| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:14 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 203/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.9.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the biodbLipidmaps package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbLipidmaps |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.9.0.tar.gz |
| StartedAt: 2024-03-27 20:40:02 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 20:45:21 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 319.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.9.0’
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbLipidmaps’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 [2024-03-27 20:40:53.339][biodb::testContext]
biodb.INFO [2024-03-27 20:40:53.343][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:53.346][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-27 20:40:53.348][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:53.351][biodb::testContext]
biodb.INFO [2024-03-27 20:40:53.364][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:53.368][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:53.382][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:53.385][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:40:53.387][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.396][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:40:53.432][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.438][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:40:53.439][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.443][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:40:53.444][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:40:53.446][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:40:53.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.451][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:40:53.453][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:40:53.454][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.461][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:40:53.463][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:40:53.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.469][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:40:53.471][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:40:53.473][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:40:53.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.481][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:40:53.483][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.487][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[2024-03-27 20:40:53.489][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:40:53.490][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:40:53.491][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:40:53.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.495][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:53.497][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:40:53.498][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:40:53.499][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:40:53.500][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:40:53.502][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:40:53.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.509][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:40:53.510][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:40:53.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.514][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:40:53.516][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:40:53.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.522][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:40:53.524][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:40:53.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.531][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:40:53.533][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:40:53.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.538][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[2024-03-27 20:40:53.540][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:40:53.542][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:40:53.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.549][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:53.550][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:40:53.556][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:40:53.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.564][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:40:53.567][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:40:53.569][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:40:53.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.583][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:40:53.643][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.689][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:40:53.691][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:53.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.698][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.700][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:53.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:53.702][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.703][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:40:53.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:53.706][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.707][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.708][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:53.708][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:53.708][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:53.708][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:53.708][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:53.710][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:53.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:53.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.720][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:53.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:53.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.727][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.729][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:40:53.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.733][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:53.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:53.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.745][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:53.747][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:53.749][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.751][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:40:53.753][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:53.754][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.757][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:53.757][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:53.757][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:53.757][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:53.757][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:53.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:53.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:53.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.771][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:53.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:53.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.777][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.779][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:40:53.782][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.784][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:40:53.786][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.788][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:53.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.792][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.794][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:53.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:53.796][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.797][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:40:53.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:53.799][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.802][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.803][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:53.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:53.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.813][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:53.816][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:53.817][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.819][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.821][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:40:53.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.825][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:53.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:53.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.836][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:53.837][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:53.839][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.841][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:40:53.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:53.844][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.845][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:53.847][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:53.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:53.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:53.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:53.857][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:53.858][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:53.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:53.861][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:53.862][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:53.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:53.870][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.919][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[2024-03-27 20:40:53.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.926][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.DEBUG[2024-03-27 20:40:53.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.933][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[2024-03-27 20:40:53.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:53.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:53.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:53.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:53.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:53.989][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:40:53.996][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:40:53.999][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:40:54.001][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:40:54.004][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:54.006][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:40:54.009][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:54.011][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:54.014][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:40:54.016][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:40:54.018][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:54.021][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:40:54.023][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:54.025][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:54.027][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:40:54.030][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:40:54.032][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:40:54.034][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:40:54.037][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:54.039][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:40:54.041][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:40:54.043][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:40:54.045][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:40:54.047][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:40:54.050][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:40:54.052][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:40:54.054][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:40:54.056][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:40:54.059][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:40:54.061][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:40:54.063][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:40:54.065][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:40:54.068][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:40:54.070][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:40:54.072][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:40:54.074][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:40:54.084][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:40:54.086][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:40:54.089][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:40:54.091][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:40:54.093][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:40:54.095][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:40:54.098][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:40:54.100][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:40:54.102][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:40:54.104][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:40:54.106][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:40:54.108][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:40:54.111][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:40:54.113][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:40:54.115][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:40:54.117][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:40:54.119][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:40:54.121][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:40:54.123][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:40:54.125][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:40:54.128][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:40:54.130][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:40:54.132][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:40:54.134][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:40:54.137][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:40:54.139][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:40:54.141][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:40:54.143][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:40:54.146][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:40:54.148][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:40:54.151][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:54.153][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:54.156][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:40:54.159][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:40:54.161][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:40:54.164][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:40:54.166][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:40:54.168][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:40:54.171][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:40:54.173][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:40:54.176][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:40:54.178][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:40:54.181][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:40:54.183][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:40:54.185][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:40:54.188][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:40:54.190][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:40:54.200][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:40:54.203][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:54.208][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:54.210][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.213][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.214][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[2024-03-27 20:40:54.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.239][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[2024-03-27 20:40:54.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.248][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[2024-03-27 20:40:54.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.258][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[2024-03-27 20:40:54.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.276][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[2024-03-27 20:40:54.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.365][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[2024-03-27 20:40:54.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:54.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:54.388][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:54.400][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:40:54.404][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:54.406][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:40:54.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:54.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:54.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:54.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:54.416][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:54.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:54.420][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:54.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:54.424][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:54.425][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:40:54.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:40:54.429][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:40:54.431][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:54.433][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:54.433][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:54.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:54.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:54.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:54.439][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:54.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:54.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:54.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:54.446][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:40:54.446][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:40:54.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:54.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:54.450][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:54.451][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:54.462][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:40:54.466][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:40:54.518][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:40:54.520][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:40:54.527][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:40:54.535][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:40:54.543][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:40:54.545][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:40:54.547][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:40:54.549][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:40:54.563][biodb::testThat]
biodb.INFO [2024-03-27 20:40:54.564][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-27 20:40:54.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:54.567][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:54.573][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-27 20:40:54.576][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:54.583][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:40:54.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:54.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:54.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:54.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:54.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:54.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:54.627][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:40:54.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:54.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:54.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:54.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:54.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:54.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:54.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.684][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:40:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:40:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:54.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:54.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:54.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:54.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.763][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:54.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:54.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.770][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:40:54.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:40:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:54.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.803][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:40:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.810][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:40:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:40:54.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.961][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.968][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:54.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:54.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:54.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:54.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:54.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:54.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:54.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:55.025][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 20:40:55.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:55.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:55.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.032][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:55.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:55.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.093][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.158][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.201][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.203][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.206][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.243][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.248][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.307][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.319][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.320][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.323][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.361][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.363][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.365][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.400][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.401][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.403][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.423][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.431][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.441][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.443][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.448][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.467][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.468][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.471][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.478][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.480][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.483][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.491][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.496][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.510][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.516][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.522][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.530][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.532][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.536][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:55.549][biodb::testThat]
biodb.INFO [2024-03-27 20:40:55.552][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-27 20:40:55.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:55.556][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:55.582][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-27 20:40:55.595][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:55.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 20:40:55.605][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:55.608][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-27 20:40:55.610][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:55.658][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:55.660][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:40:55.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:55.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:55.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:55.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:55.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:55.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:55.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:55.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:55.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:55.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:55.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.706][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:40:55.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:40:55.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:55.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:55.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:40:55.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.729][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.736][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:40:55.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.742][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:40:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:40:55.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:40:55.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.781][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:40:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:40:55.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:40:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:55.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:55.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:55.901][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 20:40:55.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-27 20:40:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-27 20:40:55.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:40:55.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:40:55.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:40:55.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:40:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:55.934][biodb::testThat]
biodb.INFO [2024-03-27 20:40:55.936][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-27 20:40:55.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:55.940][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:55.945][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.951][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:55.953][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-27 20:40:55.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:55.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:55.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:56.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:56.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:56.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:56.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:56.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:56.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:56.015][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:40:56.021][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[2024-03-27 20:40:56.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:56.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:56.080][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-03-27 20:40:57.288][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-03-27 20:40:58.023][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:58.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-03-27 20:40:58.055][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-03-27 20:40:58.058][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 20:40:58.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:58.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:58.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.078][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:58.087][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.089][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-27 20:40:58.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:58.093][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:58.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:58.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:58.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:58.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:58.345][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:40:58.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:58.387][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:40:58.389][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:58.390][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-27 20:40:58.407][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.409][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-27 20:40:58.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:58.412][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:58.441][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:58.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:58.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.463][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:58.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:58.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.531][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:40:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:40:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:40:58.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:58.559][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.560][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-27 20:40:58.561][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:58.562][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.571][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.572][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-27 20:40:58.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:58.574][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.586][biodb::testThat]
biodb.INFO [2024-03-27 20:40:58.588][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-27 20:40:58.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:58.592][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:58.598][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-27 20:40:59.444][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-27 20:40:59.955][biodb::testThat]
biodb.INFO [2024-03-27 20:40:59.957][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-27 20:40:59.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:59.960][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:59.970][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:59.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:59.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:59.976][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:59.978][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:59.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:59.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.000][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:41:00.004][biodb::testThat]
biodb.INFO [2024-03-27 20:41:00.006][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-27 20:41:00.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:41:00.009][biodb::testThat]
biodb.TRACE[2024-03-27 20:41:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:00.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:00.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:00.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:00.181][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:41:00.187][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:41:00.189][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:41:00.192][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:41:00.194][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-27 20:41:00.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:41:00.310][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:41:00.312][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:41:00.314][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:41:00.317][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-27 20:41:00.337][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:41:00.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:41:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:00.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:00.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:00.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:00.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:00.406][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-27 20:41:00.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:00.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:00.462][private$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[2024-03-27 20:41:04.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 20:41:16.083][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:16.086][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-03-27 20:41:16.096][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-03-27 20:41:17.018][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[2024-03-27 20:41:17.021][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:17.022][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:17.024][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-27 20:41:17.705][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 20:41:18.387][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:18.389][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-03-27 20:41:18.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-03-27 20:41:18.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-03-27 20:41:18.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:18.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:18.419][private$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[2024-03-27 20:41:19.099][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[2024-03-27 20:41:19.785][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:19.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-03-27 20:41:19.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-03-27 20:41:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:19.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:19.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:41:19.819][biodb::testThat]
biodb.INFO [2024-03-27 20:41:19.820][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-27 20:41:19.821][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:41:19.822][biodb::testThat]
biodb.TRACE[2024-03-27 20:41:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:41:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:41:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:19.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:19.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:19.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:19.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:19.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:19.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:19.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:19.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:19.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:19.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:19.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:19.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:19.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:19.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:19.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:19.865][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[2024-03-27 20:41:19.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:19.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:19.871][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-03-27 20:41:23.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-03-27 20:41:34.797][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:34.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-27 20:41:34.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-27 20:41:35.707][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-27 20:41:35.755][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:41:35.757][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-03-27 20:41:35.758][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 20:41:35.759][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:41:35.761][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:41:35.762][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:41:35.763][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:41:35.764][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:41:35.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:35.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:35.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:35.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:35.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:35.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:35.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:35.791][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-27 20:41:35.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:35.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:35.797][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 20:41:36.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-03-27 20:41:37.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:37.260][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-03-27 20:41:37.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-03-27 20:41:37.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:37.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:37.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:37.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:37.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:37.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:37.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:37.276][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-27 20:41:37.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:37.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:37.281][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-27 20:41:37.971][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-27 20:41:38.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:38.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-27 20:41:38.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-27 20:41:38.678][private$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[2024-03-27 20:41:38.680][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:41:38.681][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:41:38.682][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:41:38.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:38.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:38.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:38.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:38.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:38.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:38.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:38.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.732][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:41:38.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:41:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.736][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:41:38.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:41:38.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.740][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.743][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.751][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.755][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:41:38.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:38.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.759][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:41:38.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:38.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:41:38.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:41:38.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:41:38.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:41:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.779][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:41:38.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.783][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:41:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.795][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:41:38.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:38.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:38.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:38.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:38.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:38.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:38.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:38.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:41:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:41:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:41:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.867][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:41:38.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:41:38.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.875][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:41:38.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.883][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:41:38.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.887][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:41:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:38.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.891][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:41:38.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:38.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:41:38.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:41:38.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:41:38.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:41:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:41:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.914][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:41:38.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:41:38.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:41:38.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:41:38.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:38.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:38.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:41:38.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:41:38.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:38.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:38.979][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-27 20:41:38.989][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:41:39.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:39.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:39.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:39.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:39.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:39.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:39.015][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.TRACE[2024-03-27 20:41:39.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.024][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.025][private$selectFields]
biodb.TRACE[2024-03-27 20:41:39.026][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:39.027][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:39.028][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.029][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.030][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.032][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.034][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.036][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.037][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.038][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.039][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.040][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.042][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.043][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.048][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.064][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:41:39.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:39.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:39.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:39.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:39.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:39.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:39.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:39.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.083][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.084][private$selectFields]
biodb.TRACE[2024-03-27 20:41:39.085][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:39.086][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:39.087][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.088][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.089][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.091][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.092][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.093][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.095][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.096][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.097][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.098][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.099][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.101][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.102][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.107][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.110][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.115][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:41:39.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:39.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:39.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:39.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:39.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:39.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:39.125][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:41:39.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.134][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.135][private$selectFields]
biodb.TRACE[2024-03-27 20:41:39.136][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:39.137][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:39.137][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.138][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.140][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.141][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.142][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.144][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.158][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.159][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.160][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:39.161][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.162][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.164][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.165][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:39.166][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:39.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.178][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:41:39.179][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:41:39.180][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:41:39.189][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:39.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:39.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:41:39.196][biodb::testThat]
biodb.INFO [2024-03-27 20:41:39.197][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-27 20:41:39.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:41:39.198][biodb::testThat]
biodb.TRACE[2024-03-27 20:41:39.201][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:41:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:41:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:39.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:39.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:39.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:39.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:39.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:39.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:39.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:39.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:39.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:39.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:39.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:39.298][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[2024-03-27 20:41:39.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:39.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:39.304][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-27 20:41:43.327][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-27 20:41:54.216][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:41:54.219][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-27 20:41:54.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-27 20:41:55.113][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:41:55.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:55.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:55.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:55.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:55.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:55.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:55.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.190][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.191][private$selectFields]
biodb.TRACE[2024-03-27 20:41:55.192][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:55.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:55.194][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.195][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.197][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.199][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.200][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.201][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.203][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.204][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.461][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.462][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.463][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.465][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.466][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:55.467][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.479][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:41:55.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:55.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:55.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:55.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:55.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:55.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:55.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:55.489][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.497][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.498][private$selectFields]
biodb.TRACE[2024-03-27 20:41:55.499][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:55.500][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:55.500][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.501][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.502][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.504][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.505][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.506][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.508][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.509][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.510][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.511][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.512][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.514][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.514][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.527][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:41:55.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:55.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:55.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:55.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:55.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:55.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:55.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:55.537][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.545][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.545][private$selectFields]
biodb.TRACE[2024-03-27 20:41:55.546][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:55.547][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:55.548][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.549][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.550][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.552][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.553][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.554][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.556][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.556][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.557][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:55.558][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.559][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.561][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.562][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.570][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.574][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:41:55.575][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:41:55.576][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:41:55.584][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:55.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:55.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:41:55.591][biodb::testThat]
biodb.INFO [2024-03-27 20:41:55.592][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-27 20:41:55.593][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:41:55.594][biodb::testThat]
biodb.TRACE[2024-03-27 20:41:55.597][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:41:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:41:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:55.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:41:55.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:41:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:55.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:41:55.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:55.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:55.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:55.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:55.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:55.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:55.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:55.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-27 20:41:55.646][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:41:55.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-03-27 20:41:55.649][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:41:55.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-03-27 20:41:56.545][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:41:56.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:56.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:56.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:56.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:56.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:56.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:56.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:56.557][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.561][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.565][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.566][private$selectFields]
biodb.TRACE[2024-03-27 20:41:56.567][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:56.568][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:56.569][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.569][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.571][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.572][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.573][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.574][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.576][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.577][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.578][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.579][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.580][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.582][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.583][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.587][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.595][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:41:56.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:56.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:56.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:56.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:56.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:56.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:56.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:56.606][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.610][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.614][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.615][private$selectFields]
biodb.TRACE[2024-03-27 20:41:56.616][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:56.618][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:56.619][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.620][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.622][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.623][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.624][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.625][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.627][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.628][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.629][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.630][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.632][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.634][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.635][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.644][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.648][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:41:56.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:56.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:56.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:56.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:56.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:56.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:56.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:41:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.668][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.669][private$selectFields]
biodb.TRACE[2024-03-27 20:41:56.670][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:41:56.671][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:41:56.672][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.673][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.674][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.676][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.677][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.678][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.680][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.681][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.682][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:41:56.683][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.684][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.686][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.687][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:41:56.707][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.716][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:41:56.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:41:56.720][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:41:56.721][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:41:56.722][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:41:56.739][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:56.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:41:56.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:41:56.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:41:56.746][biodb::testThat]
biodb.INFO [2024-03-27 20:41:56.747][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-27 20:41:56.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:41:56.749][biodb::testThat]
biodb.DEBUG[2024-03-27 20:41:56.750][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-27 20:41:56.751][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:41:56.753][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-27 20:41:56.754][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:41:56.755][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:41:56.756][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:41:56.757][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:41:56.758][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:41:56.759][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:41:56.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:41:56.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:41:56.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:41:56.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:41:56.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:41:56.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:41:56.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:41:56.782][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-27 20:41:56.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:56.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:56.787][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:41:57.440][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:41:57.441][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:41:57.442][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:41:57.443][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:41:58.250][private$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[2024-03-27 20:41:58.253][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:58.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:58.258][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:41:58.972][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:41:58.975][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:41:58.977][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:41:58.980][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:41:59.790][private$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[2024-03-27 20:41:59.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:41:59.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:41:59.798][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:00.501][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:00.502][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:00.504][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:00.505][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:01.307][private$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[2024-03-27 20:42:01.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:01.310][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:01.312][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:02.014][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:02.016][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:02.017][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:02.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:02.817][private$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[2024-03-27 20:42:02.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:02.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:02.825][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:03.531][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:03.533][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:03.535][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:03.537][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:04.356][private$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[2024-03-27 20:42:04.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:04.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:04.367][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:05.075][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:05.077][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:05.080][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:05.083][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:05.904][private$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[2024-03-27 20:42:05.907][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:05.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:05.913][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:06.624][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:06.626][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:06.697][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:06.698][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:07.488][private$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[2024-03-27 20:42:07.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:07.494][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:07.498][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:08.159][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:08.160][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:08.162][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:08.163][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:08.965][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:08.967][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:08.968][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:08.969][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:09.582][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:09.584][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:09.585][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:09.586][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:10.352][private$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[2024-03-27 20:42:10.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:10.355][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:10.356][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:42:10.981][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:10.983][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:10.984][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:10.985][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:42:11.748][private$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[2024-03-27 20:42:11.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-27 20:42:11.753][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:42:11.754][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:42:11.755][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:42:11.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:42:11.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:11.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:11.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:11.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:11.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:11.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:42:11.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:11.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:11.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:11.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:11.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:11.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:11.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:11.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:42:11.804][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-27 20:42:11.805][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-27 20:42:11.813][biodb::testThat]
biodb.INFO [2024-03-27 20:42:11.814][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-27 20:42:11.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:11.815][biodb::testThat]
biodb.DEBUG[2024-03-27 20:42:11.823][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-27 20:42:11.824][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-27 20:42:11.825][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:42:11.827][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-27 20:42:11.828][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 20:42:11.829][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:42:11.830][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:42:11.831][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:42:11.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:42:11.833][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:42:11.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:42:11.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:11.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:11.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:11.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:11.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:11.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:11.848][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-27 20:42:11.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:11.851][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:11.853][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:12.473][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:12.474][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:12.475][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[2024-03-27 20:42:12.476][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:13.241][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:13.243][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:13.245][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:13.248][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:13.914][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:13.917][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:13.919][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[2024-03-27 20:42:13.922][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:14.751][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:14.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:14.761][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:14.762][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:15.378][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:15.379][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:15.380][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[2024-03-27 20:42:15.381][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:16.087][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:16.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:16.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:16.090][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:16.704][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:16.706][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:16.707][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[2024-03-27 20:42:16.709][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:17.418][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:17.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:17.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:17.423][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:18.066][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:18.068][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:18.070][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[2024-03-27 20:42:18.071][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:18.872][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:18.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:18.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:18.877][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:19.529][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:19.531][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:19.533][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[2024-03-27 20:42:19.534][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:20.335][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:20.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:20.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:20.339][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:20.949][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:20.951][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:20.953][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[2024-03-27 20:42:20.954][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:21.734][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:21.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:21.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:21.738][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:22.354][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:22.355][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:22.356][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[2024-03-27 20:42:22.357][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:23.118][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:23.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:23.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:23.122][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:23.745][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:23.747][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:23.749][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[2024-03-27 20:42:23.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:24.570][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:24.573][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:24.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:24.578][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:42:25.253][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:25.255][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:25.257][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[2024-03-27 20:42:25.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:42:26.078][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:26.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:42:26.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:26.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:26.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:26.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:26.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:26.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:26.105][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-27 20:42:26.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:26.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:26.116][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:26.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:26.775][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:26.777][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:26.779][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:27.579][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:27.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:27.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:27.583][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:28.204][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:28.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:28.210][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:28.212][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:29.021][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:29.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:29.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:29.025][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:29.658][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:29.661][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:29.663][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:29.666][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:30.491][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:30.494][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:30.497][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:30.500][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:31.166][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:31.167][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:31.169][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:31.170][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:31.944][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:31.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:31.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:31.948][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:32.567][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:32.568][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:32.570][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:32.571][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:33.349][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:33.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:33.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:33.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:33.970][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:33.971][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:33.973][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:33.974][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:34.735][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:34.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:34.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:34.787][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:35.417][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:35.419][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:35.421][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:35.423][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:36.233][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:36.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:36.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:36.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:36.870][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:36.872][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:36.873][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:36.874][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:37.581][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:37.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:37.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:37.585][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:38.204][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:38.206][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:38.208][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:38.210][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:39.019][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:42:39.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:39.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:39.029][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:42:39.688][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:42:39.690][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:42:39.692][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:42:39.693][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:42:40.495][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 20:42:40.499][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-03-27 20:42:40.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:42:40.504][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:42:40.506][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:42:40.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:42:40.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:40.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:40.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:40.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:40.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:40.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:42:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.533][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:42:40.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:42:40.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:40.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:40.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:40.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:40.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:40.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:42:40.562][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:42:40.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:40.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:42:40.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:42:40.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:42:40.640][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-27 20:42:40.642][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 20:42:40.643][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-27 20:42:40.832][biodb::testThat]
biodb.INFO [2024-03-27 20:42:40.833][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-27 20:42:40.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:40.835][biodb::testThat]
biodb.INFO [2024-03-27 20:42:40.894][biodb::testThat]
biodb.INFO [2024-03-27 20:42:40.895][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-27 20:42:40.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:40.897][biodb::testThat]
biodb.INFO [2024-03-27 20:42:40.904][biodb::testThat]
biodb.INFO [2024-03-27 20:42:40.905][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-27 20:42:40.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:40.907][biodb::testThat]
biodb.DEBUG[2024-03-27 20:42:40.910][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[2024-03-27 20:42:40.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:40.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:40.916][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-27 20:42:45.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-27 20:42:56.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:42:56.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-27 20:42:56.296][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-27 20:42:57.193][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:42:57.194][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:42:57.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:57.196][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:42:57.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:42:57.198][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:42:57.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:42:57.200][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:42:57.202][biodb::testThat]
biodb.INFO [2024-03-27 20:42:57.203][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-27 20:42:57.204][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:57.205][biodb::testThat]
biodb.ERROR[2024-03-27 20:42:57.221][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-27 20:42:57.241][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-27 20:42:57.255][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:42:57.256][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:42:57.258][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:42:57.259][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:42:57.260][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:57.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:57.261][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.263][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:42:57.275][biodb::testContext]
biodb.INFO [2024-03-27 20:42:57.276][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:42:57.277][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-27 20:42:57.278][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:42:57.279][biodb::testContext]
biodb.INFO [2024-03-27 20:42:57.281][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:42:57.283][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:42:57.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:42:57.288][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:42:57.289][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.293][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:42:57.294][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.298][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:42:57.326][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.330][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:42:57.331][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:42:57.332][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:42:57.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.335][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:42:57.336][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:42:57.337][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.341][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:42:57.342][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:42:57.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.345][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:42:57.346][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:42:57.347][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:42:57.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.350][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:42:57.351][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.355][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:42:57.356][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:42:57.357][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:42:57.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.360][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:42:57.361][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:42:57.362][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:42:57.363][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:42:57.364][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:42:57.365][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:42:57.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.368][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:42:57.369][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:42:57.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.373][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:42:57.374][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:42:57.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.377][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:42:57.378][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:42:57.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.382][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:42:57.383][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:42:57.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.386][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:42:57.387][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:42:57.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.391][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:42:57.392][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:42:57.395][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:42:57.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.398][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:42:57.399][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:42:57.400][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:42:57.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.404][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:42:57.406][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.421][self$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[2024-03-27 20:42:57.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:42:57.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.436][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.438][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:42:57.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:42:57.440][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.441][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:42:57.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:42:57.443][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.445][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:42:57.445][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:42:57.445][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:42:57.445][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:42:57.445][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:42:57.446][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:42:57.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:42:57.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.452][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:42:57.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:42:57.455][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.456][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.457][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:42:57.458][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.459][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:42:57.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:42:57.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.464][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.465][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.466][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:42:57.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:42:57.468][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.469][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:42:57.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:42:57.471][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.472][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.473][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:42:57.473][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:42:57.473][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:42:57.473][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:42:57.473][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:42:57.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:42:57.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:42:57.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.480][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.481][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:42:57.482][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:42:57.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.483][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.485][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:42:57.486][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.487][self$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[2024-03-27 20:42:57.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:42:57.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.492][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.494][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:42:57.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:42:57.496][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.497][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:42:57.498][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:42:57.498][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.499][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.500][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.501][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:42:57.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:42:57.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.508][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.509][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:42:57.509][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:42:57.510][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.511][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.512][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:42:57.514][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.515][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:42:57.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.517][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:42:57.518][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.519][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.520][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.522][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:42:57.523][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:42:57.524][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.525][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:42:57.526][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:42:57.526][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.527][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:57.528][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:42:57.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:42:57.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:57.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:57.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:42:57.546][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.547][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:42:57.548][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:42:57.549][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:57.550][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:57.551][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:42:57.552][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.565][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[2024-03-27 20:42:57.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.574][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[2024-03-27 20:42:57.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.578][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[2024-03-27 20:42:57.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.582][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[2024-03-27 20:42:57.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.590][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[2024-03-27 20:42:57.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.599][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[2024-03-27 20:42:57.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.616][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[2024-03-27 20:42:57.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:57.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:57.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:57.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:57.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:57.624][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[2024-03-27 20:42:57.625][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:42:57.626][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:42:57.628][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:42:57.629][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:42:57.630][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:42:57.632][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:42:57.633][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:42:57.634][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:42:57.646][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:42:57.648][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:42:57.650][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:42:57.651][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:42:57.652][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:42:57.654][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:42:57.655][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:42:57.656][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:42:57.658][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:42:57.659][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:42:57.660][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:42:57.661][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:42:57.663][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:42:57.664][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:42:57.665][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:42:57.667][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:42:57.668][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:42:57.669][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:42:57.670][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:42:57.672][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:42:57.673][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:42:57.674][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:42:57.676][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:42:57.677][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:42:57.678][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:42:57.680][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:42:57.681][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:42:57.682][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:42:57.683][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:42:57.685][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:42:57.686][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:42:57.687][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:42:57.689][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:42:57.690][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:42:57.691][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:42:57.693][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:42:57.694][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:42:57.695][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:42:57.696][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:42:57.698][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:42:57.699][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:42:57.700][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:42:57.702][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:42:57.703][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:42:57.704][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:42:57.705][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:42:57.707][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:42:57.708][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:42:57.709][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:42:57.711][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:42:57.712][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:42:57.713][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:42:57.715][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:42:57.716][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:42:57.717][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:42:57.719][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:42:57.720][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:42:57.721][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:42:57.723][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:42:57.724][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:42:57.725][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:42:57.727][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:42:57.728][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:42:57.729][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:42:57.731][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:42:57.732][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:42:57.733][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:42:57.735][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:42:57.736][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:42:57.737][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:42:57.739][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:42:57.740][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:42:58.004][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:42:58.005][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:42:58.007][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:42:58.008][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:42:58.009][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:42:58.010][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:42:58.011][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.013][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.037][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[2024-03-27 20:42:58.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.089][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[2024-03-27 20:42:58.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.107][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[2024-03-27 20:42:58.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:42:58.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:42:58.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:42:58.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:42:58.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:42:58.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:42:58.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:42:58.114][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:42:58.115][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:42:58.117][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:58.118][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:42:58.119][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:58.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:42:58.121][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:58.122][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:42:58.123][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:58.124][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:42:58.125][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:42:58.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:42:58.127][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:58.128][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:42:58.129][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:42:58.130][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:42:58.131][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:42:58.132][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:42:58.132][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:42:58.133][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:42:58.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:58.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:58.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:42:58.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:42:58.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:42:58.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:42:58.140][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:42:58.140][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:42:58.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:42:58.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:42:58.143][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:42:58.144][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:42:58.145][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:42:58.146][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:42:58.150][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:42:58.151][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:42:58.152][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:42:58.154][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:42:58.155][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:42:58.156][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:42:58.157][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:42:58.158][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:42:58.160][biodb::testThat]
biodb.INFO [2024-03-27 20:42:58.161][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-27 20:42:58.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:42:58.163][biodb::testThat]
biodb.DEBUG[2024-03-27 20:42:58.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-27 20:42:58.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:58.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:58.173][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-27 20:42:59.170][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[2024-03-27 20:42:59.851][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:42:59.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-27 20:42:59.858][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-27 20:42:59.867][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[2024-03-27 20:42:59.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:42:59.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:42:59.874][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-27 20:43:00.882][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-03-27 20:43:01.872][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:43:01.874][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-27 20:43:01.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-27 20:43:01.887][biodb::testThat]
biodb.INFO [2024-03-27 20:43:01.889][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-27 20:43:01.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:43:01.891][biodb::testThat]
biodb.INFO [2024-03-27 20:43:01.919][biodb::testThat]
biodb.INFO [2024-03-27 20:43:01.920][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-27 20:43:01.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:43:01.922][biodb::testThat]
biodb.DEBUG[2024-03-27 20:43:01.925][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 20:43:01.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:43:01.930][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:43:01.931][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 20:43:02.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 20:43:02.980][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:43:02.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-27 20:43:02.987][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-27 20:43:02.993][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[2024-03-27 20:43:02.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:43:02.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-27 20:43:03.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:43:03.001][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-27 20:43:03.008][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[2024-03-27 20:43:03.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:43:03.013][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:43:03.015][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 20:43:03.541][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 20:43:04.065][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:43:04.068][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-27 20:43:04.078][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-27 20:43:04.088][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-27 20:43:04.092][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:43:04.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:43:04.096][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-27 20:43:05.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-27 20:43:08.771][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:43:08.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-27 20:43:08.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-27 20:43:08.898][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[2024-03-27 20:43:08.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:43:08.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:43:08.904][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-03-27 20:43:10.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-03-27 20:43:13.627][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:43:13.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-27 20:43:13.635][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-27 20:43:13.752][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:43:13.754][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:43:13.755][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:43:13.756][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:43:13.757][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:13.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:13.759][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:13.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:13.760][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:43:13.765][biodb::testContext]
biodb.INFO [2024-03-27 20:43:13.766][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:43:13.767][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-27 20:43:13.768][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:43:13.769][biodb::testContext]
biodb.INFO [2024-03-27 20:43:13.771][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:43:13.773][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:43:13.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:43:13.779][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:43:13.780][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.830][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:43:13.831][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.835][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:43:13.836][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.840][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:43:13.841][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:43:13.842][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:43:13.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.846][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:43:13.847][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:43:13.848][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.851][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:43:13.852][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:43:13.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.856][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:43:13.857][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:43:13.858][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:43:13.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.862][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:43:13.863][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.867][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:43:13.868][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:43:13.869][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:43:13.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.873][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:43:13.874][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:43:13.875][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:43:13.876][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:43:13.877][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:43:13.878][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:43:13.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.882][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:43:13.883][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:43:13.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.887][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:43:13.888][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:43:13.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.891][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:43:13.892][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:43:13.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.896][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:43:13.897][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:43:13.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.901][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:43:13.902][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:43:13.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.906][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:43:13.907][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:43:13.910][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:43:13.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:13.914][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:43:13.915][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:43:13.916][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:43:13.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:13.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:13.919][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[2024-03-27 20:43:13.920][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:43:13.922][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.923][self$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[2024-03-27 20:43:13.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:43:13.926][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.927][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.928][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.930][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:43:13.931][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:43:13.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.933][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:43:13.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:43:13.935][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.937][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:43:13.937][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:43:13.937][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:43:13.937][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:43:13.937][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:43:13.938][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:43:13.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:13.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:13.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:43:13.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:13.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:13.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.945][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:43:13.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:43:13.948][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.949][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.950][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:43:13.952][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.953][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:43:13.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:43:13.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.958][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.960][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:43:13.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:43:13.962][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.963][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:43:13.964][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:43:13.966][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.967][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.968][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:43:13.968][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:43:13.968][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:43:13.968][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:43:13.968][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:43:13.969][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:43:13.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:13.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:13.972][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:43:13.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:13.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:13.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.976][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:43:13.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:43:13.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.980][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.981][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:43:13.983][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.984][self$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[2024-03-27 20:43:13.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:43:13.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:43:13.991][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:43:13.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:43:13.993][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:13.994][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:43:13.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:43:13.996][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:13.998][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:13.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:43:14.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:43:14.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.006][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:43:14.008][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:43:14.009][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.010][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.011][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:43:14.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.014][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:43:14.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:43:14.017][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.021][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:43:14.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:43:14.023][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.024][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:43:14.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:43:14.026][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.027][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.028][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:43:14.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:43:14.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.036][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:43:14.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:43:14.039][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.040][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:43:14.043][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.048][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[2024-03-27 20:43:14.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.124][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[2024-03-27 20:43:14.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.137][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:43:14.139][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:43:14.141][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:43:14.143][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:43:14.145][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:43:14.146][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:43:14.148][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:43:14.149][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:43:14.151][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:43:14.152][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:43:14.154][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:43:14.155][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:43:14.156][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:43:14.158][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:43:14.159][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:43:14.161][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:43:14.162][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:43:14.164][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:43:14.165][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:43:14.167][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:43:14.168][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:43:14.170][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:43:14.171][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:43:14.173][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:43:14.174][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:43:14.175][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:43:14.177][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:43:14.178][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:43:14.180][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:43:14.181][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:43:14.182][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:43:14.184][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:43:14.185][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:43:14.187][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:43:14.188][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:43:14.189][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:43:14.191][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:43:14.192][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:43:14.193][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:43:14.194][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:43:14.196][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:43:14.197][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:43:14.198][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:43:14.200][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:43:14.201][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:43:14.202][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:43:14.204][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:43:14.205][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:43:14.206][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:43:14.208][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:43:14.209][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:43:14.210][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:43:14.212][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:43:14.213][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:43:14.214][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:43:14.215][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:43:14.217][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:43:14.218][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:43:14.219][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:43:14.221][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:43:14.242][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:43:14.244][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:43:14.245][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:43:14.247][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:43:14.248][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:43:14.250][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:43:14.251][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:43:14.252][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:43:14.254][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:43:14.255][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:43:14.256][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:43:14.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:43:14.259][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:43:14.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:43:14.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:43:14.263][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:43:14.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:43:14.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:43:14.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:43:14.269][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:43:14.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:43:14.272][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:43:14.273][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:43:14.275][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:43:14.276][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:43:14.277][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:43:14.278][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.280][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.288][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[2024-03-27 20:43:14.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.294][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[2024-03-27 20:43:14.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.307][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[2024-03-27 20:43:14.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.313][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[2024-03-27 20:43:14.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.319][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[2024-03-27 20:43:14.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.338][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[2024-03-27 20:43:14.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:43:14.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:14.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:14.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:14.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:14.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:14.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:43:14.391][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:43:14.393][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:43:14.395][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.396][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.397][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:43:14.399][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.401][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.403][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:43:14.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:43:14.405][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.406][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:43:14.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:43:14.408][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:43:14.409][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:43:14.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:43:14.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:43:14.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:43:14.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:43:14.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:43:14.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:43:14.417][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:43:14.418][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:43:14.418][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:43:14.419][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:43:14.420][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:43:14.421][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:43:14.422][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:43:14.423][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:43:14.425][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:43:14.428][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:43:14.429][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:43:14.430][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:43:14.432][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:43:14.433][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:43:14.434][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:43:14.436][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:43:14.437][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:43:14.438][biodb::testThat]
biodb.INFO [2024-03-27 20:43:14.439][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-03-27 20:43:14.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:43:14.441][biodb::testThat]
biodb.DEBUG[2024-03-27 20:43:14.445][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 20:43:14.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:43:14.450][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-27 20:43:14.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:43:14.501][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-27 20:43:15.344][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-27 20:43:15.346][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:43:15.347][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-27 20:43:15.349][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-27 20:43:15.350][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-27 20:43:15.351][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:43:15.352][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:43:15.353][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:43:15.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:43:15.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:15.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:15.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:15.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:15.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:15.364][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:43:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.384][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:43:15.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:43:15.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:43:15.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:43:15.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.391][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.395][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:43:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.411][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:43:15.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.415][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:43:15.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:43:15.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.445][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:43:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:43:15.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:43:15.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:15.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:15.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:15.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:15.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:15.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:43:15.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.524][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:43:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:43:15.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.527][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:43:15.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:43:15.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.547][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:43:15.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.551][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:43:15.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:43:15.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.583][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:43:15.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.596][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:43:15.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.600][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:43:15.655][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-03-27 20:43:15.658][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:43:15.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:43:15.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:15.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:15.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:15.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:15.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:15.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:43:15.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:43:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:43:15.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:43:15.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:43:15.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.690][private$selectFields] Fields none
biodb.TRACE[2024-03-27 20:43:15.691][private$selectFields]
biodb.TRACE[2024-03-27 20:43:15.692][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-27 20:43:15.693][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:43:15.694][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:15.695][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.696][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.741][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.742][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.744][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.745][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.746][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.747][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.749][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.750][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.752][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.753][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.754][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.757][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.758][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.759][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.761][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.762][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.765][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.766][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.767][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.769][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.770][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.773][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.777][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.778][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.779][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.781][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.782][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.784][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.786][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.788][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.789][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.790][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.793][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.794][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.795][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.797][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.798][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.799][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.801][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.802][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:15.803][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:15.804][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.806][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.807][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.810][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.811][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.812][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.814][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.816][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.816][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.818][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.820][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.821][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.822][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.824][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.825][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.826][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.828][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.829][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.830][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.832][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.833][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.834][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.837][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-27 20:43:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.884][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:15.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:15.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:15.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.934][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:15.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.944][private$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[2024-03-27 20:43:15.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:43:15.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:15.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:15.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:15.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:15.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:15.955][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.TRACE[2024-03-27 20:43:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:43:15.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.965][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:43:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:43:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:43:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:43:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.974][private$selectFields] Fields none
biodb.TRACE[2024-03-27 20:43:15.974][private$selectFields]
biodb.TRACE[2024-03-27 20:43:15.975][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-27 20:43:15.976][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:43:15.977][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:15.978][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:15.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:15.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.982][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:15.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.985][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.986][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.987][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:15.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.989][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.990][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.991][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:15.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.993][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.994][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.995][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:15.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:15.997][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:15.998][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:15.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.001][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.002][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.003][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.004][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.005][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.006][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.008][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.009][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:16.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:16.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.012][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.013][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.016][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.017][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.018][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.020][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.021][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.022][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.023][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.024][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.025][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.027][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.028][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:16.029][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.031][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.032][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.035][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.036][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.037][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.038][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.039][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:16.040][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:43:16.041][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:16.042][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:16.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.044][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.048][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.049][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.050][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.052][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.053][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.054][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.055][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.059][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.060][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:16.061][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.063][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.064][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.065][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.067][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.068][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.069][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.071][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.071][private$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[2024-03-27 20:43:16.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:16.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:16.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:16.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:16.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:43:16.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:43:16.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:43:16.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.107][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:43:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.123][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:43:16.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:43:16.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:16.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.146][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:16.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:43:16.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:43:16.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:43:16.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:43:16.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.168][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:43:16.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:43:16.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:43:16.179][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-27 20:43:16.180][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:43:16.181][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-27 20:43:16.186][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:43:16.188][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:43:16.189][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:43:16.190][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:43:16.190][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:43:16.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:43:16.192][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:43:16.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:43:16.194][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:43:16.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 1.118 | 0.088 | 3.458 | |
| LipidmapsStructureEntry | 0.237 | 0.000 | 0.237 | |