| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:27 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 195/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.7.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: biodbLipidmaps |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2023-05-09 09:58:53 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 10:04:51 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 358.5 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LipidmapsStructureConn 2.746 0.14 5.334
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘biodbLipidmaps’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-05-09 09:59:42.514][biodb::testContext]
biodb.INFO [2023-05-09 09:59:42.517][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 09:59:42.518][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-09 09:59:42.520][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 09:59:42.521][biodb::testContext]
biodb.INFO [2023-05-09 09:59:42.541][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 09:59:42.544][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 09:59:42.554][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:59:42.555][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 09:59:42.557][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.562][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 09:59:42.589][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.593][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[2023-05-09 09:59:42.595][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 09:59:42.596][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.602][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 09:59:42.603][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 09:59:42.605][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 09:59:42.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.610][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 09:59:42.611][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 09:59:42.613][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.618][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 09:59:42.619][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 09:59:42.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.623][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[2023-05-09 09:59:42.625][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 09:59:42.626][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 09:59:42.628][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 09:59:42.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.633][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 09:59:42.635][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.640][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 09:59:42.642][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 09:59:42.643][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 09:59:42.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.649][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 09:59:42.650][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 09:59:42.652][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 09:59:42.653][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 09:59:42.654][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 09:59:42.656][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 09:59:42.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.661][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 09:59:42.663][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 09:59:42.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.668][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 09:59:42.670][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 09:59:42.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.675][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 09:59:42.676][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 09:59:42.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.682][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 09:59:42.683][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 09:59:42.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.687][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[2023-05-09 09:59:42.689][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 09:59:42.690][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 09:59:42.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.696][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 09:59:42.697][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 09:59:42.702][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 09:59:42.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.707][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 09:59:42.709][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 09:59:42.710][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 09:59:42.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.719][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 09:59:42.768][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-09 09:59:42.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:59:42.806][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.807][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.811][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 09:59:42.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:59:42.814][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.815][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 09:59:42.816][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:59:42.818][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.819][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.820][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:59:42.820][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:59:42.820][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 09:59:42.820][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 09:59:42.820][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 09:59:42.822][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:59:42.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:59:42.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.830][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:59:42.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:59:42.834][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.835][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.837][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 09:59:42.839][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.840][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 09:59:42.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:59:42.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.846][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.847][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.850][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 09:59:42.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:59:42.852][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.854][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 09:59:42.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:59:42.856][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.859][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:59:42.859][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:59:42.859][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 09:59:42.859][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 09:59:42.859][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 09:59:42.860][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:59:42.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.864][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:59:42.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.869][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:59:42.871][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:59:42.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.874][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.875][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 09:59:42.878][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.879][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-09 09:59:42.880][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.882][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:59:42.883][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.886][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.887][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.888][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 09:59:42.890][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:59:42.891][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.892][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 09:59:42.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:59:42.895][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.896][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.897][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.899][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:59:42.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:59:42.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.906][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.907][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:59:42.910][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:59:42.911][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.912][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.914][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 09:59:42.916][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.918][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 09:59:42.919][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.920][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:59:42.922][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.923][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 09:59:42.928][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:59:42.930][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.931][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 09:59:42.932][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:59:42.934][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.935][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:42.936][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.937][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:59:42.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:59:42.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:42.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:42.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:59:42.946][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:59:42.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:59:42.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:42.951][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:42.956][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:59:42.957][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:42.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:42.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:42.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:42.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:42.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.012][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[2023-05-09 09:59:43.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.053][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[2023-05-09 09:59:43.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.060][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 09:59:43.066][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 09:59:43.068][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 09:59:43.070][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 09:59:43.072][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 09:59:43.074][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 09:59:43.076][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 09:59:43.078][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 09:59:43.079][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 09:59:43.081][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 09:59:43.083][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 09:59:43.085][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 09:59:43.087][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 09:59:43.089][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 09:59:43.091][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 09:59:43.092][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 09:59:43.094][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 09:59:43.096][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 09:59:43.098][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 09:59:43.100][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 09:59:43.102][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 09:59:43.103][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 09:59:43.105][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 09:59:43.107][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 09:59:43.109][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 09:59:43.111][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 09:59:43.113][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 09:59:43.114][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 09:59:43.116][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 09:59:43.126][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 09:59:43.128][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 09:59:43.130][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 09:59:43.131][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 09:59:43.133][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 09:59:43.135][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 09:59:43.137][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 09:59:43.139][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 09:59:43.141][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 09:59:43.143][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 09:59:43.145][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 09:59:43.146][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 09:59:43.148][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 09:59:43.150][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 09:59:43.152][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 09:59:43.154][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 09:59:43.156][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 09:59:43.158][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 09:59:43.160][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 09:59:43.162][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 09:59:43.163][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 09:59:43.165][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 09:59:43.167][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 09:59:43.169][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 09:59:43.171][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 09:59:43.173][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 09:59:43.174][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 09:59:43.176][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 09:59:43.178][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 09:59:43.180][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 09:59:43.182][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 09:59:43.184][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 09:59:43.186][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 09:59:43.188][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 09:59:43.190][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 09:59:43.191][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 09:59:43.193][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 09:59:43.195][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 09:59:43.197][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 09:59:43.199][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 09:59:43.201][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 09:59:43.203][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 09:59:43.205][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 09:59:43.206][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 09:59:43.208][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 09:59:43.210][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 09:59:43.212][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 09:59:43.214][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 09:59:43.216][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 09:59:43.218][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 09:59:43.219][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 09:59:43.221][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 09:59:43.223][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 09:59:43.225][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 09:59:43.233][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 09:59:43.235][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 09:59:43.239][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 09:59:43.240][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.274][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[2023-05-09 09:59:43.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.340][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[2023-05-09 09:59:43.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.349][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[2023-05-09 09:59:43.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.357][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[2023-05-09 09:59:43.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 09:59:43.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 09:59:43.393][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-09 09:59:43.405][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 09:59:43.408][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:43.409][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 09:59:43.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:43.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 09:59:43.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:43.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 09:59:43.416][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:43.417][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 09:59:43.418][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 09:59:43.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 09:59:43.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:43.422][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-09 09:59:43.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-09 09:59:43.425][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-09 09:59:43.426][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 09:59:43.428][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 09:59:43.428][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 09:59:43.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 09:59:43.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:43.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:43.433][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 09:59:43.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 09:59:43.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 09:59:43.437][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 09:59:43.438][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 09:59:43.438][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-09 09:59:43.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 09:59:43.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 09:59:43.442][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 09:59:43.443][self$setPropertyValue]
biodb.DEBUG[2023-05-09 09:59:43.458][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-09 09:59:43.460][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 09:59:43.490][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 09:59:43.492][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-09 09:59:43.497][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 09:59:43.502][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-09 09:59:43.508][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 09:59:43.509][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 09:59:43.511][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-09 09:59:43.512][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-09 09:59:43.533][biodb::testThat]
biodb.INFO [2023-05-09 09:59:43.534][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-05-09 09:59:43.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:43.536][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:43.541][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-05-09 09:59:43.547][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:43.552][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 09:59:43.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:43.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:43.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:43.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:43.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:43.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:43.585][FUN] Functions in observer BiodbConfig: [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[2023-05-09 09:59:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:43.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:43.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 09:59:43.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 09:59:43.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.641][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:43.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:43.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.646][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:43.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:43.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:43.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:43.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:43.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:43.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:43.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.707][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 09:59:43.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:43.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.712][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 09:59:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:43.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:43.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.726][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:43.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 09:59:43.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.754][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 09:59:43.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.770][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 09:59:43.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:43.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:43.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.886][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:43.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:43.940][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-09 09:59:43.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:43.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:43.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.962][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:43.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:43.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:43.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:43.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:43.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:43.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.057][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.102][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.106][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.139][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.140][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.143][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.159][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.176][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.177][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.178][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.180][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.212][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.214][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.215][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.216][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.251][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.252][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.253][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.286][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.287][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.290][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.306][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.308][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.310][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.318][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.319][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.320][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.322][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.329][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.332][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.333][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.340][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.344][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.352][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.356][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.363][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.365][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.367][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:59:44.410][biodb::testThat]
biodb.INFO [2023-05-09 09:59:44.411][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-09 09:59:44.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:44.414][biodb::testThat]
biodb.DEBUG[2023-05-09 09:59:44.432][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-05-09 09:59:44.441][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 09:59:44.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-05-09 09:59:44.448][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:44.450][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-05-09 09:59:44.451][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 09:59:44.512][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-09 09:59:44.513][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 09:59:44.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 09:59:44.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 09:59:44.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 09:59:44.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 09:59:44.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 09:59:44.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 09:59:44.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 09:59:44.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:44.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:44.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 09:59:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 09:59:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.563][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 09:59:44.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 09:59:44.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 09:59:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.580][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 09:59:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.588][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 09:59:44.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 09:59:44.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 09:59:44.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:44.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.622][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 09:59:44.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 09:59:44.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.645][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 09:59:44.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.651][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 09:59:44.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.667][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 09:59:44.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.715][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 09:59:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 09:59:44.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 09:59:44.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:44.774][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-05-09 09:59:44.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-09 09:59:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-09 09:59:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-09 09:59:44.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-09 09:59:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-09 09:59:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-09 09:59:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 09:59:44.799][biodb::testThat]
biodb.INFO [2023-05-09 09:59:44.800][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-09 09:59:44.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:44.803][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:44.807][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.809][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.811][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:44.812][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-05-09 09:59:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:44.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:44.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:44.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:44.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:44.867][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-09 09:59:44.883][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[2023-05-09 09:59:44.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:44.912][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:44.914][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-05-09 09:59:46.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-05-09 09:59:47.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 09:59:47.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-05-09 09:59:47.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-05-09 09:59:47.447][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-05-09 09:59:47.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:47.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:47.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.472][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:59:47.475][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.476][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-05-09 09:59:47.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:47.479][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:47.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:47.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:47.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:47.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:47.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:47.707][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-09 09:59:47.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:59:47.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-09 09:59:47.742][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:47.744][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-05-09 09:59:47.765][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.767][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-05-09 09:59:47.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:47.769][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:47.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:47.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:47.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.885][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 09:59:47.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:47.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 09:59:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:47.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 09:59:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:47.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 09:59:47.903][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.904][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-09 09:59:47.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:47.907][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.913][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.915][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-09 09:59:47.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:47.917][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.923][biodb::testThat]
biodb.INFO [2023-05-09 09:59:47.924][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-09 09:59:47.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:47.927][biodb::testThat]
biodb.DEBUG[2023-05-09 09:59:47.931][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-05-09 09:59:49.290][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-05-09 09:59:50.164][biodb::testThat]
biodb.INFO [2023-05-09 09:59:50.166][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-09 09:59:50.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:50.168][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:50.180][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:50.182][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:50.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.192][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.205][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.207][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 09:59:50.215][biodb::testThat]
biodb.INFO [2023-05-09 09:59:50.217][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-05-09 09:59:50.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 09:59:50.220][biodb::testThat]
biodb.TRACE[2023-05-09 09:59:50.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:50.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:50.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 09:59:50.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 09:59:50.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:50.385][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-09 09:59:50.389][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:59:50.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-09 09:59:50.393][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:50.395][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-05-09 09:59:50.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-05-09 09:59:50.518][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 09:59:50.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-05-09 09:59:50.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 09:59:50.523][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-05-09 09:59:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 09:59:50.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 09:59:50.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:50.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 09:59:50.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 09:59:50.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 09:59:50.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 09:59:50.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 09:59:50.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-05-09 09:59:50.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 09:59:50.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 09:59:50.707][private$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[2023-05-09 09:59:55.598][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[2023-05-09 10:00:09.429][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:09.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-05-09 10:00:09.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-05-09 10:00:10.744][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[2023-05-09 10:00:10.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:10.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:10.754][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-05-09 10:00:11.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-05-09 10:00:13.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:13.127][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-05-09 10:00:13.142][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-05-09 10:00:13.266][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-05-09 10:00:13.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:13.273][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:13.275][private$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[2023-05-09 10:00:14.358][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[2023-05-09 10:00:16.335][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:00:16.345][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-05-09 10:00:16.360][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-05-09 10:00:16.390][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:16.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:00:16.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:00:16.411][biodb::testThat]
biodb.INFO [2023-05-09 10:00:16.412][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-05-09 10:00:16.413][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:00:16.415][biodb::testThat]
biodb.TRACE[2023-05-09 10:00:16.419][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:00:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:00:16.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:16.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:00:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:16.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:16.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:00:16.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:00:16.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:00:16.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:00:16.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:00:16.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:00:16.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:00:16.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:00:16.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:00:16.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:00:16.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:00:16.560][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[2023-05-09 10:00:16.565][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:00:16.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:00:16.570][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-05-09 10:00:21.032][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-05-09 10:01:20.268][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:20.283][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-05-09 10:01:20.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-05-09 10:01:21.443][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-05-09 10:01:21.509][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-09 10:01:21.511][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-05-09 10:01:21.513][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-09 10:01:21.514][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:01:21.516][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:01:21.517][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 10:01:21.518][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:01:21.520][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:01:21.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:21.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:21.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:21.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:21.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:21.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:21.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:21.557][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-05-09 10:01:21.561][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:21.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:21.564][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-05-09 10:01:22.623][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-05-09 10:01:23.694][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:23.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-05-09 10:01:23.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-05-09 10:01:23.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:23.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:23.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:23.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:23.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:23.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:23.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:23.738][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-05-09 10:01:23.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:23.743][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:23.744][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-05-09 10:01:27.239][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-05-09 10:01:28.326][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:01:28.335][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-05-09 10:01:28.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-05-09 10:01:28.363][private$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[2023-05-09 10:01:28.369][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:01:28.397][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-09 10:01:28.399][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 10:01:28.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:28.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:28.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:28.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:28.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:28.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:28.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:28.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.484][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:01:28.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:01:28.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.489][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:28.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.495][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.524][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:01:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:28.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.530][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:01:28.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:28.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:28.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:28.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:28.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.567][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:01:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.572][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 10:01:28.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.588][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:01:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:28.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:28.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:28.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:28.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:28.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:28.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:28.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:28.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:01:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.697][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:01:28.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:01:28.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:01:28.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:01:28.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:01:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.736][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:01:28.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:28.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.741][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:01:28.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:28.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:01:28.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:01:28.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.778][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:01:28.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.783][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 10:01:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:01:28.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:01:28.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:01:28.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:01:28.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:01:28.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:28.900][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-05-09 10:01:28.913][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:01:28.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:28.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:28.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:28.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:28.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:28.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:28.929][FUN] Functions in observer BiodbConfig: [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[2023-05-09 10:01:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.936][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.941][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:28.942][private$selectFields]
biodb.TRACE[2023-05-09 10:01:28.944][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:01:28.945][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:01:28.946][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:28.947][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.949][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.951][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.953][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.954][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.955][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.957][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.958][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:28.959][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:28.960][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.962][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.964][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.966][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:01:28.967][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:28.994][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-09 10:01:28.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:28.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:28.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:29.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:29.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:29.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:29.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:29.011][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.021][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.023][private$selectFields]
biodb.TRACE[2023-05-09 10:01:29.024][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:01:29.025][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:01:29.026][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.028][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.029][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.032][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.034][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.037][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.038][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.040][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.041][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.042][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.044][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.064][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.066][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:01:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.083][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-09 10:01:29.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:29.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:29.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:29.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:29.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:29.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:29.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:01:29.099][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.109][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.110][private$selectFields]
biodb.TRACE[2023-05-09 10:01:29.111][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:01:29.113][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:01:29.114][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.115][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.117][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.119][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.120][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.122][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.124][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.125][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.127][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:01:29.128][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.129][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.132][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.133][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:01:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.140][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:01:29.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.150][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-09 10:01:29.152][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:01:29.153][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:01:29.165][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:01:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:01:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:01:29.172][biodb::testThat]
biodb.INFO [2023-05-09 10:01:29.173][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-05-09 10:01:29.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:01:29.176][biodb::testThat]
biodb.TRACE[2023-05-09 10:01:29.180][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:01:29.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:01:29.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:29.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:01:29.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:01:29.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:01:29.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:01:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:01:29.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:01:29.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:01:29.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:01:29.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:01:29.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:01:29.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:01:29.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:01:29.387][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[2023-05-09 10:01:29.391][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:01:29.393][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:01:29.395][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-05-09 10:01:33.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-05-09 10:02:09.625][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:02:09.638][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-05-09 10:02:09.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-05-09 10:02:11.011][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:02:11.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:11.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:11.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:11.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:11.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:11.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:11.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:11.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.136][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.138][private$selectFields]
biodb.TRACE[2023-05-09 10:02:11.139][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:11.141][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:11.142][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.143][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.145][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.148][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.149][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.151][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.152][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.153][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.155][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.172][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.173][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.175][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.177][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.179][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:11.180][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.185][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.197][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-09 10:02:11.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:11.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:11.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:11.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:11.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:11.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:11.212][FUN] Functions in observer BiodbConfig: [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[2023-05-09 10:02:11.214][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.225][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.226][private$selectFields]
biodb.TRACE[2023-05-09 10:02:11.227][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:11.229][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:11.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.231][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.233][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.235][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.237][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.238][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.240][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.241][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.243][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.244][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.245][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.247][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.249][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.251][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.258][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.269][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-09 10:02:11.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:11.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:11.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:11.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:11.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:11.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:11.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.297][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.298][private$selectFields]
biodb.TRACE[2023-05-09 10:02:11.299][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:11.301][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:11.302][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.303][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.305][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.307][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.309][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.310][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.312][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.313][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.315][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.316][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:11.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.319][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.322][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.323][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.331][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.337][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:11.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.343][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-09 10:02:11.344][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:02:11.346][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:02:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:02:11.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:02:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:02:11.366][biodb::testThat]
biodb.INFO [2023-05-09 10:02:11.367][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-05-09 10:02:11.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:02:11.370][biodb::testThat]
biodb.TRACE[2023-05-09 10:02:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-09 10:02:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-09 10:02:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-09 10:02:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-09 10:02:11.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:11.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:02:11.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:11.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:02:11.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:11.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:11.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:11.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:11.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:11.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:11.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:02:11.524][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-05-09 10:02:11.529][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:02:11.531][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-05-09 10:02:11.533][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:02:11.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-05-09 10:02:12.687][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:02:12.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:12.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:12.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:12.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:12.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:12.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:12.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:12.704][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.715][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.716][private$selectFields]
biodb.TRACE[2023-05-09 10:02:12.717][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:12.719][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:12.720][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.721][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.723][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.724][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.725][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.727][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.728][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.730][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.732][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.733][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.734][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.738][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.739][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:12.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.757][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-05-09 10:02:12.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:12.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:12.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:12.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:12.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:12.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:12.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.779][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.784][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.786][private$selectFields]
biodb.TRACE[2023-05-09 10:02:12.787][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:12.788][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:12.789][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.791][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.792][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.795][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.796][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.797][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.800][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.801][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.802][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.804][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.805][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.808][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.809][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.816][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.821][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.827][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-05-09 10:02:12.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:12.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:12.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:12.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:12.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:12.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:12.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:12.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.854][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.856][private$selectFields]
biodb.TRACE[2023-05-09 10:02:12.858][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-09 10:02:12.859][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:02:12.861][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.862][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.864][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.866][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.868][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.869][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.871][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.872][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.879][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.880][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:02:12.882][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.884][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.885][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.886][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.888][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-05-09 10:02:12.889][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:12.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-05-09 10:02:12.909][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:02:12.910][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-09 10:02:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-09 10:02:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-09 10:02:12.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:12.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-09 10:02:12.949][biodb::testThat]
biodb.INFO [2023-05-09 10:02:12.951][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-05-09 10:02:12.952][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:02:12.954][biodb::testThat]
biodb.DEBUG[2023-05-09 10:02:12.956][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-09 10:02:12.958][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-09 10:02:12.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-09 10:02:12.962][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-09 10:02:12.964][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:02:12.965][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:02:12.967][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 10:02:12.968][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:02:12.969][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:02:12.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:12.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:12.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:13.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:13.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:13.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:13.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:02:13.006][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-05-09 10:02:13.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:13.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:13.014][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:13.983][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:13.985][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:13.986][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:13.987][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:15.164][private$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[2023-05-09 10:02:15.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:15.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:15.168][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:16.197][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:16.199][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:16.200][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:16.201][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:17.375][private$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[2023-05-09 10:02:17.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:17.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:17.379][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:18.392][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:18.393][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:18.394][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:18.396][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:19.571][private$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[2023-05-09 10:02:19.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:19.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:19.575][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:20.584][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:20.586][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:20.587][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:20.588][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:21.801][private$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[2023-05-09 10:02:21.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:21.804][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:21.806][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:22.821][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:22.822][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:22.824][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:22.825][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:24.000][private$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[2023-05-09 10:02:24.002][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:24.003][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:24.005][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:25.030][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:25.032][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:25.033][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:25.034][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:26.216][private$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[2023-05-09 10:02:26.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:26.219][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:26.221][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:27.245][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:27.247][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:27.249][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:27.250][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:28.426][private$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[2023-05-09 10:02:28.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:28.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:28.431][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:29.455][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:29.456][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:29.458][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:29.459][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:30.633][private$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[2023-05-09 10:02:30.634][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:30.635][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:30.637][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:31.668][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:31.669][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:31.671][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:31.672][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:32.857][private$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[2023-05-09 10:02:32.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:32.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:32.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-05-09 10:02:37.249][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:37.250][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:37.252][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:37.253][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-05-09 10:02:38.427][private$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[2023-05-09 10:02:38.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-05-09 10:02:38.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:02:38.468][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-05-09 10:02:38.470][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 10:02:38.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:38.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:38.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:38.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:38.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:38.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:38.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:02:38.491][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:38.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:38.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:02:38.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:02:38.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:02:38.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:02:38.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:02:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:02:38.537][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-05-09 10:02:38.538][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-09 10:02:38.547][biodb::testThat]
biodb.INFO [2023-05-09 10:02:38.548][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-09 10:02:38.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:02:38.551][biodb::testThat]
biodb.DEBUG[2023-05-09 10:02:38.562][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-05-09 10:02:38.564][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-05-09 10:02:38.566][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-09 10:02:38.568][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-05-09 10:02:38.570][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-05-09 10:02:38.572][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-09 10:02:38.573][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:02:38.575][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 10:02:38.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-09 10:02:38.578][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-09 10:02:38.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:02:38.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:02:38.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:02:38.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:02:38.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:02:38.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:02:38.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:02:38.599][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-05-09 10:02:38.603][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:38.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:38.606][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:39.629][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:39.631][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:39.632][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[2023-05-09 10:02:39.633][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:41.040][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:41.041][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:41.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:41.044][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:43.100][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:43.102][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:43.103][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[2023-05-09 10:02:43.105][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:44.285][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:44.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:44.288][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:44.290][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:45.317][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:45.319][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:45.320][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[2023-05-09 10:02:45.322][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:46.499][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:46.500][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:46.501][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:46.503][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:47.568][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:47.570][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:47.571][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[2023-05-09 10:02:47.573][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:48.747][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:48.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:48.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:48.752][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:49.777][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:49.779][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:49.780][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[2023-05-09 10:02:49.782][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:51.162][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:51.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:51.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:51.167][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:52.216][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:52.217][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:52.218][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-05-09 10:02:52.220][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:54.395][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:54.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:54.397][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:54.399][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:55.440][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:55.441][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:55.443][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[2023-05-09 10:02:55.444][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:56.622][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:56.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:56.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:56.627][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:57.661][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:57.663][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:57.664][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[2023-05-09 10:02:57.665][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:02:58.838][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:02:58.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:02:58.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:02:58.843][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:02:59.878][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:02:59.879][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:02:59.880][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[2023-05-09 10:02:59.882][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:03:01.054][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:03:01.055][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:01.056][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:01.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-05-09 10:03:02.044][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-05-09 10:03:02.045][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-05-09 10:03:02.047][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[2023-05-09 10:03:02.048][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-05-09 10:03:03.232][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-05-09 10:03:03.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:03.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:03.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:03.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:03.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:03.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:03.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:03.251][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-05-09 10:03:03.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:03.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:03.258][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-05-09 10:03:04.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-05-09 10:03:05.394][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:05.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-05-09 10:03:05.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-05-09 10:03:05.432][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-05-09 10:03:05.437][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-09 10:03:05.464][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-09 10:03:05.465][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 10:03:05.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:05.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:05.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:05.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:05.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:05.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:05.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:03:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.492][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:03:05.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:05.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:05.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:05.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:05.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:05.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:05.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:03:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:05.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:05.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:05.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.554][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:05.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:05.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:05.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:05.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.569][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:05.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.575][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:05.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:05.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:05.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:05.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:05.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:05.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:05.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:05.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:05.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:05.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:05.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:05.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.664][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 10:03:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.681][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:05.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:05.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.728][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:05.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:05.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:05.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:05.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:05.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:03:05.809][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-05-09 10:03:05.810][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-09 10:03:05.811][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-05-09 10:03:05.827][biodb::testThat]
biodb.INFO [2023-05-09 10:03:05.829][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-05-09 10:03:05.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:05.831][biodb::testThat]
biodb.INFO [2023-05-09 10:03:05.859][biodb::testThat]
biodb.INFO [2023-05-09 10:03:05.860][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-05-09 10:03:05.862][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:05.863][biodb::testThat]
biodb.INFO [2023-05-09 10:03:05.873][biodb::testThat]
biodb.INFO [2023-05-09 10:03:05.874][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-05-09 10:03:05.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:05.877][biodb::testThat]
biodb.DEBUG[2023-05-09 10:03:05.900][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[2023-05-09 10:03:05.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:05.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:05.907][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-05-09 10:03:10.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-05-09 10:03:21.295][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:21.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-05-09 10:03:21.346][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-05-09 10:03:22.712][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:22.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:22.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:22.717][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:22.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:22.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:22.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:22.722][ef$get] fields variable is a list.
biodb.INFO [2023-05-09 10:03:22.724][biodb::testThat]
biodb.INFO [2023-05-09 10:03:22.726][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-05-09 10:03:22.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:22.729][biodb::testThat]
biodb.ERROR[2023-05-09 10:03:22.746][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-05-09 10:03:22.768][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-05-09 10:03:22.783][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:03:22.784][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-09 10:03:22.786][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-09 10:03:22.787][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:03:22.788][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:22.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:22.790][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:22.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:22.793][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-09 10:03:22.807][biodb::testContext]
biodb.INFO [2023-05-09 10:03:22.808][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:03:22.809][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-05-09 10:03:22.811][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:03:22.812][biodb::testContext]
biodb.INFO [2023-05-09 10:03:22.818][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:03:22.820][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 10:03:22.825][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:22.827][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 10:03:22.828][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.835][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 10:03:22.836][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.841][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 10:03:22.843][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.848][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 10:03:22.849][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 10:03:22.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 10:03:22.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.855][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 10:03:22.857][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 10:03:22.858][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.863][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 10:03:22.864][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 10:03:22.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.869][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 10:03:22.870][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 10:03:22.872][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 10:03:22.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.877][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 10:03:22.878][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.883][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 10:03:22.885][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 10:03:22.886][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 10:03:22.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.891][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:03:22.893][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 10:03:22.894][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 10:03:22.895][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 10:03:22.897][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 10:03:22.898][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 10:03:22.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.903][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 10:03:22.905][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 10:03:22.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.909][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 10:03:22.911][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 10:03:22.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.916][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 10:03:22.917][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 10:03:22.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.922][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 10:03:22.923][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 10:03:22.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.928][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 10:03:22.929][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 10:03:22.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.933][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[2023-05-09 10:03:22.934][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:03:22.935][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 10:03:22.940][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 10:03:22.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.945][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 10:03:22.946][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 10:03:22.948][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 10:03:22.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:22.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:22.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:22.953][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 10:03:22.987][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:22.988][self$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[2023-05-09 10:03:22.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:22.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:22.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:22.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:22.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:22.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:22.998][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:22.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:23.000][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.002][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 10:03:23.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:23.004][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.007][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:23.007][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:23.007][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:03:23.007][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:03:23.007][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:03:23.008][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:23.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:23.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.017][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.018][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:23.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:23.020][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.022][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.023][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 10:03:23.026][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.027][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:03:23.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:23.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.037][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:03:23.038][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:23.039][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.041][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 10:03:23.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:23.043][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.046][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:23.046][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:23.046][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:03:23.046][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:03:23.046][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:03:23.047][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:23.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:23.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.056][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:23.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:23.060][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.061][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.063][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 10:03:23.065][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.067][self$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[2023-05-09 10:03:23.068][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.069][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:23.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.074][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.075][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.076][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:23.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:23.079][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.080][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 10:03:23.082][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:23.083][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.084][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.086][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.087][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:23.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.091][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:23.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.095][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.096][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.097][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:23.098][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:23.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.101][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.103][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 10:03:23.105][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.106][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:03:23.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:23.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.113][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.115][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.116][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:03:23.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:23.119][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.120][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 10:03:23.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:23.123][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.124][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.125][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.127][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:23.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:23.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.136][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:23.138][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:23.140][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.141][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.143][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:23.144][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.201][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[2023-05-09 10:03:23.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.207][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[2023-05-09 10:03:23.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.248][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[2023-05-09 10:03:23.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.254][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[2023-05-09 10:03:23.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.261][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[2023-05-09 10:03:23.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.267][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[2023-05-09 10:03:23.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.279][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[2023-05-09 10:03:23.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.285][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[2023-05-09 10:03:23.286][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 10:03:23.288][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 10:03:23.290][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 10:03:23.292][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 10:03:23.293][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:03:23.295][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 10:03:23.297][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 10:03:23.299][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 10:03:23.301][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 10:03:23.303][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 10:03:23.305][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:03:23.307][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 10:03:23.309][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 10:03:23.311][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 10:03:23.313][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 10:03:23.315][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:03:23.317][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 10:03:23.319][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 10:03:23.321][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:03:23.323][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 10:03:23.325][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 10:03:23.326][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 10:03:23.328][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 10:03:23.330][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 10:03:23.332][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 10:03:23.334][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 10:03:23.336][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 10:03:23.338][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 10:03:23.340][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 10:03:23.342][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 10:03:23.343][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 10:03:23.345][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 10:03:23.347][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 10:03:23.349][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 10:03:23.351][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 10:03:23.353][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 10:03:23.355][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 10:03:23.357][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 10:03:23.359][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 10:03:23.361][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 10:03:23.363][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 10:03:23.365][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 10:03:23.367][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 10:03:23.369][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 10:03:23.371][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 10:03:23.373][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 10:03:23.375][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 10:03:23.377][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 10:03:23.379][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 10:03:23.381][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 10:03:23.382][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 10:03:23.384][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 10:03:23.386][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 10:03:23.388][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 10:03:23.390][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 10:03:23.392][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 10:03:23.394][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 10:03:23.396][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 10:03:23.398][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 10:03:23.400][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 10:03:23.402][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 10:03:23.404][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 10:03:23.406][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 10:03:23.408][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 10:03:23.410][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 10:03:23.411][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 10:03:23.413][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:03:23.415][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:03:23.417][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 10:03:23.419][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 10:03:23.421][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 10:03:23.423][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 10:03:23.425][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 10:03:23.427][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 10:03:23.429][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 10:03:23.431][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 10:03:23.433][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 10:03:23.435][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 10:03:23.437][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 10:03:23.439][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 10:03:23.441][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 10:03:23.443][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 10:03:23.445][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 10:03:23.447][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 10:03:23.449][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:03:23.450][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:23.451][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.454][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.582][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[2023-05-09 10:03:23.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:23.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:23.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:23.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:23.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:23.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:23.602][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-09 10:03:23.604][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:23.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.607][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:23.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.614][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.617][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:23.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:23.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.621][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-09 10:03:23.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-09 10:03:23.624][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-09 10:03:23.625][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:23.626][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:23.626][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:23.628][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:23.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:23.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:23.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:23.635][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:23.637][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 10:03:23.637][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-09 10:03:23.639][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:23.640][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:23.641][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:23.643][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:23.644][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-09 10:03:23.646][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:03:23.650][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:23.652][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-09 10:03:23.653][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:23.655][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-09 10:03:23.657][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 10:03:23.658][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 10:03:23.659][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-09 10:03:23.661][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-09 10:03:23.663][biodb::testThat]
biodb.INFO [2023-05-09 10:03:23.664][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-05-09 10:03:23.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:23.666][biodb::testThat]
biodb.DEBUG[2023-05-09 10:03:23.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-05-09 10:03:23.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:23.694][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:23.696][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-05-09 10:03:24.798][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[2023-05-09 10:03:25.869][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:25.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-05-09 10:03:25.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-05-09 10:03:25.907][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[2023-05-09 10:03:25.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:25.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:25.915][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-05-09 10:03:27.009][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-05-09 10:03:28.119][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:28.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-05-09 10:03:28.146][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-05-09 10:03:28.163][biodb::testThat]
biodb.INFO [2023-05-09 10:03:28.164][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-05-09 10:03:28.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:28.167][biodb::testThat]
biodb.INFO [2023-05-09 10:03:28.205][biodb::testThat]
biodb.INFO [2023-05-09 10:03:28.207][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-05-09 10:03:28.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:28.209][biodb::testThat]
biodb.DEBUG[2023-05-09 10:03:28.214][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-05-09 10:03:28.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:28.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:28.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-05-09 10:03:29.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-05-09 10:03:30.037][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:30.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-05-09 10:03:30.062][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-05-09 10:03:30.071][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[2023-05-09 10:03:30.075][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:03:30.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-05-09 10:03:30.078][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:03:30.080][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-05-09 10:03:30.087][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[2023-05-09 10:03:30.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:30.093][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:30.095][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-05-09 10:03:31.027][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-05-09 10:03:31.961][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:31.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-05-09 10:03:31.986][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-05-09 10:03:31.996][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-05-09 10:03:32.000][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:32.002][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:32.004][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-05-09 10:03:33.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-05-09 10:03:35.998][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:36.008][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-05-09 10:03:36.025][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-05-09 10:03:36.172][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[2023-05-09 10:03:36.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-09 10:03:36.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-09 10:03:36.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-05-09 10:03:37.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-05-09 10:03:40.335][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-09 10:03:40.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-05-09 10:03:40.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-05-09 10:03:40.508][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:03:40.510][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-09 10:03:40.511][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-09 10:03:40.512][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:03:40.514][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:40.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:40.516][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.518][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-09 10:03:40.524][biodb::testContext]
biodb.INFO [2023-05-09 10:03:40.527][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:03:40.528][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-05-09 10:03:40.529][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-09 10:03:40.531][biodb::testContext]
biodb.INFO [2023-05-09 10:03:40.537][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:03:40.539][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-09 10:03:40.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:40.545][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-09 10:03:40.547][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.552][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-09 10:03:40.553][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.558][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-09 10:03:40.559][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.564][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-09 10:03:40.565][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-09 10:03:40.567][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-09 10:03:40.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.571][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-09 10:03:40.573][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-09 10:03:40.574][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.579][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-09 10:03:40.580][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-09 10:03:40.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.585][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-09 10:03:40.586][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-09 10:03:40.587][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-09 10:03:40.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.592][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-09 10:03:40.594][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.598][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-09 10:03:40.600][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-09 10:03:40.601][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-09 10:03:40.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.606][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:03:40.607][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-09 10:03:40.608][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-09 10:03:40.609][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-09 10:03:40.611][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-09 10:03:40.612][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-09 10:03:40.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.617][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-09 10:03:40.618][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-09 10:03:40.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.623][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-09 10:03:40.624][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-09 10:03:40.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.629][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-09 10:03:40.630][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-09 10:03:40.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.635][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-09 10:03:40.636][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-09 10:03:40.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.641][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-09 10:03:40.643][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-09 10:03:40.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.646][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[2023-05-09 10:03:40.647][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-09 10:03:40.649][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-09 10:03:40.653][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-09 10:03:40.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.657][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-09 10:03:40.659][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-09 10:03:40.660][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-09 10:03:40.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.663][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[2023-05-09 10:03:40.665][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-09 10:03:40.667][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.669][self$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[2023-05-09 10:03:40.670][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.671][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:40.672][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.678][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:40.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:40.680][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.681][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-09 10:03:40.683][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:40.684][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.685][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.687][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:40.687][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:40.687][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:03:40.687][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:03:40.687][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:03:40.688][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:40.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.692][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:40.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.697][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.698][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:40.699][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:40.700][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.702][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.703][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-09 10:03:40.705][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.707][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:03:40.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:40.711][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.712][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.713][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.715][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.716][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:03:40.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:40.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.720][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-09 10:03:40.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:40.723][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.724][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.725][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:40.725][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:40.725][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-09 10:03:40.725][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-09 10:03:40.725][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-09 10:03:40.727][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:40.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:40.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.734][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.735][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:40.738][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:40.739][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.741][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.742][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-09 10:03:40.744][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.746][self$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[2023-05-09 10:03:40.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:40.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.751][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.752][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.755][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:40.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:40.758][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.759][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-09 10:03:40.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:40.762][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.764][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:40.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:40.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.775][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:40.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:40.779][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.780][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.782][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-09 10:03:40.784][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.785][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-09 10:03:40.787][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.788][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:40.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.792][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.795][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-09 10:03:40.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:40.798][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.799][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-09 10:03:40.800][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:40.801][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.803][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:40.804][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.805][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:40.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.839][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:40.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:40.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:40.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:40.843][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.845][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:40.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:40.847][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:40.848][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:40.850][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:40.851][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:40.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:40.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:40.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:40.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:40.948][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-09 10:03:40.949][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-09 10:03:40.951][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-09 10:03:40.953][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-09 10:03:40.955][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-09 10:03:40.956][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-09 10:03:40.958][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-09 10:03:40.960][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-09 10:03:40.962][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-09 10:03:40.963][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-09 10:03:40.965][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-09 10:03:40.967][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-09 10:03:40.969][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-09 10:03:40.970][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-09 10:03:40.972][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-09 10:03:40.974][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:03:40.976][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-09 10:03:40.978][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-09 10:03:40.979][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-09 10:03:40.981][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-09 10:03:40.983][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-09 10:03:40.985][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-09 10:03:40.987][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-09 10:03:40.988][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-09 10:03:40.990][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-09 10:03:40.992][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-09 10:03:40.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-09 10:03:40.996][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-09 10:03:40.998][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-09 10:03:41.000][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-09 10:03:41.002][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-09 10:03:41.003][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-09 10:03:41.005][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-09 10:03:41.007][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-09 10:03:41.009][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-09 10:03:41.011][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-09 10:03:41.012][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-09 10:03:41.014][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-09 10:03:41.016][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-09 10:03:41.018][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-09 10:03:41.020][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-09 10:03:41.021][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-09 10:03:41.023][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-09 10:03:41.025][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-09 10:03:41.027][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-09 10:03:41.029][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-09 10:03:41.030][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-09 10:03:41.032][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-09 10:03:41.034][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-09 10:03:41.036][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-09 10:03:41.038][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-09 10:03:41.039][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-09 10:03:41.041][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-09 10:03:41.043][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-09 10:03:41.045][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-09 10:03:41.047][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-09 10:03:41.049][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-09 10:03:41.050][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-09 10:03:41.052][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-09 10:03:41.054][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-09 10:03:41.056][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-09 10:03:41.058][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-09 10:03:41.059][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-09 10:03:41.061][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-09 10:03:41.063][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-09 10:03:41.065][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-09 10:03:41.067][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-09 10:03:41.068][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-09 10:03:41.070][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-09 10:03:41.072][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-09 10:03:41.074][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-09 10:03:41.076][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-09 10:03:41.077][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-09 10:03:41.079][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-09 10:03:41.081][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-09 10:03:41.083][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-09 10:03:41.085][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-09 10:03:41.087][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-09 10:03:41.088][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-09 10:03:41.090][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-09 10:03:41.092][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-09 10:03:41.094][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-09 10:03:41.096][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-09 10:03:41.098][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-09 10:03:41.100][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-09 10:03:41.101][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-09 10:03:41.102][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.104][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.113][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[2023-05-09 10:03:41.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.169][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[2023-05-09 10:03:41.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.194][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[2023-05-09 10:03:41.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.234][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[2023-05-09 10:03:41.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-09 10:03:41.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:41.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:41.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:41.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:41.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:41.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-09 10:03:41.244][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-05-09 10:03:41.246][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:41.248][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:41.250][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-09 10:03:41.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:41.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-09 10:03:41.254][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:41.255][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-09 10:03:41.256][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:41.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-09 10:03:41.259][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-09 10:03:41.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-09 10:03:41.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:41.262][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-05-09 10:03:41.264][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-05-09 10:03:41.265][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-05-09 10:03:41.266][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-09 10:03:41.268][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-09 10:03:41.268][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-09 10:03:41.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-09 10:03:41.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:41.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:41.273][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-09 10:03:41.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-09 10:03:41.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-09 10:03:41.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-09 10:03:41.294][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-05-09 10:03:41.294][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-05-09 10:03:41.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-09 10:03:41.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-09 10:03:41.298][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-09 10:03:41.299][self$setPropertyValue]
biodb.DEBUG[2023-05-09 10:03:41.300][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-05-09 10:03:41.302][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-09 10:03:41.306][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:41.308][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-05-09 10:03:41.309][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-05-09 10:03:41.311][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-05-09 10:03:41.312][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 10:03:41.314][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-05-09 10:03:41.315][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-05-09 10:03:41.317][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-05-09 10:03:41.318][biodb::testThat]
biodb.INFO [2023-05-09 10:03:41.320][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2023-05-09 10:03:41.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-09 10:03:41.322][biodb::testThat]
biodb.DEBUG[2023-05-09 10:03:41.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-05-09 10:03:41.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-09 10:03:41.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-05-09 10:03:41.335][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-09 10:03:41.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-05-09 10:03:42.579][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-05-09 10:03:42.581][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-05-09 10:03:42.583][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-05-09 10:03:42.585][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-05-09 10:03:42.587][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-05-09 10:03:42.588][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-05-09 10:03:42.611][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-05-09 10:03:42.613][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-05-09 10:03:42.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:42.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:42.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:42.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:42.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:42.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:42.629][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.TRACE[2023-05-09 10:03:42.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:42.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:42.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.671][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:42.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.706][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:42.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.711][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:42.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:42.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:42.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.726][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:42.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:42.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:42.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.755][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 10:03:42.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.771][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.811][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.817][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.828][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:42.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:03:42.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:42.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:42.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:42.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:42.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:42.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:42.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:03:42.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:42.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:42.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:42.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.902][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:42.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-05-09 10:03:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:42.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-09 10:03:42.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.913][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.919][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:42.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:42.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.943][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:42.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:42.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.948][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-05-09 10:03:42.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:42.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:42.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:42.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:42.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.987][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:42.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.992][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-05-09 10:03:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:42.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:42.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:42.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:42.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.009][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-05-09 10:03:43.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.018][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.023][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-09 10:03:43.115][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-05-09 10:03:43.118][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-09 10:03:43.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:43.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:43.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:43.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:43.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:43.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:43.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-09 10:03:43.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 10:03:43.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 10:03:43.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 10:03:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 10:03:43.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.157][private$selectFields] Fields none
biodb.TRACE[2023-05-09 10:03:43.158][private$selectFields]
biodb.TRACE[2023-05-09 10:03:43.160][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-09 10:03:43.161][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:03:43.162][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.164][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.165][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.166][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.168][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.169][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.170][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.172][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.173][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.174][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.176][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.178][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.179][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.181][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.183][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.187][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.188][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.190][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.194][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.195][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.196][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.198][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.199][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.200][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.202][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.204][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.205][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.208][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.209][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.211][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.212][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.215][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.216][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.217][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.220][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.221][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.222][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.224][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.225][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.227][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.229][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.230][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.231][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.234][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.235][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.236][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.239][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.241][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.242][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.243][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.245][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.246][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.247][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.249][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.250][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.254][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.257][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.258][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.259][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.260][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.262][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.265][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.266][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.267][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.270][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.271][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.275][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.276][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.278][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.279][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.280][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.282][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.284][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.285][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.287][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.288][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.290][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.291][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.292][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-05-09 10:03:43.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.326][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.373][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.384][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.410][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.416][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.428][private$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[2023-05-09 10:03:43.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-09 10:03:43.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:43.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:43.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:43.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:43.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:43.443][FUN] Functions in observer BiodbConfig: [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[2023-05-09 10:03:43.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-09 10:03:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-09 10:03:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-09 10:03:43.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-09 10:03:43.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-09 10:03:43.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.481][private$selectFields] Fields none
biodb.TRACE[2023-05-09 10:03:43.482][private$selectFields]
biodb.TRACE[2023-05-09 10:03:43.484][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-05-09 10:03:43.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-09 10:03:43.486][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.488][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.489][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.492][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.496][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.497][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.498][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.500][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.502][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.504][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.505][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.508][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.513][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.514][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.516][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.518][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.519][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.523][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.525][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.526][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.527][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.547][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.549][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.550][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.551][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.553][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.554][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.555][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.558][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.559][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.560][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.563][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.564][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.565][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.568][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.572][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.574][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.575][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.577][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.579][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.582][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.584][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.585][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.587][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.589][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.590][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-05-09 10:03:43.591][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.592][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.595][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.600][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.601][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.602][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.605][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.606][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.607][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.610][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.611][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.615][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.616][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.617][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.619][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.621][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.622][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.624][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.626][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.627][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.629][ef$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.631][private$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[2023-05-09 10:03:43.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-09 10:03:43.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-09 10:03:43.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-09 10:03:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-05-09 10:03:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.678][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-05-09 10:03:43.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-09 10:03:43.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-09 10:03:43.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-09 10:03:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-09 10:03:43.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-09 10:03:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.744][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-05-09 10:03:43.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-09 10:03:43.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-09 10:03:43.759][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-05-09 10:03:43.760][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-09 10:03:43.762][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-05-09 10:03:43.765][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-09 10:03:43.767][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-05-09 10:03:43.768][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-05-09 10:03:43.769][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-09 10:03:43.770][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-09 10:03:43.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-09 10:03:43.773][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-09 10:03:43.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-09 10:03:43.775][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-09 10:03:43.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
36.415 2.303 243.656
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 2.746 | 0.140 | 5.334 | |
| LipidmapsStructureEntry | 0.475 | 0.024 | 0.499 | |