| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-03 02:35:45 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biodbLipidmaps package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 183/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.5.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: biodbLipidmaps |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbLipidmaps_1.5.0.tar.gz |
| StartedAt: 2023-02-02 01:58:17 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 02:03:01 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 283.4 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/library --timings biodbLipidmaps_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LipidmapsStructureConn 2.853 0.148 6.46
* 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/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) (2023-01-14 r83615) -- "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 [2023-02-02 01:59:14.000][biodb::testContext]
biodb.INFO [2023-02-02 01:59:14.003][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 01:59:14.004][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-02 01:59:14.006][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 01:59:14.007][biodb::testContext]
biodb.INFO [2023-02-02 01:59:14.028][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-02 01:59:14.031][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-02 01:59:14.041][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 01:59:14.042][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-02 01:59:14.044][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.049][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-02 01:59:14.077][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.083][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-02 01:59:14.085][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.090][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-02 01:59:14.092][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-02 01:59:14.094][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-02 01:59:14.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.100][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-02 01:59:14.101][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-02 01:59:14.103][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.109][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-02 01:59:14.110][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-02 01:59:14.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.116][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-02 01:59:14.118][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-02 01:59:14.120][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-02 01:59:14.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.126][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-02 01:59:14.127][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.133][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-02 01:59:14.135][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-02 01:59:14.137][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-02 01:59:14.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.142][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-02 01:59:14.144][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-02 01:59:14.145][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-02 01:59:14.147][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-02 01:59:14.149][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-02 01:59:14.150][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-02 01:59:14.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.156][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-02 01:59:14.158][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-02 01:59:14.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.163][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-02 01:59:14.165][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-02 01:59:14.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.169][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[2023-02-02 01:59:14.171][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-02 01:59:14.173][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-02 01:59:14.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.178][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-02 01:59:14.180][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-02 01:59:14.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.186][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-02 01:59:14.188][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-02 01:59:14.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.194][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-02 01:59:14.195][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-02 01:59:14.200][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-02 01:59:14.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.206][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-02 01:59:14.208][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-02 01:59:14.210][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-02 01:59:14.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.220][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-02 01:59:14.284][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.306][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-02 01:59:14.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 01:59:14.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.313][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.316][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 01:59:14.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 01:59:14.319][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.321][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-02 01:59:14.322][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 01:59:14.324][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.325][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.327][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 01:59:14.327][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 01:59:14.327][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 01:59:14.327][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 01:59:14.327][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 01:59:14.328][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 01:59:14.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 01:59:14.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.338][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 01:59:14.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 01:59:14.342][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.344][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.345][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-02 01:59:14.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.349][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 01:59:14.351][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.352][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 01:59:14.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.355][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.359][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 01:59:14.361][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 01:59:14.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.364][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-02 01:59:14.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 01:59:14.367][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.368][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 01:59:14.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 01:59:14.370][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 01:59:14.370][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 01:59:14.370][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 01:59:14.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 01:59:14.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 01:59:14.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.381][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 01:59:14.384][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 01:59:14.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.387][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.388][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-02 01:59:14.391][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.392][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-02 01:59:14.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.395][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 01:59:14.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.402][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 01:59:14.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 01:59:14.405][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.407][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-02 01:59:14.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 01:59:14.410][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.413][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 01:59:14.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 01:59:14.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.424][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.426][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 01:59:14.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 01:59:14.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.430][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.431][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-02 01:59:14.434][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.435][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 01:59:14.437][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 01:59:14.440][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.441][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.443][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.445][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 01:59:14.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 01:59:14.448][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.450][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-02 01:59:14.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 01:59:14.453][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.455][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.457][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 01:59:14.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 01:59:14.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.467][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 01:59:14.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 01:59:14.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.472][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:14.478][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 01:59:14.479][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.481][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[2023-02-02 01:59:14.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.506][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[2023-02-02 01:59:14.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.565][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[2023-02-02 01:59:14.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.584][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[2023-02-02 01:59:14.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.600][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-02 01:59:14.606][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-02 01:59:14.608][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-02 01:59:14.611][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-02 01:59:14.613][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-02 01:59:14.615][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-02 01:59:14.617][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-02 01:59:14.619][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-02 01:59:14.621][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-02 01:59:14.623][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-02 01:59:14.625][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-02 01:59:14.627][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-02 01:59:14.629][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-02 01:59:14.631][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-02 01:59:14.633][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-02 01:59:14.635][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 01:59:14.637][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-02 01:59:14.639][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-02 01:59:14.641][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-02 01:59:14.643][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-02 01:59:14.645][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-02 01:59:14.647][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-02 01:59:14.649][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-02 01:59:14.652][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-02 01:59:14.654][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-02 01:59:14.656][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-02 01:59:14.658][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-02 01:59:14.660][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-02 01:59:14.662][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-02 01:59:14.664][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-02 01:59:14.666][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-02 01:59:14.668][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-02 01:59:14.670][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-02 01:59:14.672][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-02 01:59:14.674][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-02 01:59:14.676][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-02 01:59:14.678][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-02 01:59:14.680][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-02 01:59:14.682][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-02 01:59:14.684][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-02 01:59:14.686][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-02 01:59:14.688][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-02 01:59:14.690][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-02 01:59:14.693][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-02 01:59:14.695][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-02 01:59:14.697][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-02 01:59:14.699][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-02 01:59:14.701][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-02 01:59:14.703][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-02 01:59:14.705][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-02 01:59:14.707][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-02 01:59:14.709][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-02 01:59:14.711][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-02 01:59:14.713][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-02 01:59:14.715][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-02 01:59:14.717][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-02 01:59:14.719][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-02 01:59:14.721][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-02 01:59:14.723][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-02 01:59:14.725][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-02 01:59:14.727][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-02 01:59:14.729][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-02 01:59:14.731][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-02 01:59:14.733][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-02 01:59:14.735][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-02 01:59:14.737][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-02 01:59:14.739][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-02 01:59:14.741][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-02 01:59:14.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-02 01:59:14.745][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-02 01:59:14.747][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-02 01:59:14.749][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-02 01:59:14.751][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-02 01:59:14.753][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-02 01:59:14.755][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-02 01:59:14.757][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-02 01:59:14.759][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-02 01:59:14.761][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-02 01:59:14.763][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-02 01:59:14.765][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-02 01:59:14.767][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-02 01:59:14.769][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-02 01:59:14.771][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-02 01:59:14.779][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-02 01:59:14.781][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-02 01:59:14.786][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 01:59:14.787][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.790][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.840][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[2023-02-02 01:59:14.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.858][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[2023-02-02 01:59:14.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.867][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.DEBUG[2023-02-02 01:59:14.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.876][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[2023-02-02 01:59:14.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.902][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[2023-02-02 01:59:14.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.919][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[2023-02-02 01:59:14.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 01:59:14.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:14.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:14.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:14.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:14.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:14.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:14.956][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-02 01:59:14.969][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 01:59:14.972][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.973][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.975][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.976][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 01:59:14.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.980][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.982][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 01:59:14.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 01:59:14.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 01:59:14.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:14.987][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-02 01:59:14.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-02 01:59:14.990][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-02 01:59:14.991][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-02 01:59:14.993][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 01:59:14.993][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 01:59:14.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 01:59:14.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:14.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:14.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 01:59:15.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 01:59:15.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 01:59:15.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 01:59:15.004][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 01:59:15.004][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-02 01:59:15.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 01:59:15.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 01:59:15.008][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-02 01:59:15.010][self$setPropertyValue]
biodb.DEBUG[2023-02-02 01:59:15.018][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-02 01:59:15.020][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 01:59:15.052][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 01:59:15.053][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-02 01:59:15.059][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 01:59:15.065][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-02 01:59:15.070][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 01:59:15.072][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 01:59:15.074][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-02 01:59:15.075][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-02 01:59:15.097][biodb::testThat]
biodb.INFO [2023-02-02 01:59:15.099][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-02-02 01:59:15.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:15.101][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:15.106][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-02-02 01:59:15.113][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-02 01:59:15.117][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 01:59:15.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 01:59:15.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:15.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:15.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:15.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:15.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:15.153][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.TRACE[2023-02-02 01:59:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 01:59:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 01:59:15.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.208][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 01:59:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 01:59:15.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 01:59:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 01:59:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.303][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 01:59:15.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 01:59:15.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.350][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 01:59:15.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 01:59:15.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.373][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 01:59:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:15.591][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-02-02 01:59:15.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:15.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:15.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:15.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:15.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:15.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:15.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.717][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.722][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.755][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.758][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.791][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.793][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.794][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.795][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:15.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.821][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.837][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.839][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.841][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.874][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.876][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.878][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.912][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.914][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.915][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.916][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:15.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.951][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.952][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.955][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.972][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:15.974][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:15.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.976][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.984][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.986][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:15.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:15.988][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:15.996][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:15.998][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:15.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.000][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.008][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:16.010][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:16.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.012][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.020][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.022][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.025][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.032][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.034][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.037][ef$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:16.046][biodb::testThat]
biodb.INFO [2023-02-02 01:59:16.047][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-02 01:59:16.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:16.050][biodb::testThat]
biodb.DEBUG[2023-02-02 01:59:16.070][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-02-02 01:59:16.088][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-02 01:59:16.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-02-02 01:59:16.095][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 01:59:16.097][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-02-02 01:59:16.099][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-02 01:59:16.161][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-02 01:59:16.163][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 01:59:16.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 01:59:16.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:16.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:16.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:16.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:16.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:16.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 01:59:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 01:59:16.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 01:59:16.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 01:59:16.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 01:59:16.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 01:59:16.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 01:59:16.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 01:59:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 01:59:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.234][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.240][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 01:59:16.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 01:59:16.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.265][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 01:59:16.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:16.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.271][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 01:59:16.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:16.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:16.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:16.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 01:59:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 01:59:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 01:59:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.318][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 01:59:16.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.335][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 01:59:16.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.393][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 01:59:16.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 01:59:16.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 01:59:16.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:16.449][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-02-02 01:59:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-02 01:59:16.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-02 01:59:16.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-02 01:59:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-02 01:59:16.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-02 01:59:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-02 01:59:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:16.476][biodb::testThat]
biodb.INFO [2023-02-02 01:59:16.477][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-02 01:59:16.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:16.480][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:16.484][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.485][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.487][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.488][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:16.490][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-02-02 01:59:16.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:16.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:16.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:16.550][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-02 01:59:16.569][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[2023-02-02 01:59:16.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 01:59:16.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 01:59:16.603][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-02-02 01:59:18.479][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-02-02 01:59:19.863][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 01:59:19.890][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-02-02 01:59:19.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-02-02 01:59:19.960][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-02-02 01:59:20.048][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:20.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:20.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.052][ef$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:20.055][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.056][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-02-02 01:59:20.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:20.059][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:20.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:20.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:20.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:20.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-02 01:59:20.294][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 01:59:20.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-02 01:59:20.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 01:59:20.320][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-02-02 01:59:20.343][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.344][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-02-02 01:59:20.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:20.347][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.388][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:20.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:20.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:20.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 01:59:20.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:20.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-02 01:59:20.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:20.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-02 01:59:20.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:20.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:20.500][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.502][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-02 01:59:20.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:20.504][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.511][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.512][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-02 01:59:20.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:20.515][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.521][biodb::testThat]
biodb.INFO [2023-02-02 01:59:20.522][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-02 01:59:20.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:20.525][biodb::testThat]
biodb.DEBUG[2023-02-02 01:59:20.530][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-02-02 01:59:22.238][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-02-02 01:59:23.379][biodb::testThat]
biodb.INFO [2023-02-02 01:59:23.380][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-02 01:59:23.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:23.383][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:23.419][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:23.421][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:23.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.423][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.426][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.429][ef$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:23.447][biodb::testThat]
biodb.INFO [2023-02-02 01:59:23.449][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-02-02 01:59:23.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:23.452][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:23.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:23.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:23.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 01:59:23.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 01:59:23.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:23.731][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-02 01:59:23.735][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 01:59:23.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-02 01:59:23.740][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 01:59:23.742][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-02-02 01:59:23.864][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-02 01:59:23.869][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 01:59:23.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-02 01:59:23.873][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 01:59:23.876][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-02-02 01:59:23.901][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-02 01:59:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-02 01:59:23.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-02 01:59:23.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-02 01:59:23.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:23.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:23.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:23.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:24.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-02-02 01:59:24.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 01:59:24.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 01:59:24.096][private$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[2023-02-02 01:59:28.753][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[2023-02-02 01:59:41.891][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 01:59:41.901][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-02-02 01:59:41.942][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-02-02 01:59:43.244][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[2023-02-02 01:59:43.249][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 01:59:43.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 01:59:43.253][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-02-02 01:59:44.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-02-02 01:59:45.763][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 01:59:45.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-02-02 01:59:45.814][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-02-02 01:59:45.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-02-02 01:59:45.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 01:59:45.959][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 01:59:45.961][private$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[2023-02-02 01:59:47.287][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[2023-02-02 01:59:48.659][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 01:59:48.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-02-02 01:59:48.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-02-02 01:59:48.721][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-02 01:59:48.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-02 01:59:48.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 01:59:48.776][biodb::testThat]
biodb.INFO [2023-02-02 01:59:48.777][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-02-02 01:59:48.778][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 01:59:48.780][biodb::testThat]
biodb.TRACE[2023-02-02 01:59:48.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-02 01:59:48.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-02 01:59:48.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:48.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-02 01:59:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-02 01:59:48.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:48.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:48.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:48.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 01:59:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 01:59:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 01:59:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 01:59:48.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 01:59:48.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 01:59:48.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 01:59:48.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 01:59:48.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 01:59:48.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 01:59:48.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 01:59:48.897][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[2023-02-02 01:59:48.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 01:59:48.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 01:59:48.906][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-02-02 01:59:53.724][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-02-02 02:00:03.582][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:00:03.592][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-02-02 02:00:03.632][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-02-02 02:00:04.800][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-02-02 02:00:04.863][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-02 02:00:04.865][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-02-02 02:00:04.867][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-02-02 02:00:04.869][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-02 02:00:04.870][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-02 02:00:04.871][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 02:00:04.873][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-02 02:00:04.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-02 02:00:04.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:04.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:04.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:04.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:04.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:04.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:04.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:04.910][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-02-02 02:00:04.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:04.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:04.916][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-02-02 02:00:06.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-02-02 02:00:07.547][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:00:07.557][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-02-02 02:00:07.570][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-02-02 02:00:07.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:07.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:07.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:07.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:07.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:07.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:07.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:07.591][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-02-02 02:00:07.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:07.596][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:07.598][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-02-02 02:00:08.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-02-02 02:00:10.205][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:00:10.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-02-02 02:00:10.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-02-02 02:00:10.242][private$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[2023-02-02 02:00:10.248][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-02 02:00:10.269][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-02 02:00:10.270][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 02:00:10.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:10.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:10.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:10.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:10.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:10.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:10.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:10.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:00:10.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:00:10.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.361][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:00:10.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:00:10.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.373][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.388][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.397][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:00:10.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:10.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.403][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:00:10.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:10.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:00:10.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:00:10.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:00:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:00:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:00:10.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.448][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 02:00:10.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.465][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:00:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.475][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.492][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:00:10.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:10.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:10.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:10.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:10.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:10.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:10.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:00:10.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.560][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:00:10.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:00:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.566][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:00:10.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:00:10.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.577][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:00:10.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:00:10.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.602][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:00:10.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:00:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:10.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:00:10.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:00:10.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:00:10.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:00:10.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:00:10.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.654][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 02:00:10.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:00:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.671][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:00:10.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:00:10.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.680][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.697][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:10.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:10.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:00:10.775][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-02-02 02:00:10.788][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-02 02:00:10.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:10.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:10.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:10.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:10.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:10.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:10.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:10.806][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.812][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.817][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.818][private$selectFields]
biodb.TRACE[2023-02-02 02:00:10.820][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:10.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:10.822][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.824][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.825][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.827][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.828][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.829][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.831][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.833][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.835][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.836][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.838][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.839][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.842][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.843][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:10.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.850][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.873][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-02 02:00:10.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:10.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:10.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:10.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:10.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:10.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:10.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:10.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.902][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.903][private$selectFields]
biodb.TRACE[2023-02-02 02:00:10.905][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:10.906][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:10.907][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.909][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.910][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.913][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.914][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.916][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.918][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.920][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.921][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.923][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.924][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.927][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.928][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:10.930][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-02 02:00:10.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:10.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:10.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:10.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:10.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:10.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:10.962][FUN] Functions in observer BiodbConfig: [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[2023-02-02 02:00:10.964][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.975][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.976][private$selectFields]
biodb.TRACE[2023-02-02 02:00:10.977][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:10.979][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:10.980][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.981][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.983][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.985][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.987][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.988][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.991][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:10.992][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.993][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:10.995][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.996][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:10.998][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:10.999][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.000][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:11.002][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.013][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:11.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.019][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-02 02:00:11.020][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-02 02:00:11.021][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-02 02:00:11.035][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:11.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 02:00:11.042][biodb::testThat]
biodb.INFO [2023-02-02 02:00:11.043][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-02-02 02:00:11.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:00:11.046][biodb::testThat]
biodb.TRACE[2023-02-02 02:00:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-02 02:00:11.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-02 02:00:11.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-02 02:00:11.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-02 02:00:11.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:11.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:00:11.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:11.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:11.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:11.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:11.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:11.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:11.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:11.250][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[2023-02-02 02:00:11.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:11.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:11.258][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-02-02 02:00:15.807][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-02-02 02:00:26.575][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:00:26.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-02-02 02:00:26.625][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-02-02 02:00:27.751][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-02 02:00:27.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:27.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:27.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:27.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:27.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:27.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:27.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.854][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.855][private$selectFields]
biodb.TRACE[2023-02-02 02:00:27.856][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:27.858][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:27.859][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.860][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.862][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.864][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.866][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.867][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.869][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.871][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.885][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.887][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.891][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.892][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.911][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-02 02:00:27.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:27.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:27.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:27.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:27.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:27.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:27.926][FUN] Functions in observer BiodbConfig: [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[2023-02-02 02:00:27.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.939][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.940][private$selectFields]
biodb.TRACE[2023-02-02 02:00:27.941][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:27.943][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:27.944][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.945][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.947][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.949][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.951][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.955][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.956][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.958][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:27.959][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.961][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.962][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.963][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.964][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:27.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:27.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:27.983][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-02 02:00:27.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:27.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:27.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:27.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:27.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:27.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:27.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:28.000][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.011][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:28.012][private$selectFields]
biodb.TRACE[2023-02-02 02:00:28.014][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:28.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:28.016][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:28.018][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.019][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.022][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.023][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.025][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.026][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.027][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.029][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:28.030][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:28.031][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.033][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.036][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.037][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:28.038][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.050][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:28.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.056][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-02 02:00:28.057][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-02 02:00:28.090][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-02 02:00:28.102][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:28.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:28.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 02:00:28.109][biodb::testThat]
biodb.INFO [2023-02-02 02:00:28.110][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-02-02 02:00:28.111][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:00:28.113][biodb::testThat]
biodb.TRACE[2023-02-02 02:00:28.117][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-02 02:00:28.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-02 02:00:28.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-02 02:00:28.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-02 02:00:28.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:28.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:00:28.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:28.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:00:28.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:28.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:28.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:28.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:28.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:28.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:28.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:28.233][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-02-02 02:00:28.238][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 02:00:28.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-02-02 02:00:28.241][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 02:00:28.332][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-02-02 02:00:29.415][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-02 02:00:29.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:29.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:29.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:29.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:29.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:29.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:29.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:29.433][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.438][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.443][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.445][private$selectFields]
biodb.TRACE[2023-02-02 02:00:29.446][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:29.447][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:29.449][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.450][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.451][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.454][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.455][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.457][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.459][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.461][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.462][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.463][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.465][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.467][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.469][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:29.470][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.487][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-02 02:00:29.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:29.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:29.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:29.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:29.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:29.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:29.502][FUN] Functions in observer BiodbConfig: [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[2023-02-02 02:00:29.503][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.514][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.516][private$selectFields]
biodb.TRACE[2023-02-02 02:00:29.517][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:29.518][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:29.519][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.521][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.522][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.525][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.528][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.529][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.530][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.532][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.533][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.534][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.536][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.537][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.538][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.540][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:29.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.552][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.558][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-02 02:00:29.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:29.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:29.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:29.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:29.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:29.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:29.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:29.575][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.580][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.585][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.587][private$selectFields]
biodb.TRACE[2023-02-02 02:00:29.588][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-02 02:00:29.589][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:00:29.591][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.592][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.594][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.595][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.596][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.598][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.599][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.602][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.603][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.604][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:00:29.606][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.607][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.610][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.611][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-02 02:00:29.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:29.629][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-02 02:00:29.631][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-02 02:00:29.632][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-02 02:00:29.661][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:29.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-02 02:00:29.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:29.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-02 02:00:29.668][biodb::testThat]
biodb.INFO [2023-02-02 02:00:29.669][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-02-02 02:00:29.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:00:29.671][biodb::testThat]
biodb.DEBUG[2023-02-02 02:00:29.674][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-02 02:00:29.676][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-02 02:00:29.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-02 02:00:29.680][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-02 02:00:29.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-02 02:00:29.683][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-02 02:00:29.684][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 02:00:29.686][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-02 02:00:29.687][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-02 02:00:29.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:29.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:29.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:29.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:29.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:29.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:29.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:29.722][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-02-02 02:00:29.725][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:29.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:29.728][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:30.931][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:30.933][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:30.934][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:30.936][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:32.356][private$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[2023-02-02 02:00:32.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:32.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:32.360][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:33.651][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:33.652][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:33.654][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:33.655][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:35.127][private$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[2023-02-02 02:00:35.128][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:35.130][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:35.132][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:36.389][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:36.391][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:36.392][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:36.393][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:37.850][private$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[2023-02-02 02:00:37.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:37.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:37.855][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:39.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:39.169][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:39.171][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:39.172][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:40.625][private$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[2023-02-02 02:00:40.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:40.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:40.629][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:41.875][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:41.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:41.878][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:41.879][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:43.318][private$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[2023-02-02 02:00:43.319][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:43.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:43.322][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:44.570][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:44.571][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:44.572][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:44.574][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:46.032][private$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[2023-02-02 02:00:46.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:46.035][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:46.037][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:47.317][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:47.319][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:47.320][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:47.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:48.758][private$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[2023-02-02 02:00:48.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:48.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:48.762][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:50.032][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:50.034][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:50.035][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:50.036][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:51.487][private$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[2023-02-02 02:00:51.489][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:51.490][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:51.492][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:52.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:52.761][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:52.762][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:52.763][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:54.205][private$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[2023-02-02 02:00:54.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:54.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:54.210][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-02 02:00:55.489][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:55.491][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:55.492][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-02 02:00:55.494][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-02 02:00:56.982][private$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[2023-02-02 02:00:56.992][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-02-02 02:00:56.998][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-02 02:00:57.018][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-02 02:00:57.019][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 02:00:57.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:57.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:57.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:57.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:57.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:57.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:57.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:00:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:57.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:57.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:57.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:00:57.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:00:57.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:00:57.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:00:57.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:00:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:00:57.084][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-02 02:00:57.085][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-02 02:00:57.094][biodb::testThat]
biodb.INFO [2023-02-02 02:00:57.096][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-02 02:00:57.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:00:57.099][biodb::testThat]
biodb.DEBUG[2023-02-02 02:00:57.112][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-02-02 02:00:57.113][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-02-02 02:00:57.115][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-02 02:00:57.117][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-02-02 02:00:57.119][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-02-02 02:00:57.121][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-02 02:00:57.122][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-02 02:00:57.124][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 02:00:57.125][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-02 02:00:57.126][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-02 02:00:57.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:00:57.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:00:57.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:00:57.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:00:57.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:00:57.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:00:57.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:00:57.148][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-02-02 02:00:57.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:57.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:57.155][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:00:58.392][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:00:58.393][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:00:58.394][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[2023-02-02 02:00:58.396][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:00:59.832][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:00:59.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:00:59.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:00:59.836][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:01.105][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:01.106][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:01.108][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[2023-02-02 02:01:01.109][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:02.556][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:02.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:02.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:02.561][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:03.808][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:03.810][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:03.811][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[2023-02-02 02:01:03.812][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:05.264][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:05.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:05.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:05.269][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:06.524][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:06.525][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:06.527][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[2023-02-02 02:01:06.528][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:09.172][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:09.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:09.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:09.176][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:10.432][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:10.433][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:10.435][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[2023-02-02 02:01:10.436][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:11.890][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:11.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:11.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:11.895][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:13.105][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:13.106][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:13.108][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[2023-02-02 02:01:13.109][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:14.550][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:14.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:14.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:14.554][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:15.746][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:15.747][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:15.749][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[2023-02-02 02:01:15.750][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:17.208][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:17.209][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:17.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:17.212][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:18.504][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:18.505][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:18.507][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[2023-02-02 02:01:18.508][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:19.974][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:19.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:19.977][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:19.978][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:21.229][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:21.230][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:21.231][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[2023-02-02 02:01:21.233][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:22.679][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:22.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:22.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:22.683][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-02 02:01:23.954][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-02 02:01:23.956][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-02 02:01:23.957][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[2023-02-02 02:01:23.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-02 02:01:25.414][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-02 02:01:25.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:01:25.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:25.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:25.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:25.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:25.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:25.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:25.432][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-02-02 02:01:25.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:25.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:25.439][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-02-02 02:01:26.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-02-02 02:01:28.038][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:28.048][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-02-02 02:01:28.064][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-02-02 02:01:28.080][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-02-02 02:01:28.085][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-02 02:01:28.154][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-02 02:01:28.156][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 02:01:28.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:01:28.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:28.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:28.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:28.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:28.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:28.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:01:28.176][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:01:28.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:01:28.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:28.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:28.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:28.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:28.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:28.208][FUN] Functions in observer BiodbConfig: [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[2023-02-02 02:01:28.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:01:28.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:01:28.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:01:28.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:01:28.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.246][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:01:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:01:28.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.252][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:01:28.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:01:28.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:01:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:01:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.267][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:01:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:01:28.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:01:28.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:01:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.282][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:01:28.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:01:28.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:01:28.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:01:28.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.297][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:01:28.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:01:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:01:28.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:01:28.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:01:28.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:01:28.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:01:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:01:28.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:01:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:01:28.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.353][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:01:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.359][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 02:01:28.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.376][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:01:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:28.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:28.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.423][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.434][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:01:28.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:01:28.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:01:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:28.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:01:28.506][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-02-02 02:01:28.507][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-02 02:01:28.508][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-02-02 02:01:28.525][biodb::testThat]
biodb.INFO [2023-02-02 02:01:28.527][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-02-02 02:01:28.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:28.529][biodb::testThat]
biodb.INFO [2023-02-02 02:01:28.578][biodb::testThat]
biodb.INFO [2023-02-02 02:01:28.580][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-02-02 02:01:28.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:28.582][biodb::testThat]
biodb.INFO [2023-02-02 02:01:28.592][biodb::testThat]
biodb.INFO [2023-02-02 02:01:28.594][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-02-02 02:01:28.595][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:28.596][biodb::testThat]
biodb.DEBUG[2023-02-02 02:01:28.601][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[2023-02-02 02:01:28.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:28.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:28.610][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-02-02 02:01:33.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-02-02 02:01:43.266][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:43.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-02-02 02:01:43.321][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-02-02 02:01:44.490][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:01:44.491][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:01:44.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:44.494][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:01:44.495][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:01:44.497][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:01:44.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:01:44.499][ef$get] fields variable is a list.
biodb.INFO [2023-02-02 02:01:44.502][biodb::testThat]
biodb.INFO [2023-02-02 02:01:44.503][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-02-02 02:01:44.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:44.505][biodb::testThat]
biodb.ERROR[2023-02-02 02:01:44.524][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-02-02 02:01:44.543][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-02-02 02:01:44.556][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-02 02:01:44.558][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-02 02:01:44.560][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-02 02:01:44.561][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-02 02:01:44.562][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:44.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:44.565][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.567][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-02 02:01:44.582][biodb::testContext]
biodb.INFO [2023-02-02 02:01:44.583][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 02:01:44.585][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-02-02 02:01:44.586][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 02:01:44.588][biodb::testContext]
biodb.INFO [2023-02-02 02:01:44.594][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-02 02:01:44.596][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-02 02:01:44.601][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:01:44.603][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-02 02:01:44.604][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.608][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[2023-02-02 02:01:44.609][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-02 02:01:44.611][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.616][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-02 02:01:44.618][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.623][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-02 02:01:44.624][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-02 02:01:44.626][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-02 02:01:44.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.631][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-02 02:01:44.632][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-02 02:01:44.634][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.639][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-02 02:01:44.641][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-02 02:01:44.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.646][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-02 02:01:44.648][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-02 02:01:44.649][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-02 02:01:44.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.655][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-02 02:01:44.656][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.662][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-02 02:01:44.663][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-02 02:01:44.665][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-02 02:01:44.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.670][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-02 02:01:44.672][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-02 02:01:44.673][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-02 02:01:44.675][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-02 02:01:44.676][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-02 02:01:44.678][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-02 02:01:44.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.683][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-02 02:01:44.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-02 02:01:44.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.690][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-02 02:01:44.691][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-02 02:01:44.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.696][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-02 02:01:44.698][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-02 02:01:44.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.703][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-02 02:01:44.705][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-02 02:01:44.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.710][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-02 02:01:44.711][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-02 02:01:44.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.716][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-02 02:01:44.718][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-02 02:01:44.722][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-02 02:01:44.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.727][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-02 02:01:44.729][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-02 02:01:44.730][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-02 02:01:44.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.736][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-02 02:01:44.738][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.739][self$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[2023-02-02 02:01:44.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:01:44.744][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.745][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.749][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:01:44.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:01:44.752][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.754][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-02 02:01:44.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:01:44.756][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.758][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.759][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:01:44.759][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:01:44.759][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 02:01:44.759][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 02:01:44.759][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 02:01:44.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:01:44.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.764][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:01:44.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.770][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:01:44.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:01:44.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.776][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.777][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-02 02:01:44.780][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.781][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 02:01:44.783][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.784][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:01:44.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.789][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.790][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.791][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 02:01:44.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:01:44.794][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.796][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-02 02:01:44.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:01:44.799][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.802][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:01:44.802][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:01:44.802][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 02:01:44.802][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 02:01:44.802][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 02:01:44.803][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:01:44.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.807][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:01:44.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.813][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:01:44.816][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:01:44.817][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.818][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.820][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-02 02:01:44.822][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.824][self$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[2023-02-02 02:01:44.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:01:44.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.834][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:01:44.835][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:01:44.837][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.838][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-02 02:01:44.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:01:44.841][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.842][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.844][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:01:44.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:01:44.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.855][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:01:44.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:01:44.859][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.892][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.894][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-02 02:01:44.896][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.898][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 02:01:44.899][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:01:44.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.905][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.907][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.908][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 02:01:44.910][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:01:44.911][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.913][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-02 02:01:44.914][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:01:44.916][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.917][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:44.919][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.920][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:01:44.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.925][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:01:44.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:44.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:44.929][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:01:44.931][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:01:44.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:01:44.935][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:44.937][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:44.939][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:01:44.941][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.976][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[2023-02-02 02:01:44.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.982][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[2023-02-02 02:01:44.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:44.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:44.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:44.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:44.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:44.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.030][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[2023-02-02 02:01:45.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.059][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-02 02:01:45.061][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-02 02:01:45.063][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-02 02:01:45.065][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-02 02:01:45.067][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-02 02:01:45.069][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-02 02:01:45.071][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-02 02:01:45.073][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-02 02:01:45.076][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-02 02:01:45.078][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-02 02:01:45.080][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-02 02:01:45.082][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-02 02:01:45.084][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-02 02:01:45.086][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-02 02:01:45.089][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-02 02:01:45.091][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 02:01:45.093][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-02 02:01:45.095][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-02 02:01:45.097][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-02 02:01:45.099][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-02 02:01:45.102][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-02 02:01:45.104][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-02 02:01:45.106][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-02 02:01:45.108][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-02 02:01:45.110][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-02 02:01:45.113][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-02 02:01:45.115][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-02 02:01:45.117][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-02 02:01:45.119][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-02 02:01:45.122][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-02 02:01:45.124][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-02 02:01:45.126][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-02 02:01:45.128][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-02 02:01:45.130][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-02 02:01:45.133][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-02 02:01:45.135][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-02 02:01:45.137][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-02 02:01:45.139][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-02 02:01:45.142][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-02 02:01:45.144][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-02 02:01:45.146][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-02 02:01:45.149][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-02 02:01:45.151][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-02 02:01:45.153][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-02 02:01:45.155][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-02 02:01:45.157][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-02 02:01:45.160][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-02 02:01:45.162][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-02 02:01:45.164][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-02 02:01:45.167][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-02 02:01:45.169][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-02 02:01:45.171][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-02 02:01:45.174][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-02 02:01:45.176][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-02 02:01:45.178][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-02 02:01:45.180][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-02 02:01:45.182][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-02 02:01:45.184][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-02 02:01:45.187][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-02 02:01:45.189][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-02 02:01:45.191][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-02 02:01:45.193][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-02 02:01:45.195][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-02 02:01:45.197][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-02 02:01:45.199][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-02 02:01:45.201][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-02 02:01:45.203][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-02 02:01:45.205][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-02 02:01:45.208][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-02 02:01:45.210][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-02 02:01:45.212][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-02 02:01:45.214][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-02 02:01:45.216][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-02 02:01:45.218][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-02 02:01:45.220][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-02 02:01:45.222][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-02 02:01:45.224][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-02 02:01:45.226][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-02 02:01:45.228][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-02 02:01:45.231][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-02 02:01:45.233][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-02 02:01:45.235][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-02 02:01:45.237][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-02 02:01:45.239][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-02 02:01:45.241][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-02 02:01:45.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:01:45.244][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.246][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.248][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[2023-02-02 02:01:45.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.257][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[2023-02-02 02:01:45.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.284][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.DEBUG[2023-02-02 02:01:45.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.338][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[2023-02-02 02:01:45.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.365][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[2023-02-02 02:01:45.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.382][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[2023-02-02 02:01:45.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.391][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[2023-02-02 02:01:45.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:01:45.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:01:45.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:01:45.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:01:45.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:01:45.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:01:45.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:01:45.419][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-02 02:01:45.421][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:01:45.423][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:45.425][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-02 02:01:45.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:45.428][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:01:45.429][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:45.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:01:45.432][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:45.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:01:45.434][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:01:45.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:01:45.437][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:45.439][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-02 02:01:45.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-02 02:01:45.441][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-02 02:01:45.443][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-02 02:01:45.444][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:01:45.444][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:01:45.446][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:01:45.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:45.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:45.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:01:45.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:01:45.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:01:45.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:01:45.455][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 02:01:45.455][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-02 02:01:45.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:01:45.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:01:45.459][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-02 02:01:45.460][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:01:45.462][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-02 02:01:45.464][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 02:01:45.469][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:01:45.470][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-02 02:01:45.472][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:01:45.474][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-02 02:01:45.476][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 02:01:45.477][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 02:01:45.479][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-02 02:01:45.480][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-02 02:01:45.482][biodb::testThat]
biodb.INFO [2023-02-02 02:01:45.484][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-02-02 02:01:45.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:45.486][biodb::testThat]
biodb.DEBUG[2023-02-02 02:01:45.491][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-02-02 02:01:45.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:45.499][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:45.501][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-02-02 02:01:46.772][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[2023-02-02 02:01:48.079][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:48.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-02-02 02:01:48.104][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-02-02 02:01:48.120][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[2023-02-02 02:01:48.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:48.125][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:48.128][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-02-02 02:01:49.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-02-02 02:01:50.779][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:50.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-02-02 02:01:50.804][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-02-02 02:01:50.850][biodb::testThat]
biodb.INFO [2023-02-02 02:01:50.851][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-02-02 02:01:50.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:50.854][biodb::testThat]
biodb.INFO [2023-02-02 02:01:50.889][biodb::testThat]
biodb.INFO [2023-02-02 02:01:50.891][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-02-02 02:01:50.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:01:50.893][biodb::testThat]
biodb.DEBUG[2023-02-02 02:01:50.898][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-02-02 02:01:50.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:50.904][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:50.906][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-02-02 02:01:52.053][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-02-02 02:01:53.144][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:53.154][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-02-02 02:01:53.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-02-02 02:01:53.178][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[2023-02-02 02:01:53.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 02:01:53.184][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-02-02 02:01:53.185][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 02:01:53.187][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-02-02 02:01:53.194][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[2023-02-02 02:01:53.198][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:53.199][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:53.202][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-02-02 02:01:54.320][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-02-02 02:01:55.456][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:01:55.474][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-02-02 02:01:55.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-02-02 02:01:55.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-02-02 02:01:55.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:01:55.506][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:01:55.508][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-02-02 02:01:57.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-02-02 02:02:00.498][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:02:00.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-02-02 02:02:00.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-02-02 02:02:00.682][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[2023-02-02 02:02:00.686][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-02 02:02:00.687][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-02 02:02:00.708][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-02-02 02:02:02.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-02-02 02:02:05.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-02 02:02:05.720][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-02-02 02:02:05.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-02-02 02:02:05.880][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-02 02:02:05.882][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-02 02:02:05.883][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-02 02:02:05.884][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-02 02:02:05.885][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:05.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:05.888][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:05.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:05.890][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-02 02:02:05.896][biodb::testContext]
biodb.INFO [2023-02-02 02:02:05.897][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 02:02:05.899][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-02-02 02:02:05.900][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-02 02:02:05.901][biodb::testContext]
biodb.INFO [2023-02-02 02:02:05.907][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-02 02:02:05.909][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-02 02:02:05.914][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:02:05.915][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-02 02:02:05.917][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.921][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[2023-02-02 02:02:05.922][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-02 02:02:05.923][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.928][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-02 02:02:05.930][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.933][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[2023-02-02 02:02:05.935][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-02 02:02:05.936][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-02 02:02:05.938][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-02 02:02:05.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.942][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-02 02:02:05.944][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-02 02:02:05.945][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.950][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-02 02:02:05.952][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-02 02:02:05.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.957][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-02 02:02:05.958][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-02 02:02:05.960][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-02 02:02:05.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.965][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-02 02:02:05.966][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.971][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-02 02:02:05.973][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-02 02:02:05.974][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-02 02:02:05.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.979][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-02 02:02:05.980][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-02 02:02:05.982][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-02 02:02:05.983][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-02 02:02:05.985][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-02 02:02:05.986][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-02 02:02:05.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.991][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-02 02:02:05.993][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-02 02:02:05.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:05.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:05.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:05.998][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-02 02:02:05.999][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-02 02:02:06.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.004][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-02 02:02:06.005][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-02 02:02:06.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.010][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-02 02:02:06.012][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-02 02:02:06.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.017][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-02 02:02:06.018][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-02 02:02:06.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.023][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-02 02:02:06.025][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-02 02:02:06.029][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-02 02:02:06.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.034][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-02 02:02:06.035][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-02 02:02:06.037][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-02 02:02:06.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.042][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-02 02:02:06.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.046][self$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[2023-02-02 02:02:06.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.049][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:02:06.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.053][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.055][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:02:06.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:02:06.058][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.060][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-02 02:02:06.061][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:02:06.062][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.064][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:02:06.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:02:06.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 02:02:06.065][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 02:02:06.065][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 02:02:06.066][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:02:06.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:02:06.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.074][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.076][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.077][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:02:06.078][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:02:06.079][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.081][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.082][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-02 02:02:06.085][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.086][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 02:02:06.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.089][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:02:06.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.093][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.096][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 02:02:06.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:02:06.098][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.100][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-02 02:02:06.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:02:06.103][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.105][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:02:06.105][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:02:06.105][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-02 02:02:06.105][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-02 02:02:06.105][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-02 02:02:06.107][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:02:06.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:02:06.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.115][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.116][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:02:06.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:02:06.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.121][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.123][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-02 02:02:06.125][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.127][self$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[2023-02-02 02:02:06.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.129][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:02:06.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.136][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:02:06.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:02:06.139][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.140][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-02 02:02:06.142][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:02:06.143][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.144][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.146][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:02:06.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:02:06.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.156][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.158][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:02:06.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:02:06.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.180][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.189][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-02 02:02:06.191][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.193][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-02 02:02:06.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:02:06.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.200][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.201][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-02 02:02:06.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:02:06.206][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.207][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-02 02:02:06.208][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:02:06.210][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.211][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.213][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.214][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:02:06.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.218][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:02:06.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.222][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.223][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.225][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:02:06.226][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:02:06.227][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.229][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.230][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:02:06.232][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.282][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[2023-02-02 02:02:06.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.307][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[2023-02-02 02:02:06.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.338][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-02 02:02:06.340][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-02 02:02:06.342][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-02 02:02:06.344][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-02 02:02:06.346][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-02 02:02:06.348][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-02 02:02:06.350][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-02 02:02:06.352][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-02 02:02:06.354][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-02 02:02:06.356][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-02 02:02:06.358][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-02 02:02:06.359][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-02 02:02:06.361][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-02 02:02:06.363][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-02 02:02:06.365][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-02 02:02:06.367][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 02:02:06.369][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-02 02:02:06.371][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-02 02:02:06.373][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-02 02:02:06.375][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-02 02:02:06.377][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-02 02:02:06.379][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-02 02:02:06.381][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-02 02:02:06.383][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-02 02:02:06.385][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-02 02:02:06.387][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-02 02:02:06.389][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-02 02:02:06.391][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-02 02:02:06.393][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-02 02:02:06.395][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-02 02:02:06.397][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-02 02:02:06.399][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-02 02:02:06.400][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-02 02:02:06.403][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-02 02:02:06.405][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-02 02:02:06.407][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-02 02:02:06.409][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-02 02:02:06.411][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-02 02:02:06.413][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-02 02:02:06.415][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-02 02:02:06.417][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-02 02:02:06.419][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-02 02:02:06.421][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-02 02:02:06.423][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-02 02:02:06.425][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-02 02:02:06.427][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-02 02:02:06.429][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-02 02:02:06.431][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-02 02:02:06.433][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-02 02:02:06.435][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-02 02:02:06.439][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-02 02:02:06.441][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-02 02:02:06.443][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-02 02:02:06.445][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-02 02:02:06.447][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-02 02:02:06.449][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-02 02:02:06.451][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-02 02:02:06.453][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-02 02:02:06.455][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-02 02:02:06.457][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-02 02:02:06.459][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-02 02:02:06.461][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-02 02:02:06.463][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-02 02:02:06.465][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-02 02:02:06.467][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-02 02:02:06.469][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-02 02:02:06.471][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-02 02:02:06.473][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-02 02:02:06.475][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-02 02:02:06.477][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-02 02:02:06.479][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-02 02:02:06.481][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-02 02:02:06.483][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-02 02:02:06.485][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-02 02:02:06.487][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-02 02:02:06.489][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-02 02:02:06.491][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-02 02:02:06.493][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-02 02:02:06.495][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-02 02:02:06.497][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-02 02:02:06.498][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-02 02:02:06.500][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-02 02:02:06.502][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-02 02:02:06.504][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-02 02:02:06.506][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-02 02:02:06.508][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-02 02:02:06.509][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.511][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.574][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[2023-02-02 02:02:06.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.582][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[2023-02-02 02:02:06.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.591][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[2023-02-02 02:02:06.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.608][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[2023-02-02 02:02:06.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.616][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[2023-02-02 02:02:06.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.632][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[2023-02-02 02:02:06.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-02 02:02:06.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:06.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:06.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:06.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:06.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:06.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-02 02:02:06.676][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-02 02:02:06.678][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:02:06.680][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.682][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.683][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.684][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-02 02:02:06.686][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.687][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.688][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.690][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.691][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-02 02:02:06.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-02 02:02:06.694][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.695][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-02 02:02:06.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-02 02:02:06.698][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-02 02:02:06.699][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-02 02:02:06.701][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-02 02:02:06.701][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-02 02:02:06.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-02 02:02:06.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-02 02:02:06.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-02 02:02:06.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-02 02:02:06.709][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-02 02:02:06.711][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-02 02:02:06.711][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-02 02:02:06.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-02 02:02:06.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-02 02:02:06.715][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-02 02:02:06.716][self$setPropertyValue]
biodb.DEBUG[2023-02-02 02:02:06.717][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-02 02:02:06.719][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-02 02:02:06.724][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:02:06.725][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-02 02:02:06.726][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-02 02:02:06.728][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-02 02:02:06.730][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 02:02:06.731][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-02 02:02:06.733][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-02 02:02:06.734][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-02 02:02:06.736][biodb::testThat]
biodb.INFO [2023-02-02 02:02:06.737][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2023-02-02 02:02:06.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-02 02:02:06.740][biodb::testThat]
biodb.DEBUG[2023-02-02 02:02:06.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-02-02 02:02:06.750][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-02 02:02:06.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-02-02 02:02:06.754][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-02 02:02:06.833][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-02-02 02:02:07.939][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-02-02 02:02:07.940][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-02 02:02:07.943][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-02-02 02:02:07.945][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-02-02 02:02:07.947][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-02-02 02:02:07.948][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-02 02:02:07.969][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-02 02:02:07.970][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-02 02:02:07.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:02:07.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:07.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:07.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:07.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:07.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:07.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:02:07.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:07.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:07.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:07.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:07.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:07.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.022][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:02:08.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:02:08.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.028][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:02:08.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:02:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.034][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.049][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.055][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.064][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:02:08.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.070][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:02:08.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.079][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.110][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:02:08.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.115][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 02:02:08.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.132][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:02:08.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.180][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:02:08.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:02:08.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:08.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:08.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:08.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:08.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:08.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:02:08.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.269][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:02:08.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-02 02:02:08.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:02:08.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-02 02:02:08.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.286][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.295][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.311][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:02:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-02 02:02:08.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.380][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:02:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-02 02:02:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.403][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-02 02:02:08.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.413][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-02 02:02:08.489][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-02-02 02:02:08.491][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-02 02:02:08.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:02:08.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:08.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:08.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:08.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:08.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:08.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-02 02:02:08.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.521][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-02 02:02:08.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-02 02:02:08.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.527][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-02 02:02:08.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-02 02:02:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.533][private$selectFields] Fields none
biodb.TRACE[2023-02-02 02:02:08.534][private$selectFields]
biodb.TRACE[2023-02-02 02:02:08.535][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-02-02 02:02:08.537][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:02:08.538][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.540][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.544][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.549][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.551][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.552][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.555][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.556][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.558][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.560][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.562][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.563][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.566][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.567][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.569][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.570][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.572][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.573][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.577][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.580][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.583][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.584][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.586][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.588][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.591][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.594][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.595][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.597][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.599][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.601][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.602][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.605][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.610][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.612][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.613][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.616][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.617][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.622][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.623][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.624][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.627][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.629][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.630][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.631][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.633][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.636][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.641][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.643][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.644][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.647][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.648][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.650][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.651][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.652][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.654][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.655][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.658][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.659][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.661][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.664][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.665][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.666][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.668][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.669][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.670][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.672][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.675][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.676][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-02-02 02:02:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.737][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.742][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.748][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.759][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.819][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.837][private$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[2023-02-02 02:02:08.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-02 02:02:08.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:08.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:08.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:08.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:08.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:08.852][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.TRACE[2023-02-02 02:02:08.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-02 02:02:08.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.866][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-02 02:02:08.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-02 02:02:08.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-02 02:02:08.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-02 02:02:08.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.880][private$selectFields] Fields none
biodb.TRACE[2023-02-02 02:02:08.881][private$selectFields]
biodb.TRACE[2023-02-02 02:02:08.883][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-02-02 02:02:08.884][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-02 02:02:08.885][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.887][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.891][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.894][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.897][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.898][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.899][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.902][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.903][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.905][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.908][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.910][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.913][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.914][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.916][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.919][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.920][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.923][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.924][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.925][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.927][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.930][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.931][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.934][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.935][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.938][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.939][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.941][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.942][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.943][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.945][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.946][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.947][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.949][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.950][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.952][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:08.956][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.957][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.958][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:08.960][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:08.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.962][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.964][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:08.965][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:08.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.968][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.969][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.971][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:08.972][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.973][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.975][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.976][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-02 02:02:08.977][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:08.979][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:08.980][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.982][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:08.986][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.987][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.988][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.990][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:08.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.992][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.994][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.995][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:08.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:08.998][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:08.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.003][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.005][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:09.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:09.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.009][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.010][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:09.011][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:09.013][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.014][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.015][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.017][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.018][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.019][ef$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.021][private$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[2023-02-02 02:02:09.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:09.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:09.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:09.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:09.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-02 02:02:09.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-02 02:02:09.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-02 02:02:09.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.061][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.066][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-02 02:02:09.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-02 02:02:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-02 02:02:09.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:09.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:09.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:09.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.135][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-02 02:02:09.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-02 02:02:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:09.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:09.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:09.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-02 02:02:09.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-02 02:02:09.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.162][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.167][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-02 02:02:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-02 02:02:09.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-02 02:02:09.178][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-02-02 02:02:09.180][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-02 02:02:09.181][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-02-02 02:02:09.185][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-02 02:02:09.186][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-02 02:02:09.188][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-02 02:02:09.189][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-02 02:02:09.190][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-02 02:02:09.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-02 02:02:09.193][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-02 02:02:09.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-02 02:02:09.195][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-02 02:02:09.196][FUN] Functions in observer 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
31.087 1.595 177.774
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 2.853 | 0.148 | 6.460 | |
| LipidmapsStructureEntry | 0.500 | 0.000 | 0.528 | |