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 11:36:19 -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. |
Package: biodbLipidmaps |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz |
StartedAt: 2024-05-03 21:09:34 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 21:14:47 -0400 (Fri, 03 May 2024) |
EllapsedTime: 313.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbLipidmaps.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.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: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK * this is package ‘biodbLipidmaps’ version ‘1.10.0’ * 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 166 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’ for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbLipidmaps’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location 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: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbLipidmaps) 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 [2024-05-03 21:10:20.927][biodb::testContext] biodb.INFO [2024-05-03 21:10:20.930][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:10:20.931][biodb::testContext] Test context - Generic tests biodb.INFO [2024-05-03 21:10:20.932][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:10:20.933][biodb::testContext] biodb.INFO [2024-05-03 21:10:20.940][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:10:20.943][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:10:20.951][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:10:20.952][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:10:20.953][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:10:20.954][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:20.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:20.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:20.957][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:10:20.978][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:10:20.979][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:20.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:20.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:20.982][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:10:20.983][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:10:20.984][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:20.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:20.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:20.987][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:10:20.988][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:10:20.989][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:10:20.990][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:20.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:20.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:20.993][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:10:20.994][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:10:20.995][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:10:20.996][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:20.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:20.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:20.999][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:10:21.000][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:10:21.001][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.004][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:10:21.005][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:10:21.006][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:10:21.007][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.009][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:10:21.011][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:10:21.011][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.014][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:10:21.015][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:10:21.016][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:10:21.017][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.020][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:10:21.021][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:10:21.022][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:10:21.023][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:10:21.024][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:10:21.025][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:10:21.026][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.029][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:10:21.030][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:10:21.031][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.034][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:10:21.035][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:10:21.036][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.039][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:10:21.040][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:10:21.041][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.044][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:10:21.045][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:10:21.046][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.049][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:10:21.050][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:10:21.051][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.054][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:10:21.055][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:10:21.058][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:10:21.059][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.069][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:10:21.070][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:10:21.072][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:10:21.073][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.080][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:10:21.120][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.173][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-03 21:10:21.175][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.176][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:10:21.177][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.178][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:10:21.179][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.180][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:10:21.181][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:10:21.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:10:21.183][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.184][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:10:21.185][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:10:21.186][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.187][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.188][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:10:21.188][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:10:21.188][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:10:21.188][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:10:21.188][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:10:21.189][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:10:21.190][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.192][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:10:21.193][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.195][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:10:21.196][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.197][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:10:21.198][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:10:21.199][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.200][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.201][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:10:21.203][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.204][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:10:21.206][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.207][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:10:21.208][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:10:21.210][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.211][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:10:21.212][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:10:21.213][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:10:21.214][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.215][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:10:21.216][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:10:21.217][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.218][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.219][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:10:21.219][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:10:21.219][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:10:21.219][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:10:21.219][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:10:21.220][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:10:21.221][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.223][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:10:21.224][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.224][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.225][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:10:21.226][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.227][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:10:21.228][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:10:21.229][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.230][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.231][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:10:21.233][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.234][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-03 21:10:21.235][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.236][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:10:21.237][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.238][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:10:21.239][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.240][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:10:21.241][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:10:21.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:10:21.243][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.244][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:10:21.245][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:10:21.246][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.247][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.248][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.249][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:10:21.250][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.252][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:10:21.253][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.254][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:10:21.255][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.256][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:10:21.257][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:10:21.258][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.259][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.260][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:10:21.262][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.263][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:10:21.264][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.265][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:10:21.266][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:10:21.268][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:10:21.270][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:10:21.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:10:21.272][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.273][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:10:21.274][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:10:21.275][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.276][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.277][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.278][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:10:21.279][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.281][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:10:21.282][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.283][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:10:21.284][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.285][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:10:21.286][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:10:21.287][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.288][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.292][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:10:21.293][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.294][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[2024-05-03 21:10:21.295][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.300][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.304][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.309][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.312][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[2024-05-03 21:10:21.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.317][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.322][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.325][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[2024-05-03 21:10:21.326][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.331][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.335][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.339][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.344][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.348][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.357][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.362][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.366][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.370][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:10:21.375][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:10:21.376][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:10:21.377][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:10:21.379][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:10:21.380][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:10:21.381][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:10:21.382][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:10:21.384][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:10:21.385][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:10:21.386][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:10:21.387][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:10:21.389][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:10:21.390][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:10:21.391][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:10:21.392][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:10:21.394][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:10:21.395][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:10:21.396][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:10:21.398][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:10:21.399][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:10:21.400][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:10:21.401][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:10:21.403][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:10:21.404][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:10:21.405][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:10:21.406][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:10:21.408][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:10:21.409][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:10:21.410][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:10:21.411][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:10:21.413][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:10:21.414][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:10:21.415][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:10:21.417][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:10:21.418][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:10:21.419][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:10:21.425][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:10:21.426][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:10:21.427][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:10:21.429][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:10:21.430][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:10:21.431][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:10:21.432][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:10:21.434][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:10:21.435][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:10:21.436][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:10:21.437][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:10:21.439][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:10:21.440][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:10:21.441][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:10:21.442][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:10:21.444][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:10:21.445][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:10:21.446][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:10:21.447][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:10:21.449][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:10:21.450][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:10:21.451][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:10:21.452][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:10:21.454][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:10:21.455][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:10:21.456][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:10:21.457][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:10:21.459][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:10:21.460][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:10:21.461][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:10:21.462][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:10:21.464][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:10:21.465][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:10:21.466][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:10:21.467][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:10:21.469][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:10:21.470][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:10:21.471][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:10:21.472][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:10:21.474][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:10:21.475][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:10:21.476][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:10:21.478][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:10:21.479][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:10:21.480][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:10:21.481][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:10:21.487][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:10:21.488][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:10:21.492][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:10:21.492][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.494][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.499][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.504][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[2024-05-03 21:10:21.505][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.511][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.516][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.521][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[2024-05-03 21:10:21.522][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.528][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.533][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.539][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.545][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.551][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.556][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.562][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.568][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.573][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.578][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[2024-05-03 21:10:21.579][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.585][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.590][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:10:21.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:10:21.597][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-03 21:10:21.605][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:10:21.607][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.608][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:10:21.609][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.610][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:10:21.611][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:10:21.613][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:10:21.615][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:10:21.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:10:21.616][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.617][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-03 21:10:21.618][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-03 21:10:21.619][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-03 21:10:21.620][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:10:21.621][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:10:21.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:10:21.622][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:10:21.623][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.625][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:10:21.625][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:10:21.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:10:21.627][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:10:21.628][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:10:21.628][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-03 21:10:21.629][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:10:21.630][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:10:21.631][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:10:21.632][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:10:21.637][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-03 21:10:21.638][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:10:21.666][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:10:21.668][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-03 21:10:21.672][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:10:21.676][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-03 21:10:21.680][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:10:21.681][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:10:21.682][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-03 21:10:21.683][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-03 21:10:21.692][biodb::testThat] biodb.INFO [2024-05-03 21:10:21.693][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-03 21:10:21.694][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:21.695][biodb::testThat] biodb.TRACE[2024-05-03 21:10:21.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv". biodb.DEBUG[2024-05-03 21:10:21.701][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-03 21:10:21.704][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:10:21.713][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:21.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:21.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:21.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:21.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:21.729][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:21.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:10:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:21.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:21.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.768][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:21.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:21.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:21.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.799][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:21.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:21.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:21.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:21.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:21.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:21.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.810][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:10:21.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.814][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:10:21.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:21.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:21.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:21.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:21.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:21.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.833][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:10:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.837][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:10:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.848][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:10:21.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:21.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.926][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.937][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:21.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:21.963][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001. biodb.TRACE[2024-05-03 21:10:21.965][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:21.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:21.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.969][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:21.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:21.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:21.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:21.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.976][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:21.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:21.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:21.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:21.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:21.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:21.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.049][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.072][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.073][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.074][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.075][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.098][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.099][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.100][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.101][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.145][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.146][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.147][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.148][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.149][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.159][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.162][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.170][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.171][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.172][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.173][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.195][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.196][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.197][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.198][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.216][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.220][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.221][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.222][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.222][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.233][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.234][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.235][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.236][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.240][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.241][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.242][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.243][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.246][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.247][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.248][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.249][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.253][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.254][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.255][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.255][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.259][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.260][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.261][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.262][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.266][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.267][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.267][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.268][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:22.275][biodb::testThat] biodb.INFO [2024-05-03 21:10:22.276][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-03 21:10:22.276][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:22.277][biodb::testThat] biodb.DEBUG[2024-05-03 21:10:22.290][private$loadEntries] Creating entries from ids [1]: "LMFA00000001". biodb.DEBUG[2024-05-03 21:10:22.297][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)... biodb.TRACE[2024-05-03 21:10:22.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001". biodb.TRACE[2024-05-03 21:10:22.303][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:10:22.304][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv". biodb.DEBUG[2024-05-03 21:10:22.305][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:10:22.327][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-03 21:10:22.328][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:10:22.330][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:22.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:22.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:22.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:22.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:22.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:22.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:10:22.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:22.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:22.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:10:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:10:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.362][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:22.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:10:22.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.365][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:22.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:10:22.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.369][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.373][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:10:22.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.377][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:10:22.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.384][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:10:22.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.388][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:10:22.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:22.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:10:22.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:10:22.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.407][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:10:22.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.411][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:10:22.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.422][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:10:22.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.444][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.448][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.455][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:10:22.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:10:22.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:10:22.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:22.481][self$createEntryFromContent] Accession numbers: LMFA00000001. biodb.TRACE[2024-05-03 21:10:22.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-03 21:10:22.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-03 21:10:22.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-03 21:10:22.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-03 21:10:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-03 21:10:22.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-03 21:10:22.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:22.499][biodb::testThat] biodb.INFO [2024-05-03 21:10:22.500][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-03 21:10:22.501][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:22.502][biodb::testThat] biodb.TRACE[2024-05-03 21:10:22.504][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.505][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.506][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.507][ef$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:22.508][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name". biodb.TRACE[2024-05-03 21:10:22.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:22.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:22.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:22.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:22.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:22.548][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-05-03 21:10:22.554][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[2024-05-03 21:10:22.574][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:10:22.575][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:10:22.576][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride". biodb.TRACE[2024-05-03 21:10:23.358][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride). biodb.DEBUG[2024-05-03 21:10:24.355][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:10:24.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content" biodb.TRACE[2024-05-03 21:10:24.372][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request" biodb.DEBUG[2024-05-03 21:10:24.374][function(conn, opt)] With found IDs [1]: "LMFA00000001". biodb.TRACE[2024-05-03 21:10:24.385][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:24.386][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:24.387][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.388][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:24.392][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.393][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-03 21:10:24.393][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:24.394][biodb::testThat] biodb.TRACE[2024-05-03 21:10:24.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:24.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:24.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:24.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:24.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:24.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:24.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:24.538][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-05-03 21:10:24.541][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:10:24.556][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-03 21:10:24.558][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:10:24.559][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.INFO [2024-05-03 21:10:24.577][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.579][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-03 21:10:24.579][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:24.580][biodb::testThat] biodb.TRACE[2024-05-03 21:10:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.607][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:24.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:24.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:24.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:24.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:10:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:10:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:24.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:10:24.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:24.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:24.684][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.685][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-03 21:10:24.686][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:24.687][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.696][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.697][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-03 21:10:24.698][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:24.699][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.706][biodb::testThat] biodb.INFO [2024-05-03 21:10:24.707][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-03 21:10:24.708][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:24.709][biodb::testThat] biodb.DEBUG[2024-05-03 21:10:24.713][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001". biodb.DEBUG[2024-05-03 21:10:25.535][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001. biodb.INFO [2024-05-03 21:10:26.013][biodb::testThat] biodb.INFO [2024-05-03 21:10:26.015][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-03 21:10:26.017][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:26.018][biodb::testThat] biodb.TRACE[2024-05-03 21:10:26.028][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:26.030][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:26.032][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.034][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.036][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.038][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.039][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.041][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:26.044][biodb::testThat] biodb.INFO [2024-05-03 21:10:26.046][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-05-03 21:10:26.047][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:26.049][biodb::testThat] biodb.TRACE[2024-05-03 21:10:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:26.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:26.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:10:26.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:10:26.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:26.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-05-03 21:10:26.178][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:10:26.179][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-03 21:10:26.180][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:10:26.182][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.DEBUG[2024-05-03 21:10:26.239][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-05-03 21:10:26.242][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:10:26.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-05-03 21:10:26.244][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:10:26.246][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.TRACE[2024-05-03 21:10:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:26.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:26.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-03 21:10:26.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-03 21:10:26.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:26.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:26.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:26.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.DEBUG[2024-05-03 21:10:26.323][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:10:26.324][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:10:26.339][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.TRACE[2024-05-03 21:10:30.535][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06). biodb.DEBUG[2024-05-03 21:10:41.909][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:10:41.911][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content" biodb.TRACE[2024-05-03 21:10:41.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request" biodb.DEBUG[2024-05-03 21:10:42.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.DEBUG[2024-05-03 21:10:42.885][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:10:42.886][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:10:42.888][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.TRACE[2024-05-03 21:10:43.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06). biodb.DEBUG[2024-05-03 21:10:44.255][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:10:44.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content" biodb.TRACE[2024-05-03 21:10:44.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request" biodb.DEBUG[2024-05-03 21:10:44.285][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06". biodb.DEBUG[2024-05-03 21:10:44.289][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:10:44.290][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:10:44.292][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06". biodb.TRACE[2024-05-03 21:10:44.975][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06). biodb.DEBUG[2024-05-03 21:10:45.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:10:45.704][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content" biodb.TRACE[2024-05-03 21:10:45.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request" biodb.TRACE[2024-05-03 21:10:45.749][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-03 21:10:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-03 21:10:45.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:10:45.768][biodb::testThat] biodb.INFO [2024-05-03 21:10:45.770][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-05-03 21:10:45.771][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:10:45.772][biodb::testThat] biodb.TRACE[2024-05-03 21:10:45.776][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:10:45.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:10:45.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-03 21:10:45.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-03 21:10:45.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:45.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:45.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:10:45.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:10:45.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:10:45.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:10:45.806][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:10:45.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:10:45.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:10:45.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:10:45.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:10:45.814][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:10:45.815][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[2024-05-03 21:10:45.819][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[2024-05-03 21:10:45.822][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:10:45.823][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:10:45.825][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01". biodb.TRACE[2024-05-03 21:10:49.926][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01). biodb.DEBUG[2024-05-03 21:11:00.821][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:11:00.824][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content" biodb.TRACE[2024-05-03 21:11:00.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request" biodb.DEBUG[2024-05-03 21:11:01.841][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003". biodb.DEBUG[2024-05-03 21:11:01.892][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-03 21:11:01.894][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003". biodb.TRACE[2024-05-03 21:11:01.896][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE". biodb.TRACE[2024-05-03 21:11:01.897][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-03 21:11:01.898][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:11:01.899][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:11:01.900][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-03 21:11:01.901][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-03 21:11:01.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:01.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:01.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:01.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:01.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:01.928][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:01.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:01.930][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". biodb.DEBUG[2024-05-03 21:11:01.933][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:01.934][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:01.936][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". biodb.TRACE[2024-05-03 21:11:02.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv). biodb.DEBUG[2024-05-03 21:11:03.307][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-03 21:11:03.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content" biodb.TRACE[2024-05-03 21:11:03.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request" biodb.DEBUG[2024-05-03 21:11:03.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:03.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:03.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:03.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:03.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:03.324][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:03.325][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[2024-05-03 21:11:03.326][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv". biodb.DEBUG[2024-05-03 21:11:03.329][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:03.330][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:03.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv". biodb.TRACE[2024-05-03 21:11:04.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv). biodb.DEBUG[2024-05-03 21:11:04.739][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-03 21:11:04.742][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content" biodb.TRACE[2024-05-03 21:11:04.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request" biodb.TRACE[2024-05-03 21:11:04.747][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv" biodb.DEBUG[2024-05-03 21:11:04.748][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-03 21:11:04.749][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-03 21:11:04.750][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:11:04.752][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:04.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:04.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:04.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:04.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:04.777][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:04.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:04.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:11:04.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:11:04.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.800][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:11:04.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:11:04.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.807][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.811][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:11:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.822][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:11:04.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:04.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:11:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:11:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.829][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:11:04.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:11:04.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.840][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:11:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:11:04.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.855][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:11:04.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.858][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.869][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:11:04.884][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:04.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:04.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:04.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:04.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:04.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:04.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:04.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:11:04.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.919][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:11:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:11:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:11:04.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:11:04.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:11:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:11:04.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:11:04.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:04.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.946][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:11:04.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:04.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:11:04.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:11:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:11:04.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:11:04.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.964][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:11:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.968][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:11:04.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:11:04.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.978][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:11:04.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:11:04.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.982][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:04.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:04.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:04.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:05.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:05.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:11:05.029][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003. biodb.DEBUG[2024-05-03 21:11:05.038][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-03 21:11:05.040][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:05.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:05.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:05.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:05.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:05.057][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:05.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:05.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.066][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.067][private$selectFields] biodb.TRACE[2024-05-03 21:11:05.068][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:05.069][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:05.070][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.071][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.072][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.073][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.073][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.074][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.075][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.076][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.077][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.078][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.079][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.080][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.081][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.081][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.082][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.083][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.088][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.091][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.103][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-03 21:11:05.104][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:05.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:05.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:05.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:05.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:05.111][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:05.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.120][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.121][private$selectFields] biodb.TRACE[2024-05-03 21:11:05.122][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:05.123][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:05.124][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.125][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.126][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.126][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.127][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.128][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.129][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.130][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.132][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.133][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.134][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.136][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.137][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.138][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.139][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.140][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.147][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.159][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-03 21:11:05.161][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:05.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:05.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:05.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:05.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:05.173][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:05.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:05.176][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.187][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.189][private$selectFields] biodb.TRACE[2024-05-03 21:11:05.190][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:05.191][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:05.193][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.194][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.196][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.197][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.199][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.200][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.202][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.203][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.205][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.206][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.208][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:05.209][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.227][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.228][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.229][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.230][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:05.231][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.235][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.242][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-03 21:11:05.243][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-03 21:11:05.244][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-03 21:11:05.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-03 21:11:05.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-03 21:11:05.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:11:05.260][biodb::testThat] biodb.INFO [2024-05-03 21:11:05.261][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-05-03 21:11:05.262][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:11:05.262][biodb::testThat] biodb.TRACE[2024-05-03 21:11:05.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:11:05.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:11:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-03 21:11:05.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-03 21:11:05.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:05.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:05.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:11:05.336][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:05.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:05.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:05.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:05.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:05.344][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:05.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:05.360][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[2024-05-03 21:11:05.363][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:05.364][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:05.366][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375". biodb.TRACE[2024-05-03 21:11:09.296][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375). biodb.DEBUG[2024-05-03 21:11:20.535][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:11:20.539][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content" biodb.TRACE[2024-05-03 21:11:20.556][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request" biodb.DEBUG[2024-05-03 21:11:22.053][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-03 21:11:22.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:22.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:22.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:22.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:22.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:22.104][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:22.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:22.125][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.180][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.182][private$selectFields] biodb.TRACE[2024-05-03 21:11:22.184][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:22.186][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:22.187][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.189][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.191][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.193][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.195][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.196][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.198][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.200][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.202][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.204][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.544][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.546][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.549][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.551][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.552][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.554][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:22.556][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.570][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.577][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-03 21:11:22.579][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:22.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:22.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:22.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:22.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:22.593][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:22.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.609][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.610][private$selectFields] biodb.TRACE[2024-05-03 21:11:22.612][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:22.613][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:22.615][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.616][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.618][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.619][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.621][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.622][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.624][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.626][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.627][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.628][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.630][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.631][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.633][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.634][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.636][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.637][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:22.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.650][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.656][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-03 21:11:22.658][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:22.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:22.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:22.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:22.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:22.670][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:22.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:22.673][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.679][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.685][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.686][private$selectFields] biodb.TRACE[2024-05-03 21:11:22.687][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:22.688][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:22.690][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.691][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.693][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.694][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.696][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.697][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.699][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.700][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.702][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.703][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.705][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:22.706][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.708][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.709][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.711][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.712][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:22.714][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.733][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-03 21:11:22.734][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-03 21:11:22.736][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-03 21:11:22.749][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-03 21:11:22.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-03 21:11:22.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:11:22.760][biodb::testThat] biodb.INFO [2024-05-03 21:11:22.762][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-05-03 21:11:22.763][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:11:22.765][biodb::testThat] biodb.TRACE[2024-05-03 21:11:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-03 21:11:22.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-03 21:11:22.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-03 21:11:22.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-03 21:11:22.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:22.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:11:22.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:22.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:11:22.811][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:22.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:22.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:22.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:22.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:22.819][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:22.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:22.823][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01". biodb.DEBUG[2024-05-03 21:11:22.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:11:22.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3". biodb.TRACE[2024-05-03 21:11:22.829][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:11:22.882][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content". biodb.DEBUG[2024-05-03 21:11:24.353][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-03 21:11:24.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:24.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:24.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:24.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:24.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:24.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:24.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:24.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.380][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.387][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.389][private$selectFields] biodb.TRACE[2024-05-03 21:11:24.390][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:24.392][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:24.393][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.395][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.397][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.398][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.400][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.401][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.403][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.405][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.406][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.408][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.409][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.411][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.413][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.414][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.416][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.417][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:24.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.425][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.432][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.438][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001]. biodb.DEBUG[2024-05-03 21:11:24.440][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:24.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:24.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:24.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:24.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:24.455][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:24.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:24.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.473][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.474][private$selectFields] biodb.TRACE[2024-05-03 21:11:24.476][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:24.477][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:24.478][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.480][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.482][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.484][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.485][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.486][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.487][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.489][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.491][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.492][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.494][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.495][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.497][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.499][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.501][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.502][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:24.504][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.523][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002]. biodb.DEBUG[2024-05-03 21:11:24.524][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:24.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:24.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:24.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:24.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:24.538][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:24.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:11:24.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.556][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.558][private$selectFields] biodb.TRACE[2024-05-03 21:11:24.560][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-03 21:11:24.561][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:11:24.563][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.564][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.565][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.566][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.567][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.568][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.570][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.571][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.573][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.574][private$selectFields] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.575][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:11:24.576][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.577][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.578][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.579][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.580][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()" biodb.TRACE[2024-05-03 21:11:24.581][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:24.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:24.630][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003]. biodb.DEBUG[2024-05-03 21:11:24.632][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-03 21:11:24.633][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-03 21:11:24.662][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-03 21:11:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-03 21:11:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-03 21:11:24.675][biodb::testThat] biodb.INFO [2024-05-03 21:11:24.677][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2024-05-03 21:11:24.679][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:11:24.681][biodb::testThat] biodb.DEBUG[2024-05-03 21:11:24.684][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2024-05-03 21:11:24.685][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)... biodb.TRACE[2024-05-03 21:11:24.687][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2024-05-03 21:11:24.688][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-03 21:11:24.690][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-03 21:11:24.691][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:11:24.692][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:11:24.693][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-03 21:11:24.694][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-03 21:11:24.717][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:24.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:24.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:24.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:24.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:24.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:24.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:24.736][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.DEBUG[2024-05-03 21:11:24.741][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:24.743][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:24.746][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:25.479][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:25.481][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:25.483][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:25.485][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:26.273][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:26.275][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:26.277][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:26.280][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:26.958][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:26.959][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:26.961][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:26.962][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:27.766][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:27.767][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:27.769][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:27.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:28.434][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:28.435][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:28.436][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:28.437][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:29.202][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:29.203][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:29.204][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:29.205][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:29.871][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:29.872][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:29.873][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:29.874][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:30.634][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:30.635][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:30.636][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:30.637][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:31.322][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:31.323][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:31.324][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:31.325][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:32.091][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:32.092][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:32.093][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:32.095][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:32.747][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:32.749][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:32.751][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:32.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:33.457][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:33.458][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:33.459][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:33.461][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:34.103][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:34.104][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:34.105][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:34.106][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:34.909][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:34.911][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:34.913][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:34.916][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:35.563][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:35.565][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:35.567][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:35.568][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:36.374][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:36.377][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:36.379][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:36.382][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:37.042][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:37.043][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:37.044][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:37.045][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:37.808][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:37.810][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:37.811][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:37.812][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". biodb.TRACE[2024-05-03 21:11:38.437][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:38.438][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:38.439][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:38.440][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv). biodb.INFO [2024-05-03 21:11:39.203][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server... biodb.TRACE[2024-05-03 21:11:39.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv" biodb.DEBUG[2024-05-03 21:11:39.211][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-03 21:11:39.214][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-03 21:11:39.216][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:11:39.220][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:39.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:39.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:39.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:39.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:39.236][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:39.238][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.TRACE[2024-05-03 21:11:39.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:39.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:39.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.250][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:11:39.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:11:39.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:11:39.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:11:39.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:11:39.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:11:39.286][self$createEntryFromContent] Accession numbers: NA. biodb.DEBUG[2024-05-03 21:11:39.287][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2024-05-03 21:11:39.294][biodb::testThat] biodb.INFO [2024-05-03 21:11:39.295][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2024-05-03 21:11:39.296][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:11:39.297][biodb::testThat] biodb.DEBUG[2024-05-03 21:11:39.303][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013" biodb.DEBUG[2024-05-03 21:11:39.304][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013". biodb.DEBUG[2024-05-03 21:11:39.305][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-03 21:11:39.306][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013". biodb.TRACE[2024-05-03 21:11:39.307][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE". biodb.TRACE[2024-05-03 21:11:39.308][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-03 21:11:39.309][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:11:39.310][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:11:39.311][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-03 21:11:39.312][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-03 21:11:39.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:39.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:39.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:39.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:39.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:39.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:39.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:39.324][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.DEBUG[2024-05-03 21:11:39.327][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:39.328][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:39.329][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:39.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:39.947][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:39.949][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:39.951][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:40.710][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:40.711][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:40.712][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:40.713][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:41.326][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:41.327][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:41.328][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:41.329][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:42.038][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:42.040][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:42.043][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:42.045][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:42.724][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:42.727][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:42.729][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:42.731][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:43.540][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:43.542][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:43.544][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:43.547][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:44.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:44.169][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:44.170][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:44.171][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:44.938][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:44.940][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:44.942][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:44.944][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:45.595][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:45.596][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:45.597][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:45.598][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:46.361][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:46.363][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:46.365][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:46.368][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:47.015][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:47.016][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:47.017][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:47.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:47.778][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:47.779][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:47.780][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:47.782][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:48.404][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:48.405][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:48.406][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:48.407][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:49.217][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:49.220][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:49.222][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:49.225][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:49.887][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:49.888][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:49.890][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:49.891][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:50.722][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:50.723][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:50.725][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:50.727][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:51.370][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:51.372][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:51.374][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:51.375][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:52.171][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:52.173][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:52.174][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:52.175][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". biodb.TRACE[2024-05-03 21:11:52.792][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:52.793][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:52.794][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:52.795][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv). biodb.INFO [2024-05-03 21:11:53.553][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:53.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:11:53.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:11:53.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:11:53.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:11:53.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:11:53.562][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:11:53.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:11:53.564][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.DEBUG[2024-05-03 21:11:53.566][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:53.567][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:53.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:11:54.189][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:54.190][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:54.191][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:54.192][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:11:54.952][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:54.953][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:54.954][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:54.956][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:11:55.579][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:55.580][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:55.581][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:55.582][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:11:56.352][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:56.355][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:56.357][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:56.360][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:11:57.020][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:57.022][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:57.024][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:57.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:11:57.752][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:57.754][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:57.756][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:57.759][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:11:58.416][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:58.419][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:58.421][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:58.423][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:11:59.226][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:11:59.227][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:11:59.228][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:11:59.229][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:11:59.842][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:11:59.843][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:11:59.844][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:11:59.845][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:00.613][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:12:00.614][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:00.615][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:00.616][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:12:01.236][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:12:01.237][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:12:01.238][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:12:01.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:01.999][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:12:02.000][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:02.001][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:02.002][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:12:02.632][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:12:02.633][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:12:02.634][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:12:02.664][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:03.427][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:12:03.428][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:03.429][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:03.430][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:12:04.075][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:12:04.077][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:12:04.078][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:12:04.080][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:04.848][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:12:04.850][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:04.852][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:04.854][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:12:05.496][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:12:05.498][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:12:05.501][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:12:05.503][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:06.322][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.DEBUG[2024-05-03 21:12:06.325][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:06.327][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:06.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". biodb.TRACE[2024-05-03 21:12:07.018][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist. biodb.TRACE[2024-05-03 21:12:07.019][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-03 21:12:07.021][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-03 21:12:07.022][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv). biodb.INFO [2024-05-03 21:12:07.789][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server... biodb.TRACE[2024-05-03 21:12:07.796][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv" biodb.DEBUG[2024-05-03 21:12:07.800][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-03 21:12:07.803][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-03 21:12:07.806][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:12:07.811][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:07.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:07.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:07.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:07.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:07.832][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:07.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:12:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.846][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:12:07.858][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:07.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:07.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:07.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:07.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:07.868][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:07.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:12:07.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:07.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:07.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:12:07.924][self$createEntryFromContent] Accession numbers: NA, NA. biodb.DEBUG[2024-05-03 21:12:07.925][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-03 21:12:07.926][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL" biodb.INFO [2024-05-03 21:12:08.103][biodb::testThat] biodb.INFO [2024-05-03 21:12:08.104][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2024-05-03 21:12:08.105][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:08.106][biodb::testThat] biodb.INFO [2024-05-03 21:12:08.161][biodb::testThat] biodb.INFO [2024-05-03 21:12:08.162][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2024-05-03 21:12:08.163][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:08.164][biodb::testThat] biodb.INFO [2024-05-03 21:12:08.171][biodb::testThat] biodb.INFO [2024-05-03 21:12:08.172][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2024-05-03 21:12:08.173][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:08.174][biodb::testThat] biodb.DEBUG[2024-05-03 21:12:08.176][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[2024-05-03 21:12:08.179][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:08.180][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:08.182][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV". biodb.TRACE[2024-05-03 21:12:12.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV). biodb.DEBUG[2024-05-03 21:12:23.378][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:23.381][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content" biodb.TRACE[2024-05-03 21:12:23.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request" biodb.TRACE[2024-05-03 21:12:24.273][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:24.274][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:24.275][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:24.276][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:24.277][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:24.278][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:24.279][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:24.280][ef$get] fields variable is a list. biodb.INFO [2024-05-03 21:12:24.281][biodb::testThat] biodb.INFO [2024-05-03 21:12:24.282][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. "). biodb.INFO [2024-05-03 21:12:24.283][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:24.284][biodb::testThat] biodb.ERROR[2024-05-03 21:12:24.296][conn$annotateMzValues] No column named "mz" was found inside data frame. biodb.ERROR[2024-05-03 21:12:24.312][ef$checkIsDefined] Field(s) "foo" is/are not defined. biodb.INFO [2024-05-03 21:12:24.324][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:12:24.325][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-03 21:12:24.326][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-03 21:12:24.327][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:12:24.328][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.330][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.331][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-03 21:12:24.341][biodb::testContext] biodb.INFO [2024-05-03 21:12:24.342][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:12:24.343][biodb::testContext] Test context - Web services tests biodb.INFO [2024-05-03 21:12:24.344][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:12:24.345][biodb::testContext] biodb.INFO [2024-05-03 21:12:24.347][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:12:24.348][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:12:24.352][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:24.353][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:12:24.354][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:12:24.355][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.357][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:12:24.358][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:12:24.359][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.362][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:12:24.362][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:12:24.388][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.391][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:12:24.392][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:12:24.393][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:12:24.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.397][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:12:24.398][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:12:24.399][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:12:24.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.402][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:12:24.403][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:12:24.404][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.406][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:12:24.407][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:12:24.408][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:12:24.409][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.411][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:12:24.412][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:12:24.413][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.416][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:12:24.417][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:12:24.418][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:12:24.418][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.421][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:12:24.422][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:12:24.423][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:12:24.424][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:12:24.425][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:12:24.426][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:12:24.426][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.429][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:12:24.430][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:12:24.431][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.434][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:12:24.435][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:12:24.436][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.438][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:12:24.439][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:12:24.440][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.442][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:12:24.443][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:12:24.444][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.447][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:12:24.448][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:12:24.449][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.451][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:12:24.452][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:12:24.455][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:12:24.456][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.459][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:12:24.459][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:12:24.460][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:12:24.461][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.464][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:12:24.466][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.467][self$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[2024-05-03 21:12:24.468][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.468][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:24.469][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:24.471][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.472][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:24.473][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:24.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:24.475][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.476][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:12:24.477][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:24.478][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.479][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.480][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:24.480][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:24.480][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:12:24.480][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:12:24.480][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:12:24.481][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:24.481][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.483][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:24.484][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.486][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:24.487][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.497][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:24.498][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:24.499][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.500][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.501][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:12:24.503][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.504][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:12:24.505][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.506][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:24.507][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:24.509][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:24.511][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:12:24.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:24.513][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.514][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:12:24.514][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:24.515][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.516][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.517][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:24.517][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:24.517][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:12:24.517][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:12:24.517][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:12:24.518][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:24.519][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.521][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:24.522][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.523][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:24.524][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.525][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:24.526][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:24.527][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.528][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.529][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:12:24.531][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.531][self$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[2024-05-03 21:12:24.532][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.533][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:24.534][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:24.536][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.537][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:24.538][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:24.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:24.540][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.541][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:12:24.542][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:24.543][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.543][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.544][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.545][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:24.546][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.548][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:24.549][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.551][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:24.551][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.552][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:24.553][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:24.554][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.555][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.556][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:12:24.558][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.559][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:12:24.560][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.561][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:24.561][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.562][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:24.563][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.564][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:24.565][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:12:24.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:24.567][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.568][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:12:24.569][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:24.570][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.571][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.572][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.573][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:24.573][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.575][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:24.576][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.578][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:24.579][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.580][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:24.580][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:24.581][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.582][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.583][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:24.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.586][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.590][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.604][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.613][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.617][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.625][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.629][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.632][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[2024-05-03 21:12:24.633][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.637][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.641][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.645][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.649][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[2024-05-03 21:12:24.649][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.654][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.657][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[2024-05-03 21:12:24.658][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.662][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.665][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[2024-05-03 21:12:24.666][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:12:24.668][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:12:24.669][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:12:24.670][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:12:24.672][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:12:24.673][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:12:24.674][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:12:24.675][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:12:24.677][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:12:24.678][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:12:24.679][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:12:24.681][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:12:24.682][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:12:24.683][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:12:24.684][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:12:24.686][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:12:24.687][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:12:24.688][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:12:24.689][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:12:24.691][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:12:24.692][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:12:24.693][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:12:24.695][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:12:24.696][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:12:24.697][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:12:24.708][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:12:24.710][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:12:24.711][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:12:24.712][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:12:24.714][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:12:24.715][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:12:24.716][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:12:24.717][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:12:24.719][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:12:24.720][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:12:24.721][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:12:24.722][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:12:24.724][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:12:24.725][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:12:24.726][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:12:24.727][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:12:24.729][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:12:24.730][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:12:24.731][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:12:24.732][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:12:24.734][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:12:24.735][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:12:24.736][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:12:24.738][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:12:24.739][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:12:24.740][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:12:24.741][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:12:24.743][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:12:24.744][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:12:24.745][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:12:24.746][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:12:24.748][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:12:24.749][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:12:24.750][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:12:24.751][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:12:24.753][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:12:24.754][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:12:24.755][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:12:24.756][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:12:24.758][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:12:24.759][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:12:24.760][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:12:24.761][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:12:24.763][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:12:24.764][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:12:24.765][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:12:24.766][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:12:24.768][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:12:24.769][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:12:24.770][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:12:24.771][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:12:24.773][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:12:24.774][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:12:24.775][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:12:24.777][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:12:24.778][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:12:24.779][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:12:24.780][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:12:24.782][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:12:24.783][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:12:24.784][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:24.785][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.787][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.788][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.794][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.809][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.815][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[2024-05-03 21:12:24.816][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.821][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.826][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.DEBUG[2024-05-03 21:12:24.827][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.832][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[2024-05-03 21:12:24.833][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.838][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.844][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.850][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.855][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.861][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.867][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.873][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.878][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.884][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.889][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[2024-05-03 21:12:24.890][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:24.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:24.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:24.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:24.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:24.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:24.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:24.896][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-03 21:12:24.897][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:24.899][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.900][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:12:24.901][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.902][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:24.914][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:24.916][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:24.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:24.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:24.920][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.921][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-03 21:12:24.922][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-03 21:12:24.923][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-03 21:12:24.924][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:12:24.925][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:24.925][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:24.926][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:24.926][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.928][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:24.929][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:24.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:24.931][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:24.932][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:12:24.932][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-03 21:12:24.933][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:24.933][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:24.934][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:24.935][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:24.936][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-03 21:12:24.938][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:12:24.941][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:24.942][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-03 21:12:24.943][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:24.944][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-03 21:12:24.945][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:12:24.946][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:12:24.947][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-03 21:12:24.948][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-03 21:12:24.950][biodb::testThat] biodb.INFO [2024-05-03 21:12:24.951][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. "). biodb.INFO [2024-05-03 21:12:24.951][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:24.952][biodb::testThat] biodb.DEBUG[2024-05-03 21:12:24.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride". biodb.DEBUG[2024-05-03 21:12:24.959][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:24.960][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:24.962][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride". biodb.TRACE[2024-05-03 21:12:25.956][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride). biodb.DEBUG[2024-05-03 21:12:26.924][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:26.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content" biodb.TRACE[2024-05-03 21:12:26.937][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request" biodb.DEBUG[2024-05-03 21:12:26.955][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[2024-05-03 21:12:26.962][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:26.964][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:26.968][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty". biodb.TRACE[2024-05-03 21:12:27.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty). biodb.DEBUG[2024-05-03 21:12:28.369][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:28.373][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content" biodb.TRACE[2024-05-03 21:12:28.381][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request" biodb.INFO [2024-05-03 21:12:28.401][biodb::testThat] biodb.INFO [2024-05-03 21:12:28.404][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. "). biodb.INFO [2024-05-03 21:12:28.406][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:28.408][biodb::testThat] biodb.INFO [2024-05-03 21:12:28.643][biodb::testThat] biodb.INFO [2024-05-03 21:12:28.644][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. "). biodb.INFO [2024-05-03 21:12:28.645][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:28.646][biodb::testThat] biodb.DEBUG[2024-05-03 21:12:28.649][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001". biodb.DEBUG[2024-05-03 21:12:28.651][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:28.652][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:28.654][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001". biodb.TRACE[2024-05-03 21:12:29.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001). biodb.DEBUG[2024-05-03 21:12:29.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:29.711][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content" biodb.TRACE[2024-05-03 21:12:29.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request" biodb.DEBUG[2024-05-03 21:12:29.719][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[2024-05-03 21:12:29.721][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:12:29.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646". biodb.TRACE[2024-05-03 21:12:29.724][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:12:29.725][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content". biodb.DEBUG[2024-05-03 21:12:29.730][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[2024-05-03 21:12:29.733][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:29.734][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:29.735][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001". biodb.TRACE[2024-05-03 21:12:30.256][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001). biodb.DEBUG[2024-05-03 21:12:30.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:30.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content" biodb.TRACE[2024-05-03 21:12:30.793][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request" biodb.DEBUG[2024-05-03 21:12:30.800][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid". biodb.DEBUG[2024-05-03 21:12:30.803][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:30.804][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:30.806][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid". biodb.TRACE[2024-05-03 21:12:32.234][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid). biodb.DEBUG[2024-05-03 21:12:35.568][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:35.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content" biodb.TRACE[2024-05-03 21:12:35.575][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request" biodb.DEBUG[2024-05-03 21:12:35.700][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[2024-05-03 21:12:35.704][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-03 21:12:35.705][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-03 21:12:35.707][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6". biodb.TRACE[2024-05-03 21:12:36.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6). biodb.DEBUG[2024-05-03 21:12:40.540][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-03 21:12:40.543][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content" biodb.TRACE[2024-05-03 21:12:40.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request" biodb.INFO [2024-05-03 21:12:40.673][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:12:40.674][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-03 21:12:40.675][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-03 21:12:40.676][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:12:40.677][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:40.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:40.679][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.681][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-03 21:12:40.686][biodb::testContext] biodb.INFO [2024-05-03 21:12:40.687][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:12:40.688][biodb::testContext] Test context - Some other custom tests biodb.INFO [2024-05-03 21:12:40.689][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-03 21:12:40.690][biodb::testContext] biodb.INFO [2024-05-03 21:12:40.692][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:12:40.694][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-03 21:12:40.698][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:40.699][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-03 21:12:40.700][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-03 21:12:40.701][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.704][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-03 21:12:40.705][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-03 21:12:40.706][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.708][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-03 21:12:40.709][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-03 21:12:40.710][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.713][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-03 21:12:40.713][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-03 21:12:40.714][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-03 21:12:40.715][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.718][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-03 21:12:40.719][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-03 21:12:40.720][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-03 21:12:40.720][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.723][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-03 21:12:40.724][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-03 21:12:40.725][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.728][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-03 21:12:40.729][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-03 21:12:40.730][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-03 21:12:40.731][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.733][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-03 21:12:40.734][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-03 21:12:40.735][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.738][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-03 21:12:40.739][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-03 21:12:40.740][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-03 21:12:40.741][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.744][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:12:40.745][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-03 21:12:40.746][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-03 21:12:40.747][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-03 21:12:40.748][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-03 21:12:40.749][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-03 21:12:40.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.753][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-03 21:12:40.754][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-03 21:12:40.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.758][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-03 21:12:40.759][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-03 21:12:40.760][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.763][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-03 21:12:40.764][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-03 21:12:40.765][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.768][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-03 21:12:40.769][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-03 21:12:40.770][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.773][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-03 21:12:40.774][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-03 21:12:40.775][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.778][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-03 21:12:40.779][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-03 21:12:40.782][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-03 21:12:40.783][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.786][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-03 21:12:40.787][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-03 21:12:40.788][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-03 21:12:40.789][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.792][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-03 21:12:40.794][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.795][self$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[2024-05-03 21:12:40.796][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.797][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:40.798][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:40.800][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:40.802][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:40.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:40.805][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.806][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-03 21:12:40.807][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:40.808][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.809][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.810][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:40.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:40.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:12:40.810][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:12:40.810][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:12:40.811][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:40.812][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.814][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:40.815][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.817][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:40.818][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.819][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:40.820][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:40.821][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.822][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.823][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-03 21:12:40.825][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.826][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:12:40.827][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.828][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:40.829][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:40.831][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:40.834][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:12:40.835][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:40.836][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.837][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-03 21:12:40.838][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:40.839][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.840][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.841][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:40.841][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:40.841][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-03 21:12:40.841][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-03 21:12:40.841][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-03 21:12:40.842][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:40.843][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.845][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:40.846][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.848][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:40.849][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.850][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:40.851][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:40.852][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.853][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.854][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-03 21:12:40.856][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.857][self$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[2024-05-03 21:12:40.858][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.859][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:40.860][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:40.863][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.864][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:40.865][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:40.866][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:40.867][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.868][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-03 21:12:40.869][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:40.870][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.871][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.872][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.873][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:40.874][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.876][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:40.877][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.879][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:40.880][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.881][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:40.882][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:40.883][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.884][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.885][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-03 21:12:40.887][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.888][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-03 21:12:40.889][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.890][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:40.891][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:40.893][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:40.896][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-03 21:12:40.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:40.898][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.899][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-03 21:12:40.900][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:40.902][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.903][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-03 21:12:40.904][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.905][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:40.906][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.908][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:40.909][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:40.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:40.911][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:40.912][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.913][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:40.914][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:40.915][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-03 21:12:40.916][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:40.918][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:40.919][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.921][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.925][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.930][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.935][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.939][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[2024-05-03 21:12:40.940][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.943][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[2024-05-03 21:12:40.962][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.979][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.982][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[2024-05-03 21:12:40.983][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.988][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.992][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:40.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:40.996][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:40.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:40.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:40.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.001][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.010][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.014][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.018][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[2024-05-03 21:12:41.019][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.023][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.028][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-03 21:12:41.029][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-03 21:12:41.031][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-03 21:12:41.032][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-03 21:12:41.033][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-03 21:12:41.035][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-03 21:12:41.036][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-03 21:12:41.038][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-03 21:12:41.039][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-03 21:12:41.040][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-03 21:12:41.042][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-03 21:12:41.043][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-03 21:12:41.044][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-03 21:12:41.046][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-03 21:12:41.047][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-03 21:12:41.048][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:12:41.050][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-03 21:12:41.051][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-03 21:12:41.052][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-03 21:12:41.054][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-03 21:12:41.055][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-03 21:12:41.057][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-03 21:12:41.058][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-03 21:12:41.059][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-03 21:12:41.061][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-03 21:12:41.062][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-03 21:12:41.063][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-03 21:12:41.065][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-03 21:12:41.066][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-03 21:12:41.068][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-03 21:12:41.069][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-03 21:12:41.070][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-03 21:12:41.072][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-03 21:12:41.073][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-03 21:12:41.074][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-03 21:12:41.075][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-03 21:12:41.077][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-03 21:12:41.078][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-03 21:12:41.079][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-03 21:12:41.081][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-03 21:12:41.082][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-03 21:12:41.083][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-03 21:12:41.084][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-03 21:12:41.086][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-03 21:12:41.087][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-03 21:12:41.088][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-03 21:12:41.089][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-03 21:12:41.091][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-03 21:12:41.092][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-03 21:12:41.093][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-03 21:12:41.094][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-03 21:12:41.096][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-03 21:12:41.097][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-03 21:12:41.098][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-03 21:12:41.099][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-03 21:12:41.101][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-03 21:12:41.102][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-03 21:12:41.103][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-03 21:12:41.105][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-03 21:12:41.106][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-03 21:12:41.107][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-03 21:12:41.108][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-03 21:12:41.110][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-03 21:12:41.111][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-03 21:12:41.112][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-03 21:12:41.113][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-03 21:12:41.115][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-03 21:12:41.116][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-03 21:12:41.117][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-03 21:12:41.119][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-03 21:12:41.120][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-03 21:12:41.121][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-03 21:12:41.122][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-03 21:12:41.124][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-03 21:12:41.125][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-03 21:12:41.126][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-03 21:12:41.128][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-03 21:12:41.129][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-03 21:12:41.130][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-03 21:12:41.131][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-03 21:12:41.133][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-03 21:12:41.134][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-03 21:12:41.135][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-03 21:12:41.137][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-03 21:12:41.138][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-03 21:12:41.139][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-03 21:12:41.140][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.142][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.143][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.150][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.156][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.162][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.168][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.174][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.181][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.187][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.193][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.199][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.206][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.212][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.217][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[2024-05-03 21:12:41.218][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.223][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[2024-05-03 21:12:41.224][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.229][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[2024-05-03 21:12:41.230][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.236][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.243][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-03 21:12:41.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:41.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:41.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:41.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:41.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:41.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-03 21:12:41.249][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-03 21:12:41.251][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:41.253][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-03 21:12:41.254][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-03 21:12:41.255][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-03 21:12:41.256][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-03 21:12:41.257][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:41.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-03 21:12:41.259][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:41.260][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-03 21:12:41.261][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-03 21:12:41.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-03 21:12:41.263][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-03 21:12:41.264][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-03 21:12:41.265][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-03 21:12:41.267][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-03 21:12:41.268][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-03 21:12:41.268][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-03 21:12:41.269][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-03 21:12:41.270][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:41.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:41.271][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-03 21:12:41.272][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-03 21:12:41.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-03 21:12:41.274][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-03 21:12:41.275][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-03 21:12:41.275][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-03 21:12:41.276][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-03 21:12:41.277][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-03 21:12:41.278][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-03 21:12:41.279][self$setPropertyValue] biodb.DEBUG[2024-05-03 21:12:41.280][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-03 21:12:41.282][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-03 21:12:41.285][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:41.286][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-03 21:12:41.287][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-03 21:12:41.289][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-03 21:12:41.290][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:12:41.291][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-03 21:12:41.292][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-03 21:12:41.293][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-03 21:12:41.294][biodb::testThat] biodb.INFO [2024-05-03 21:12:41.295][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. "). biodb.INFO [2024-05-03 21:12:41.296][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-03 21:12:41.297][biodb::testThat] biodb.DEBUG[2024-05-03 21:12:41.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV". biodb.DEBUG[2024-05-03 21:12:41.304][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-03 21:12:41.305][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030". biodb.TRACE[2024-05-03 21:12:41.307][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-03 21:12:41.351][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content". biodb.DEBUG[2024-05-03 21:12:42.266][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002". biodb.DEBUG[2024-05-03 21:12:42.268][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)... biodb.TRACE[2024-05-03 21:12:42.269][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002". biodb.TRACE[2024-05-03 21:12:42.271][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-03 21:12:42.272][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv". biodb.DEBUG[2024-05-03 21:12:42.273][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-03 21:12:42.275][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s). biodb.DEBUG[2024-05-03 21:12:42.276][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-03 21:12:42.278][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:42.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:42.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:42.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:42.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:42.286][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:42.287][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.TRACE[2024-05-03 21:12:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.308][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:12:42.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:12:42.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.312][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:12:42.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:12:42.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.316][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.333][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:12:42.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.337][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:12:42.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.345][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.357][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:12:42.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.361][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:12:42.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:12:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:12:42.426][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:42.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:42.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:42.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:42.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:42.434][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:42.435][FUN] Functions in observer BiodbConfig: [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[2024-05-03 21:12:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:12:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-03 21:12:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-03 21:12:42.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-03 21:12:42.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.465][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.481][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:12:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.485][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-03 21:12:42.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.506][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:12:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-03 21:12:42.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-03 21:12:42.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-03 21:12:42.580][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002. biodb.DEBUG[2024-05-03 21:12:42.582][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-03 21:12:42.584][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:42.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:42.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:42.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:42.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:42.592][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:42.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-03 21:12:42.595][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:12:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:12:42.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.607][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:12:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:12:42.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.611][private$selectFields] Fields none biodb.TRACE[2024-05-03 21:12:42.612][private$selectFields] biodb.TRACE[2024-05-03 21:12:42.613][private$selectFields] Fields is null: TRUE biodb.TRACE[2024-05-03 21:12:42.614][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:12:42.615][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.616][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.617][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.618][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.619][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.620][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.621][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.639][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.640][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.641][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.642][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.643][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.644][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.645][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.646][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.647][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.648][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.648][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.649][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.650][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.651][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.652][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.653][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.654][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.655][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.656][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.657][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.658][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.658][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.659][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.660][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.661][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.662][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.663][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.664][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.665][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.666][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.666][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.667][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.668][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.669][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.670][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.671][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.672][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.673][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.674][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.675][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.676][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.677][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.677][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.678][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.679][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.680][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.681][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.682][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.683][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.684][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.685][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.686][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.686][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.687][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.688][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.689][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.690][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.691][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.692][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.693][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.694][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.695][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.695][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.696][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.697][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.698][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.699][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.700][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.701][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.702][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.703][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.703][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.704][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.705][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.706][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.707][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.708][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.709][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.710][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.711][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.712][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.713][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.713][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.714][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.715][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.716][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.717][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.718][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.719][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.720][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.721][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.722][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.723][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()" biodb.TRACE[2024-05-03 21:12:42.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.753][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.761][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.765][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.807][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.820][private$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[2024-05-03 21:12:42.821][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-03 21:12:42.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:42.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:42.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:42.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:42.828][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:42.829][FUN] Functions in observer BiodbConfig: [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[2024-05-03 21:12:42.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-03 21:12:42.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-03 21:12:42.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-03 21:12:42.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-03 21:12:42.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-03 21:12:42.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.846][private$selectFields] Fields none biodb.TRACE[2024-05-03 21:12:42.847][private$selectFields] biodb.TRACE[2024-05-03 21:12:42.848][private$selectFields] Fields is null: TRUE biodb.TRACE[2024-05-03 21:12:42.849][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-03 21:12:42.849][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.850][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.851][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.852][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.853][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.854][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.855][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.856][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.857][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.858][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.859][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.860][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.861][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.862][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.863][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.863][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.864][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.865][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.866][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.867][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.868][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.869][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.870][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.871][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.872][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.873][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.874][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.875][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.876][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.876][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.877][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.878][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.879][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.880][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.881][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.882][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.883][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.884][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.885][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.886][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.887][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.888][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.889][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.889][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.890][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.891][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.892][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.893][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.894][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.895][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.896][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.897][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.898][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.899][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.900][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.901][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.901][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.902][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.903][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.904][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.905][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.906][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.907][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.908][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.909][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.910][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.911][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id" biodb.TRACE[2024-05-03 21:12:42.912][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.913][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.914][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.915][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.916][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.917][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.918][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.918][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.919][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.920][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.921][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.922][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.923][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.924][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.925][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.926][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.927][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.928][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:42.929][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.930][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.931][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:42.932][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:42.932][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.933][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.934][ef$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:42.935][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:42.936][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.937][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.938][ef$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.939][ef$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:42.940][ef$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.941][ef$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.942][private$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[2024-05-03 21:12:42.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-03 21:12:42.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-03 21:12:42.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-03 21:12:42.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.978][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.982][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-03 21:12:42.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.993][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:42.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-03 21:12:42.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:42.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-03 21:12:43.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:43.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:43.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-03 21:12:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-03 21:12:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:43.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:43.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:43.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:43.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-03 21:12:43.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-03 21:12:43.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.046][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.050][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-03 21:12:43.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-03 21:12:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-03 21:12:43.059][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...]. biodb.DEBUG[2024-05-03 21:12:43.060][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s). biodb.DEBUG[2024-05-03 21:12:43.061][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.INFO [2024-05-03 21:12:43.068][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-03 21:12:43.070][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-03 21:12:43.071][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-03 21:12:43.072][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-03 21:12:43.073][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-03 21:12:43.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-03 21:12:43.075][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-03 21:12:43.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-03 21:12:43.077][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-03 21:12:43.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ── any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE `actual`: TRUE `expected`: FALSE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_false(...) ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ───────────── any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE `actual`: TRUE `expected`: FALSE One of the entries is NULL. Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_false(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ] Error: Test failures Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
name | user | system | elapsed | |
LipidmapsStructureConn | 0.994 | 0.092 | 2.866 | |
LipidmapsStructureEntry | 0.136 | 0.002 | 0.137 | |