Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:18 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
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 | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: biodbLipidmaps |
Version: 1.10.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz |
StartedAt: 2024-05-04 05:24:01 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 05:25:41 -0000 (Sat, 04 May 2024) |
EllapsedTime: 100.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbLipidmaps.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK * this is package ‘biodbLipidmaps’ version ‘1.10.0’ * 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 whether startup messages can be suppressed ... 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 161 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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) Warning message: In fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbLipidmaps") biodb.INFO [2024-05-04 05:25:10.740][biodb::testContext] biodb.INFO [2024-05-04 05:25:10.742][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:10.744][biodb::testContext] Test context - Generic tests biodb.INFO [2024-05-04 05:25:10.745][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:10.747][biodb::testContext] biodb.INFO [2024-05-04 05:25:10.755][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:10.758][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 05:25:10.767][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:10.768][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 05:25:10.770][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 05:25:10.771][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.776][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 05:25:10.804][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 05:25:10.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.809][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 05:25:10.811][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 05:25:10.812][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.816][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 05:25:10.818][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 05:25:10.819][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 05:25:10.821][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.825][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 05:25:10.826][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 05:25:10.828][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 05:25:10.829][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.833][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 05:25:10.835][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 05:25:10.836][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.840][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 05:25:10.841][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 05:25:10.843][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 05:25:10.844][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.848][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 05:25:10.850][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 05:25:10.851][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.855][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 05:25:10.857][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 05:25:10.858][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 05:25:10.860][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.864][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:10.865][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 05:25:10.867][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 05:25:10.868][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 05:25:10.870][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 05:25:10.871][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 05:25:10.872][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.877][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 05:25:10.878][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 05:25:10.879][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.883][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 05:25:10.885][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 05:25:10.886][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.890][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 05:25:10.892][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 05:25:10.893][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.897][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 05:25:10.899][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 05:25:10.900][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.909][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 05:25:10.910][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 05:25:10.912][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.916][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:10.917][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 05:25:10.922][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 05:25:10.923][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.926][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[2024-05-04 05:25:10.928][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 05:25:10.929][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 05:25:10.931][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 05:25:10.932][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:10.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:10.939][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 05:25:10.989][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.025][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 05:25:11.027][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.028][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:11.029][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:11.032][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:11.035][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:11.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:11.038][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.039][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 05:25:11.041][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:11.042][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.043][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.045][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:11.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:11.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:11.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:11.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:11.046][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:11.047][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.050][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:11.051][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.054][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:11.055][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.056][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:11.057][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:11.059][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.060][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.062][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 05:25:11.064][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.066][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:11.067][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.068][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:11.070][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:11.072][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:11.075][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:11.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:11.078][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.079][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 05:25:11.080][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:11.082][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.083][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.084][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:11.084][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:11.084][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:11.084][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:11.084][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:11.086][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:11.087][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.090][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:11.091][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.093][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:11.095][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.096][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:11.097][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:11.099][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.100][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.102][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 05:25:11.104][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.105][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 05:25:11.107][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.108][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:11.109][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:11.112][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:11.115][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:11.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:11.118][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.119][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 05:25:11.120][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:11.122][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.123][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.124][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.126][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:11.127][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.130][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:11.131][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.133][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:11.135][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.136][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:11.137][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:11.139][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.140][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.142][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 05:25:11.144][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.145][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:11.147][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.148][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:11.150][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.151][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:11.152][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:11.155][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:11.157][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:11.158][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.159][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 05:25:11.161][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:11.162][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.163][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.165][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.166][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:11.167][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.170][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:11.171][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.174][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:11.175][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.177][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:11.178][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:11.179][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.180][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.185][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:11.187][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.189][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.196][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.202][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.208][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.214][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.227][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.233][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.240][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.246][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.252][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.258][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.265][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.271][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.276][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[2024-05-04 05:25:11.277][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.284][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.290][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.295][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[2024-05-04 05:25:11.296][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 05:25:11.302][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 05:25:11.304][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 05:25:11.306][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 05:25:11.308][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 05:25:11.310][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 05:25:11.312][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 05:25:11.314][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 05:25:11.316][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 05:25:11.318][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 05:25:11.320][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 05:25:11.322][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 05:25:11.324][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 05:25:11.326][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 05:25:11.328][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 05:25:11.330][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:11.332][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 05:25:11.335][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 05:25:11.337][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 05:25:11.339][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 05:25:11.341][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 05:25:11.343][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 05:25:11.345][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 05:25:11.347][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 05:25:11.349][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 05:25:11.351][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 05:25:11.353][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 05:25:11.355][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 05:25:11.357][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 05:25:11.359][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 05:25:11.361][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 05:25:11.363][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 05:25:11.365][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 05:25:11.367][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 05:25:11.369][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 05:25:11.371][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 05:25:11.373][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 05:25:11.382][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 05:25:11.385][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 05:25:11.387][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 05:25:11.389][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 05:25:11.391][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 05:25:11.393][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 05:25:11.395][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 05:25:11.397][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 05:25:11.399][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 05:25:11.401][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 05:25:11.403][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 05:25:11.405][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 05:25:11.407][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 05:25:11.409][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 05:25:11.411][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 05:25:11.413][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 05:25:11.415][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 05:25:11.417][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 05:25:11.419][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 05:25:11.421][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 05:25:11.424][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 05:25:11.426][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 05:25:11.428][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 05:25:11.430][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 05:25:11.432][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 05:25:11.434][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 05:25:11.436][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 05:25:11.438][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 05:25:11.441][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 05:25:11.443][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 05:25:11.445][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 05:25:11.447][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 05:25:11.449][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 05:25:11.451][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 05:25:11.453][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 05:25:11.455][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 05:25:11.457][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 05:25:11.459][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 05:25:11.461][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 05:25:11.463][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 05:25:11.465][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 05:25:11.467][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 05:25:11.469][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 05:25:11.471][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 05:25:11.473][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 05:25:11.475][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 05:25:11.483][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 05:25:11.485][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:11.489][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:11.490][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.493][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.494][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[2024-05-04 05:25:11.500][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.508][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[2024-05-04 05:25:11.509][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.518][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.527][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.536][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.544][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.553][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.562][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.570][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.578][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[2024-05-04 05:25:11.579][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.588][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.597][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.606][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.614][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.623][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.632][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.640][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:11.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:11.650][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-04 05:25:11.663][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:11.665][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.667][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 05:25:11.668][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.669][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:11.671][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:11.674][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:11.676][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:11.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:11.679][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.680][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-04 05:25:11.682][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-04 05:25:11.683][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-04 05:25:11.685][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 05:25:11.686][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:11.686][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:11.687][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:11.689][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.691][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:11.692][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:11.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:11.695][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:11.696][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-04 05:25:11.696][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-04 05:25:11.698][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:11.699][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:11.700][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:11.702][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:11.710][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-04 05:25:11.712][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:11.749][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:11.750][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-04 05:25:11.755][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:11.760][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-04 05:25:11.765][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:11.767][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:11.768][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-04 05:25:11.770][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-04 05:25:11.781][biodb::testThat] biodb.INFO [2024-05-04 05:25:11.782][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 05:25:11.784][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:11.785][biodb::testThat] biodb.TRACE[2024-05-04 05:25:11.790][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv". biodb.DEBUG[2024-05-04 05:25:11.792][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 05:25:11.797][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:11.807][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:11.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:11.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:11.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:11.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:11.827][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:11.828][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:25:11.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:11.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:11.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:11.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.876][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:11.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:11.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.881][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.887][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:11.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:11.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:11.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:11.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:11.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:11.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:11.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:11.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:11.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:11.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:11.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:11.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:11.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:11.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.982][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:11.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:11.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:11.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:11.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:11.999][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:12.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.114][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:12.166][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001. biodb.TRACE[2024-05-04 05:25:12.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:12.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:12.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:12.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.180][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:12.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:12.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:12.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.278][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.284][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.290][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.322][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.324][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.325][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.326][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.361][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.363][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.364][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.366][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.436][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.437][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.439][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.440][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.474][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.476][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.477][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.479][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.513][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.515][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.516][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.517][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.552][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.554][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.555][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.557][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.575][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.576][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.578][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.579][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.586][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.587][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.589][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.590][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.597][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.598][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.600][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.601][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.607][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.609][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.610][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.612][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.618][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.620][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.621][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.623][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.629][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.631][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.632][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.634][ef$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:12.644][biodb::testThat] biodb.INFO [2024-05-04 05:25:12.646][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 05:25:12.647][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:12.649][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:12.668][private$loadEntries] Creating entries from ids [1]: "LMFA00000001". biodb.DEBUG[2024-05-04 05:25:12.678][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 05:25:12.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001". biodb.TRACE[2024-05-04 05:25:12.684][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:12.686][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv". biodb.DEBUG[2024-05-04 05:25:12.688][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 05:25:12.723][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 05:25:12.725][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:12.737][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:12.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:12.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:12.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:12.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:12.750][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:12.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:12.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:12.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:12.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.785][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:12.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:12.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.797][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:12.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.808][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:12.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.820][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:12.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:12.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:12.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.855][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.861][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:12.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.878][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:12.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:12.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:12.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:12.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:12.969][self$createEntryFromContent] Accession numbers: LMFA00000001. biodb.TRACE[2024-05-04 05:25:12.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 05:25:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 05:25:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 05:25:12.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 05:25:12.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:12.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 05:25:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 05:25:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:12.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:12.997][biodb::testThat] biodb.INFO [2024-05-04 05:25:12.998][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 05:25:13.000][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.001][biodb::testThat] biodb.TRACE[2024-05-04 05:25:13.005][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.007][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.008][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.010][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:13.011][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name". biodb.TRACE[2024-05-04 05:25:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:13.075][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-05-04 05:25:13.082][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[2024-05-04 05:25:13.112][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:13.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-04 05:25:13.137][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:13.139][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.DEBUG[2024-05-04 05:25:13.142][function(conn, opt)] With found IDs [1]: "LMFA00000001". biodb.TRACE[2024-05-04 05:25:13.157][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:13.159][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:13.160][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.162][ef$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:13.167][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.168][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 05:25:13.170][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.171][biodb::testThat] biodb.TRACE[2024-05-04 05:25:13.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:13.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:13.377][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[2024-05-04 05:25:13.381][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:13.383][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-04 05:25:13.385][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:13.387][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.INFO [2024-05-04 05:25:13.409][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.410][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 05:25:13.412][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.413][biodb::testThat] biodb.TRACE[2024-05-04 05:25:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:13.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.461][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:13.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:13.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.528][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.533][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:13.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:13.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:13.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:13.556][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.558][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 05:25:13.559][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.560][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.570][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.572][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 05:25:13.573][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.574][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.584][biodb::testThat] biodb.INFO [2024-05-04 05:25:13.586][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 05:25:13.587][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:13.588][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:13.593][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001". biodb.DEBUG[2024-05-04 05:25:17.707][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001. biodb.INFO [2024-05-04 05:25:23.907][biodb::testThat] biodb.INFO [2024-05-04 05:25:23.909][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 05:25:23.911][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:23.913][biodb::testThat] biodb.TRACE[2024-05-04 05:25:23.928][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:23.931][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:23.933][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:23.935][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:23.937][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:23.940][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:23.942][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:23.944][ef$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:23.947][biodb::testThat] biodb.INFO [2024-05-04 05:25:23.950][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-05-04 05:25:23.952][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:23.954][biodb::testThat] biodb.TRACE[2024-05-04 05:25:23.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:23.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:23.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:23.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:23.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:23.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:23.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:23.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:23.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:24.257][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[2024-05-04 05:25:24.264][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:24.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-04 05:25:24.269][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:24.272][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.DEBUG[2024-05-04 05:25:24.387][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[2024-05-04 05:25:24.391][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:24.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-04 05:25:24.395][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:24.397][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.TRACE[2024-05-04 05:25:24.415][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 05:25:24.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 05:25:24.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 05:25:24.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 05:25:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:24.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:24.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:24.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:24.474][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[2024-05-04 05:25:24.479][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:24.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359". biodb.TRACE[2024-05-04 05:25:24.482][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:24.598][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content". biodb.DEBUG[2024-05-04 05:25:26.090][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[2024-05-04 05:25:26.095][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:26.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3". biodb.TRACE[2024-05-04 05:25:26.099][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:26.101][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content". biodb.DEBUG[2024-05-04 05:25:26.129][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[2024-05-04 05:25:26.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:26.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54". biodb.TRACE[2024-05-04 05:25:26.138][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:26.141][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content". biodb.TRACE[2024-05-04 05:25:26.162][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 05:25:26.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 05:25:26.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:26.178][biodb::testThat] biodb.INFO [2024-05-04 05:25:26.180][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-05-04 05:25:26.181][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:26.182][biodb::testThat] biodb.TRACE[2024-05-04 05:25:26.187][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 05:25:26.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 05:25:26.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:26.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 05:25:26.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 05:25:26.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:26.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:26.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:26.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:26.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:26.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:26.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:26.226][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:26.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:26.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:26.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:26.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:26.238][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:26.239][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[2024-05-04 05:25:26.244][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[2024-05-04 05:25:26.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:26.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3". biodb.TRACE[2024-05-04 05:25:26.253][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:26.360][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content". biodb.DEBUG[2024-05-04 05:25:27.479][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003". biodb.DEBUG[2024-05-04 05:25:27.548][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-04 05:25:27.550][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003". biodb.TRACE[2024-05-04 05:25:27.552][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-04 05:25:27.555][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv". biodb.DEBUG[2024-05-04 05:25:27.556][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 05:25:27.558][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-04 05:25:27.560][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:27.562][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:27.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:27.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:27.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:27.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:27.573][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:27.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.602][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:27.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:27.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:27.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:27.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.614][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.636][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:27.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:27.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:27.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:27.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:27.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.703][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:27.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.709][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:27.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.726][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:27.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:27.770][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:27.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:27.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:27.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:27.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:27.781][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:27.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:27.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.805][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:27.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:27.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.811][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:27.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:27.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.822][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:27.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.838][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:27.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.844][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:27.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:27.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:27.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:27.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:27.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.872][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:27.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.878][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:27.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.895][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:27.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:27.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.938][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:27.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:27.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:27.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:27.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:27.992][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003. biodb.DEBUG[2024-05-04 05:25:28.005][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 05:25:28.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:28.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:28.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:28.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:28.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:28.018][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:28.020][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.TRACE[2024-05-04 05:25:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.032][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.033][private$selectFields] biodb.TRACE[2024-05-04 05:25:28.034][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:28.036][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:28.037][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.038][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.040][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.041][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.043][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.044][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.045][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.047][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.048][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.049][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.051][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.052][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.053][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.055][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.056][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.057][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.088][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-04 05:25:28.089][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:28.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:28.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:28.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:28.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:28.101][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:28.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:28.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.115][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.138][private$selectFields] biodb.TRACE[2024-05-04 05:25:28.139][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:28.140][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:28.142][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.143][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.144][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.146][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.147][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.148][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.150][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.151][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.152][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.154][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.155][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.156][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.158][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.159][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.160][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.162][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:28.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.168][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.179][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-04 05:25:28.181][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:28.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:28.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:28.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:28.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:28.192][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:28.193][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:25:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.200][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.205][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.206][private$selectFields] biodb.TRACE[2024-05-04 05:25:28.208][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:28.209][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:28.210][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.212][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.213][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.214][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.215][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.217][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.218][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.219][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.221][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.222][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.223][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:28.225][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.226][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.227][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.229][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.230][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:28.231][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:28.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.248][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-04 05:25:28.249][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 05:25:28.250][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 05:25:28.263][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 05:25:28.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 05:25:28.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:28.272][biodb::testThat] biodb.INFO [2024-05-04 05:25:28.274][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-05-04 05:25:28.275][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:28.276][biodb::testThat] biodb.TRACE[2024-05-04 05:25:28.280][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 05:25:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 05:25:28.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 05:25:28.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 05:25:28.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:28.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:28.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:28.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:28.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:28.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:28.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:28.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:28.425][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:28.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:28.431][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[2024-05-04 05:25:28.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:28.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6". biodb.TRACE[2024-05-04 05:25:28.439][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:28.555][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content". biodb.DEBUG[2024-05-04 05:25:29.738][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 05:25:29.776][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:29.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:29.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:29.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:29.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:29.788][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:29.790][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.TRACE[2024-05-04 05:25:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.816][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.855][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.856][private$selectFields] biodb.TRACE[2024-05-04 05:25:29.858][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:29.859][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:29.861][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.862][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.864][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.865][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.867][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.868][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.870][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.871][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.873][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.874][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.917][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.918][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.920][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.921][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.922][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.924][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:29.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.931][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.937][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.943][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-04 05:25:29.945][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:29.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:29.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:29.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:29.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:29.957][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:29.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:29.960][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.972][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.973][private$selectFields] biodb.TRACE[2024-05-04 05:25:29.974][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:29.976][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:29.977][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.979][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.980][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.982][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.983][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.985][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.986][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.988][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.989][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:29.991][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.992][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:29.994][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.996][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:29.997][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:29.998][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.000][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:30.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.012][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.018][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-04 05:25:30.020][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:30.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:30.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:30.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:30.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:30.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:30.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.045][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:30.047][private$selectFields] biodb.TRACE[2024-05-04 05:25:30.048][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:30.049][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:30.051][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:30.052][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.054][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.055][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.056][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.058][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.059][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.060][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.062][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.063][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:30.065][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:30.066][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.067][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.069][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.070][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.071][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:30.073][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.078][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.090][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-04 05:25:30.092][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 05:25:30.093][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 05:25:30.105][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 05:25:30.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 05:25:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:30.115][biodb::testThat] biodb.INFO [2024-05-04 05:25:30.117][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-05-04 05:25:30.118][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:30.119][biodb::testThat] biodb.TRACE[2024-05-04 05:25:30.143][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 05:25:30.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 05:25:30.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 05:25:30.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 05:25:30.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:30.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:30.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:30.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:30.182][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:30.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:30.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:30.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:30.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:30.193][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:30.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:30.199][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[2024-05-04 05:25:30.204][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:30.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3". biodb.TRACE[2024-05-04 05:25:30.208][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:30.300][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content". biodb.DEBUG[2024-05-04 05:25:31.642][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 05:25:31.644][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:31.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:31.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:31.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:31.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:31.655][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:31.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:31.658][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.663][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.668][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.670][private$selectFields] biodb.TRACE[2024-05-04 05:25:31.671][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:31.672][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:31.674][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.675][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.677][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.678][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.679][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.680][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.682][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.683][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.684][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.686][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.687][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.688][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.690][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.691][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.692][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.694][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.700][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.711][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-04 05:25:31.713][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:31.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:31.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:31.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:31.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:31.724][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:31.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:31.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.738][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.739][private$selectFields] biodb.TRACE[2024-05-04 05:25:31.740][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:31.741][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:31.743][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.744][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.745][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.747][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.749][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.750][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.752][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.753][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.754][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.755][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.757][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.758][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.759][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.761][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.762][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.763][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:31.765][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.775][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.781][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-04 05:25:31.782][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:31.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:31.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:31.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:31.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:31.794][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:31.796][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:25:31.797][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.802][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.808][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.809][private$selectFields] biodb.TRACE[2024-05-04 05:25:31.811][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 05:25:31.812][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:31.813][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.815][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.816][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.817][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.819][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.820][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.822][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.823][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.824][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.826][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.827][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:31.828][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.830][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.831][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.832][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.834][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-04 05:25:31.835][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.847][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.853][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-04 05:25:31.854][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 05:25:31.856][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 05:25:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 05:25:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 05:25:31.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:31.889][biodb::testThat] biodb.INFO [2024-05-04 05:25:31.890][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2024-05-04 05:25:31.892][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:31.893][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:31.895][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2024-05-04 05:25:31.896][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 05:25:31.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2024-05-04 05:25:31.900][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:31.903][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv". biodb.DEBUG[2024-05-04 05:25:31.904][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 05:25:31.906][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 05:25:31.907][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:31.909][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:31.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:31.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:31.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:31.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:31.920][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:31.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:31.923][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:31.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:31.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:31.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:31.965][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2024-05-04 05:25:31.967][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2024-05-04 05:25:31.977][biodb::testThat] biodb.INFO [2024-05-04 05:25:31.979][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2024-05-04 05:25:31.980][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:31.981][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:31.993][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013" biodb.DEBUG[2024-05-04 05:25:31.994][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013". biodb.DEBUG[2024-05-04 05:25:31.996][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-04 05:25:31.998][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013". biodb.TRACE[2024-05-04 05:25:32.000][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-04 05:25:32.004][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv". biodb.DEBUG[2024-05-04 05:25:32.005][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 05:25:32.007][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-04 05:25:32.009][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:32.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:32.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:32.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:32.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:32.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:32.024][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:32.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:32.047][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:32.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:32.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:32.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:32.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:32.059][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:32.060][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.TRACE[2024-05-04 05:25:32.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:32.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:32.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:32.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:32.167][self$createEntryFromContent] Accession numbers: NA, NA. biodb.DEBUG[2024-05-04 05:25:32.169][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 05:25:32.170][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL" biodb.INFO [2024-05-04 05:25:32.366][biodb::testThat] biodb.INFO [2024-05-04 05:25:32.367][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2024-05-04 05:25:32.369][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:32.370][biodb::testThat] biodb.INFO [2024-05-04 05:25:32.428][biodb::testThat] biodb.INFO [2024-05-04 05:25:32.429][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2024-05-04 05:25:32.431][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:32.432][biodb::testThat] biodb.INFO [2024-05-04 05:25:32.443][biodb::testThat] biodb.INFO [2024-05-04 05:25:32.444][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2024-05-04 05:25:32.446][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:32.447][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:32.451][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[2024-05-04 05:25:32.455][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:32.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030". biodb.TRACE[2024-05-04 05:25:32.459][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:32.570][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content". biodb.TRACE[2024-05-04 05:25:33.757][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:33.759][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:33.761][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:33.762][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:33.764][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:33.765][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:33.767][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:33.768][ef$get] fields variable is a list. biodb.INFO [2024-05-04 05:25:33.771][biodb::testThat] biodb.INFO [2024-05-04 05:25:33.772][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. "). biodb.INFO [2024-05-04 05:25:33.773][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:33.775][biodb::testThat] biodb.ERROR[2024-05-04 05:25:33.795][conn$annotateMzValues] No column named "mz" was found inside data frame. biodb.ERROR[2024-05-04 05:25:33.821][ef$checkIsDefined] Field(s) "foo" is/are not defined. biodb.INFO [2024-05-04 05:25:33.841][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 05:25:33.843][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-04 05:25:33.845][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-04 05:25:33.846][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 05:25:33.847][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:33.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:33.850][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:33.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:33.852][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.853][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 05:25:33.868][biodb::testContext] biodb.INFO [2024-05-04 05:25:33.869][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:33.871][biodb::testContext] Test context - Web services tests biodb.INFO [2024-05-04 05:25:33.872][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:33.873][biodb::testContext] biodb.INFO [2024-05-04 05:25:33.876][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:33.878][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 05:25:33.883][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:33.885][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 05:25:33.887][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 05:25:33.888][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.892][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 05:25:33.894][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 05:25:33.895][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.899][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 05:25:33.900][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 05:25:33.902][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.906][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 05:25:33.907][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 05:25:33.909][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 05:25:33.910][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.913][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[2024-05-04 05:25:33.914][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 05:25:33.916][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 05:25:33.917][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 05:25:33.919][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.923][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 05:25:33.924][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 05:25:33.926][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.930][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 05:25:33.931][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 05:25:33.933][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 05:25:33.934][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.938][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 05:25:33.940][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 05:25:33.941][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.945][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 05:25:33.946][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 05:25:33.948][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 05:25:33.949][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.953][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:33.954][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 05:25:33.956][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 05:25:33.957][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 05:25:33.959][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 05:25:33.960][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 05:25:33.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.965][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 05:25:33.967][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 05:25:33.968][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.972][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 05:25:33.973][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 05:25:33.974][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.978][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 05:25:33.979][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 05:25:33.981][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.985][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 05:25:33.986][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 05:25:33.987][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.991][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 05:25:33.993][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 05:25:33.994][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:33.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:33.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:33.999][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:34.001][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 05:25:34.006][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 05:25:34.007][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.011][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 05:25:34.013][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 05:25:34.014][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 05:25:34.015][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.020][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 05:25:34.022][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.024][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 05:25:34.025][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.027][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:34.028][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:34.031][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:34.034][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:34.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:34.037][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.038][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 05:25:34.040][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:34.041][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.043][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.044][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:34.044][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:34.044][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:34.044][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:34.044][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:34.046][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:34.047][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.050][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:34.052][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.054][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:34.056][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.057][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:34.058][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:34.060][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.061][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.063][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 05:25:34.066][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.067][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:34.069][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.070][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:34.072][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.073][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:34.074][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:34.077][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:34.079][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:34.080][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.082][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 05:25:34.083][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:34.084][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.086][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.087][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:34.087][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:34.087][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:34.087][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:34.087][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:34.089][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:34.090][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.093][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:34.094][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.097][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:34.098][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.100][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:34.101][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:34.102][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.104][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.106][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 05:25:34.108][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.110][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 05:25:34.111][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.112][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:34.114][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.115][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:34.117][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.118][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:34.120][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:34.121][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:34.122][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.124][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 05:25:34.125][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:34.127][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.128][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.129][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.131][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:34.132][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.135][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:34.136][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.137][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.139][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:34.140][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.142][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:34.143][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:34.144][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.146][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.147][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 05:25:34.150][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.151][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:34.152][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.154][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:34.155][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.157][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:34.158][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:34.161][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:34.162][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:34.164][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.165][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 05:25:34.191][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:34.193][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.194][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.196][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.197][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:34.198][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.200][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.201][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:34.203][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.205][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:34.207][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.208][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:34.209][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:34.211][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.212][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.214][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:34.215][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.218][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.224][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.231][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.237][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.243][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.250][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.257][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.263][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.270][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.276][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.281][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[2024-05-04 05:25:34.282][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.289][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.294][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[2024-05-04 05:25:34.295][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.300][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[2024-05-04 05:25:34.301][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.307][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.319][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.324][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[2024-05-04 05:25:34.326][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 05:25:34.328][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 05:25:34.330][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 05:25:34.332][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 05:25:34.334][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 05:25:34.336][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 05:25:34.338][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 05:25:34.340][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 05:25:34.342][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 05:25:34.344][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 05:25:34.346][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 05:25:34.348][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 05:25:34.350][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 05:25:34.352][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 05:25:34.354][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 05:25:34.356][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:34.358][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 05:25:34.360][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 05:25:34.362][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 05:25:34.364][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 05:25:34.366][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 05:25:34.368][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 05:25:34.370][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 05:25:34.372][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 05:25:34.374][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 05:25:34.376][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 05:25:34.378][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 05:25:34.381][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 05:25:34.383][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 05:25:34.385][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 05:25:34.387][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 05:25:34.389][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 05:25:34.391][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 05:25:34.393][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 05:25:34.395][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 05:25:34.397][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 05:25:34.399][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 05:25:34.401][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 05:25:34.404][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 05:25:34.406][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 05:25:34.408][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 05:25:34.410][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 05:25:34.412][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 05:25:34.414][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 05:25:34.416][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 05:25:34.418][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 05:25:34.420][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 05:25:34.422][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 05:25:34.424][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 05:25:34.426][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 05:25:34.429][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 05:25:34.431][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 05:25:34.433][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 05:25:34.435][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 05:25:34.437][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 05:25:34.439][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 05:25:34.441][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 05:25:34.443][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 05:25:34.445][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 05:25:34.447][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 05:25:34.449][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 05:25:34.451][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 05:25:34.453][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 05:25:34.455][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 05:25:34.456][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 05:25:34.459][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 05:25:34.461][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 05:25:34.463][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 05:25:34.465][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 05:25:34.467][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 05:25:34.469][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 05:25:34.471][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 05:25:34.473][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 05:25:34.475][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 05:25:34.477][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 05:25:34.479][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 05:25:34.481][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 05:25:34.483][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 05:25:34.485][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 05:25:34.487][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 05:25:34.489][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 05:25:34.491][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 05:25:34.493][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 05:25:34.495][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 05:25:34.497][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:34.499][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:34.500][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.503][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.504][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.DEBUG[2024-05-04 05:25:34.505][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.513][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[2024-05-04 05:25:34.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.522][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.531][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.540][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.547][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[2024-05-04 05:25:34.549][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.556][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.DEBUG[2024-05-04 05:25:34.557][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.565][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[2024-05-04 05:25:34.566][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.574][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.582][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[2024-05-04 05:25:34.583][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.610][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.618][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.626][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.634][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.642][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.650][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.658][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:34.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:34.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:34.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:34.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:34.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:34.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:34.667][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-04 05:25:34.669][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:34.671][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.673][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 05:25:34.674][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.675][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:34.677][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:34.679][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:34.682][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:34.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:34.685][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.686][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-04 05:25:34.687][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-04 05:25:34.689][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-04 05:25:34.690][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 05:25:34.691][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:34.691][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:34.693][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:34.694][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.695][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.696][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:34.698][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:34.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:34.700][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:34.701][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-04 05:25:34.701][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-04 05:25:34.703][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:34.704][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:34.705][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:34.706][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:34.708][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-04 05:25:34.710][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:34.715][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:34.716][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-04 05:25:34.718][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:34.719][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-04 05:25:34.721][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:34.722][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:34.724][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-04 05:25:34.726][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-04 05:25:34.727][biodb::testThat] biodb.INFO [2024-05-04 05:25:34.729][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. "). biodb.INFO [2024-05-04 05:25:34.730][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:34.731][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:34.736][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[2024-05-04 05:25:34.742][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8". biodb.TRACE[2024-05-04 05:25:34.745][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.748][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content". biodb.DEBUG[2024-05-04 05:25:34.760][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[2024-05-04 05:25:34.764][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.766][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0". biodb.TRACE[2024-05-04 05:25:34.768][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.771][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content". biodb.INFO [2024-05-04 05:25:34.785][biodb::testThat] biodb.INFO [2024-05-04 05:25:34.786][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. "). biodb.INFO [2024-05-04 05:25:34.788][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:34.789][biodb::testThat] biodb.INFO [2024-05-04 05:25:34.828][biodb::testThat] biodb.INFO [2024-05-04 05:25:34.829][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. "). biodb.INFO [2024-05-04 05:25:34.831][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:34.832][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:34.837][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[2024-05-04 05:25:34.841][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646". biodb.TRACE[2024-05-04 05:25:34.845][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.848][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content". biodb.DEBUG[2024-05-04 05:25:34.855][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[2024-05-04 05:25:34.860][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646". biodb.TRACE[2024-05-04 05:25:34.864][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.866][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content". biodb.DEBUG[2024-05-04 05:25:34.875][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[2024-05-04 05:25:34.879][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.882][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7". biodb.TRACE[2024-05-04 05:25:34.884][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.887][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content". biodb.DEBUG[2024-05-04 05:25:34.897][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[2024-05-04 05:25:34.901][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:34.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e". biodb.TRACE[2024-05-04 05:25:34.905][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:34.924][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content". biodb.DEBUG[2024-05-04 05:25:35.081][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[2024-05-04 05:25:35.086][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:35.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971". biodb.TRACE[2024-05-04 05:25:35.089][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:35.110][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content". biodb.INFO [2024-05-04 05:25:35.266][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 05:25:35.268][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-04 05:25:35.270][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-04 05:25:35.271][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 05:25:35.272][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.274][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.277][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.278][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 05:25:35.283][biodb::testContext] biodb.INFO [2024-05-04 05:25:35.284][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:35.285][biodb::testContext] Test context - Some other custom tests biodb.INFO [2024-05-04 05:25:35.287][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 05:25:35.288][biodb::testContext] biodb.INFO [2024-05-04 05:25:35.291][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:35.293][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 05:25:35.298][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:35.299][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 05:25:35.301][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 05:25:35.302][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.306][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 05:25:35.307][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 05:25:35.309][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.312][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 05:25:35.314][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 05:25:35.315][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.319][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 05:25:35.320][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 05:25:35.322][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 05:25:35.323][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.327][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 05:25:35.328][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 05:25:35.330][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 05:25:35.331][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.335][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 05:25:35.336][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 05:25:35.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.340][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[2024-05-04 05:25:35.341][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 05:25:35.343][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 05:25:35.344][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 05:25:35.345][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.349][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 05:25:35.374][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 05:25:35.375][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.379][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 05:25:35.380][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 05:25:35.382][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 05:25:35.383][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.386][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:35.388][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 05:25:35.389][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 05:25:35.390][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 05:25:35.392][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 05:25:35.393][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 05:25:35.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.397][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[2024-05-04 05:25:35.398][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 05:25:35.399][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 05:25:35.400][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.404][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 05:25:35.405][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 05:25:35.406][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.410][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 05:25:35.412][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 05:25:35.413][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.417][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 05:25:35.418][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 05:25:35.419][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.423][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 05:25:35.424][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 05:25:35.425][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.429][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 05:25:35.430][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 05:25:35.436][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 05:25:35.437][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.441][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 05:25:35.442][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 05:25:35.443][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 05:25:35.445][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.449][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 05:25:35.452][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.453][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 05:25:35.454][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.456][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:35.457][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:35.460][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.461][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:35.462][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:35.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:35.465][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.466][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 05:25:35.468][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:35.469][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.471][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.472][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:35.472][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:35.472][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:35.472][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:35.472][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:35.473][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:35.475][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.477][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:35.479][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.481][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:35.482][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.484][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:35.485][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:35.486][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.488][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.489][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 05:25:35.492][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.493][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:35.494][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.496][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:35.497][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.498][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:35.500][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.501][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:35.503][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:35.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:35.505][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.507][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 05:25:35.508][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:35.509][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.511][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.512][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:35.512][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:35.512][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 05:25:35.512][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 05:25:35.512][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 05:25:35.514][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:35.515][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.518][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:35.519][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.521][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:35.523][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.524][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:35.525][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:35.527][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.528][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.530][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 05:25:35.532][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.534][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 05:25:35.535][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.537][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:35.538][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.539][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:35.541][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.542][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:35.544][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:35.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:35.546][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.548][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 05:25:35.549][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:35.550][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.552][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.553][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.554][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:35.556][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.558][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:35.560][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.562][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:35.563][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.565][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:35.566][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:35.567][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.569][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.570][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 05:25:35.573][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.574][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 05:25:35.575][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.577][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:35.578][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.579][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:35.581][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:35.583][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 05:25:35.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:35.586][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.587][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 05:25:35.589][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:35.590][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.592][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 05:25:35.593][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.594][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:35.596][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.598][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:35.599][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:35.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:35.602][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:35.603][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.605][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:35.606][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:35.607][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 05:25:35.608][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:35.610][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:35.612][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.614][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.627][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.633][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.639][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.645][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.651][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.657][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.663][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.670][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.676][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.682][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.688][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.694][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.700][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.707][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.713][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.719][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 05:25:35.721][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 05:25:35.723][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 05:25:35.725][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 05:25:35.727][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 05:25:35.729][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 05:25:35.731][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 05:25:35.733][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 05:25:35.735][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 05:25:35.737][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 05:25:35.738][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 05:25:35.740][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 05:25:35.742][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 05:25:35.744][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 05:25:35.746][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 05:25:35.748][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:35.750][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 05:25:35.752][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 05:25:35.754][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 05:25:35.756][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 05:25:35.758][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 05:25:35.778][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 05:25:35.781][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 05:25:35.783][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 05:25:35.785][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 05:25:35.787][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 05:25:35.789][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 05:25:35.791][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 05:25:35.793][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 05:25:35.795][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 05:25:35.797][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 05:25:35.799][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 05:25:35.801][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 05:25:35.803][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 05:25:35.805][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 05:25:35.807][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 05:25:35.809][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 05:25:35.811][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 05:25:35.813][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 05:25:35.815][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 05:25:35.817][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 05:25:35.820][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 05:25:35.822][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 05:25:35.824][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 05:25:35.826][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 05:25:35.828][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 05:25:35.830][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 05:25:35.832][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 05:25:35.834][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 05:25:35.836][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 05:25:35.838][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 05:25:35.840][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 05:25:35.842][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 05:25:35.844][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 05:25:35.846][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 05:25:35.848][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 05:25:35.850][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 05:25:35.852][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 05:25:35.854][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 05:25:35.856][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 05:25:35.858][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 05:25:35.860][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 05:25:35.862][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 05:25:35.864][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 05:25:35.865][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 05:25:35.867][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 05:25:35.869][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 05:25:35.871][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 05:25:35.873][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 05:25:35.875][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 05:25:35.877][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 05:25:35.879][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 05:25:35.881][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 05:25:35.883][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 05:25:35.885][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 05:25:35.887][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 05:25:35.889][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 05:25:35.891][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 05:25:35.893][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 05:25:35.895][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 05:25:35.897][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 05:25:35.899][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 05:25:35.901][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 05:25:35.903][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 05:25:35.905][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 05:25:35.906][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 05:25:35.908][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.910][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.913][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[2024-05-04 05:25:35.915][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.923][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.932][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.939][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[2024-05-04 05:25:35.941][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.949][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.958][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.966][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.975][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.983][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:35.992][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:35.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:35.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:35.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:35.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:35.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:35.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.000][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.008][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.017][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.025][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.034][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.043][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.051][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 05:25:36.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:36.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:36.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:36.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:36.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:36.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 05:25:36.061][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-04 05:25:36.062][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:36.065][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 05:25:36.066][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 05:25:36.068][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 05:25:36.069][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 05:25:36.070][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:36.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 05:25:36.073][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:36.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 05:25:36.076][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 05:25:36.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 05:25:36.078][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 05:25:36.080][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-04 05:25:36.081][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-04 05:25:36.082][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-04 05:25:36.084][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 05:25:36.085][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 05:25:36.085][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 05:25:36.086][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 05:25:36.088][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:36.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:36.090][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 05:25:36.092][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 05:25:36.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 05:25:36.094][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 05:25:36.095][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-04 05:25:36.095][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-04 05:25:36.097][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 05:25:36.098][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 05:25:36.099][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 05:25:36.101][self$setPropertyValue] biodb.DEBUG[2024-05-04 05:25:36.102][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-04 05:25:36.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 05:25:36.109][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:36.110][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-04 05:25:36.111][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-04 05:25:36.113][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-04 05:25:36.115][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:36.116][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 05:25:36.118][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-04 05:25:36.119][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-04 05:25:36.121][biodb::testThat] biodb.INFO [2024-05-04 05:25:36.122][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. "). biodb.INFO [2024-05-04 05:25:36.124][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 05:25:36.125][biodb::testThat] biodb.DEBUG[2024-05-04 05:25:36.130][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[2024-05-04 05:25:36.135][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 05:25:36.137][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030". biodb.TRACE[2024-05-04 05:25:36.138][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 05:25:36.227][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content". biodb.DEBUG[2024-05-04 05:25:37.326][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002". biodb.DEBUG[2024-05-04 05:25:37.328][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-04 05:25:37.331][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002". biodb.TRACE[2024-05-04 05:25:37.333][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-04 05:25:37.335][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[2024-05-04 05:25:37.336][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 05:25:37.338][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-04 05:25:37.340][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 05:25:37.343][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:37.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:37.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:37.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:37.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:37.355][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:37.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:37.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.388][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:37.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:37.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.394][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.400][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.424][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.431][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:37.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.462][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:37.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.468][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:37.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.486][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:37.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.528][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:37.562][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:37.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:37.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:37.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:37.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:37.573][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:37.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:37.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.603][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:37.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 05:25:37.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:37.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 05:25:37.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.614][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.642][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 05:25:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:37.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.676][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 05:25:37.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.692][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 05:25:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.703][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.714][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 05:25:37.806][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002. biodb.DEBUG[2024-05-04 05:25:37.810][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 05:25:37.812][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:37.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:37.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:37.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:37.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:37.825][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:37.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:37.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:37.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:37.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:37.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:37.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:37.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:37.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.854][private$selectFields] Fields none biodb.TRACE[2024-05-04 05:25:37.855][private$selectFields] biodb.TRACE[2024-05-04 05:25:37.857][private$selectFields] Fields is null: TRUE biodb.TRACE[2024-05-04 05:25:37.858][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:37.859][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:37.861][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.862][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.864][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.865][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.867][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.868][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.870][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.871][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.873][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.874][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.876][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.877][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.878][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.880][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.881][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.883][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.884][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.885][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.887][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.888][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.890][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.891][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.892][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.894][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.895][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.897][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.898][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.900][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.901][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.903][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.904][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.905][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.907][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.909][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.910][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.911][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.913][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.914][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.916][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.917][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.919][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.920][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.922][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.923][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.925][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.926][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.928][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.929][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.931][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.932][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.933][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.935][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.936][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.938][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.939][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.940][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.942][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.943][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.945][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.946][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.947][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.949][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.950][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.951][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.953][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:37.954][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:37.955][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:37.957][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:37.958][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.960][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.961][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.962][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:37.964][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.965][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.966][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.968][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:37.969][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.970][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.972][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.973][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:37.974][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.976][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.977][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.978][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:37.980][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.981][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.982][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:37.984][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:37.985][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.986][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.988][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:37.989][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:37.991][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.992][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.993][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.995][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:37.996][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:37.997][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:37.999][private$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[2024-05-04 05:25:38.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.035][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.133][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.146][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...]. biodb.DEBUG[2024-05-04 05:25:38.147][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 05:25:38.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:38.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:38.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:38.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:38.159][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:38.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 05:25:38.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:38.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:38.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 05:25:38.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 05:25:38.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:38.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 05:25:38.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:38.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 05:25:38.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.206][private$selectFields] Fields none biodb.TRACE[2024-05-04 05:25:38.207][private$selectFields] biodb.TRACE[2024-05-04 05:25:38.208][private$selectFields] Fields is null: TRUE biodb.TRACE[2024-05-04 05:25:38.209][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 05:25:38.211][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:38.212][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.214][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.215][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.216][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.217][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.219][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.220][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.221][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.223][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.224][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.225][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.227][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.228][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.229][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.231][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.232][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.233][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.235][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.236][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.237][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.238][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.240][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.241][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.243][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.244][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.245][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.247][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.248][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.250][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.251][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.253][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.254][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.255][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.257][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.258][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.259][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.261][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.262][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.263][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.265][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.266][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.267][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.269][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.270][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.271][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.273][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.274][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.275][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.277][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.278][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.279][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.280][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.282][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.283][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.284][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.286][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.287][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.288][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.290][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.291][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.292][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.294][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.295][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.296][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.297][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:38.299][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-04 05:25:38.300][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.302][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.303][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.304][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.305][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.307][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.308][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.309][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.310][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.312][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.313][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.314][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.316][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.317][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.318][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.320][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.321][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.322][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.324][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.325][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.326][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.327][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.329][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.330][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.331][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.333][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.334][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.335][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.337][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.338][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.339][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.341][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.342][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()" biodb.TRACE[2024-05-04 05:25:38.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 05:25:38.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 05:25:38.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 05:25:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 05:25:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 05:25:38.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 05:25:38.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 05:25:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 05:25:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 05:25:38.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 05:25:38.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.471][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 05:25:38.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 05:25:38.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 05:25:38.482][private$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[2024-05-04 05:25:38.484][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 05:25:38.485][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.INFO [2024-05-04 05:25:38.493][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 05:25:38.495][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-04 05:25:38.497][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-04 05:25:38.498][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 05:25:38.499][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 05:25:38.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 05:25:38.502][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 05:25:38.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 05:25:38.504][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 05:25:38.505][FUN] Functions in observer 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 161 ] ══ 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 161 ] Error: Test failures Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
name | user | system | elapsed | |
LipidmapsStructureConn | 0.816 | 0.058 | 0.877 | |
LipidmapsStructureEntry | 0.261 | 0.005 | 0.267 | |