| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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 | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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: 2024-07-21 22:09:09 -0400 (Sun, 21 Jul 2024) |
| EndedAt: 2024-07-21 22:14:01 -0400 (Sun, 21 Jul 2024) |
| EllapsedTime: 292.7 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 4.4.1 (2024-06-14)
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 [2024-07-21 22:09:55.622][biodb::testContext]
biodb.INFO [2024-07-21 22:09:55.625][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:09:55.626][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-21 22:09:55.627][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:09:55.628][biodb::testContext]
biodb.INFO [2024-07-21 22:09:55.636][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:09:55.638][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 22:09:55.646][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:09:55.648][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 22:09:55.649][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.653][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 22:09:55.674][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.678][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 22:09:55.679][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.683][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 22:09:55.684][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 22:09:55.685][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 22:09:55.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.696][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 22:09:55.697][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 22:09:55.699][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.703][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 22:09:55.704][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 22:09:55.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.707][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[2024-07-21 22:09:55.708][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 22:09:55.709][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 22:09:55.710][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 22:09:55.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.714][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 22:09:55.715][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.719][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 22:09:55.720][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 22:09:55.721][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 22:09:55.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.725][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:09:55.726][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 22:09:55.727][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 22:09:55.728][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 22:09:55.729][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 22:09:55.730][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 22:09:55.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.733][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[2024-07-21 22:09:55.734][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 22:09:55.735][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 22:09:55.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.739][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 22:09:55.741][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 22:09:55.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.743][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[2024-07-21 22:09:55.744][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 22:09:55.746][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 22:09:55.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.749][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 22:09:55.751][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 22:09:55.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.754][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 22:09:55.756][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 22:09:55.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.760][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:09:55.761][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 22:09:55.765][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 22:09:55.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.769][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 22:09:55.770][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 22:09:55.771][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 22:09:55.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.779][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 22:09:55.819][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.860][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-21 22:09:55.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:09:55.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.865][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.868][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:09:55.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:09:55.870][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.871][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 22:09:55.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:09:55.874][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.875][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:09:55.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:09:55.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:09:55.876][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:09:55.876][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:09:55.877][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:09:55.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:09:55.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.884][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:09:55.886][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:09:55.887][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.888][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.889][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 22:09:55.891][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.892][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:09:55.894][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:09:55.896][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.897][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.898][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.900][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:09:55.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:09:55.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.903][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 22:09:55.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:09:55.905][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.907][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:09:55.907][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:09:55.907][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:09:55.907][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:09:55.907][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:09:55.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:09:55.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:09:55.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.915][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:09:55.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:09:55.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.919][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.920][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 22:09:55.922][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.923][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-21 22:09:55.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:09:55.926][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.927][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.928][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.930][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:09:55.931][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:09:55.932][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.933][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 22:09:55.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:09:55.935][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.937][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.938][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:09:55.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:09:55.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.945][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:09:55.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:09:55.948][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.949][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.950][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 22:09:55.952][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.953][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:09:55.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:09:55.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.961][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:09:55.962][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:09:55.963][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.964][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 22:09:55.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:09:55.966][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.967][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:55.968][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.969][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:09:55.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.972][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:09:55.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:55.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:55.974][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:09:55.975][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:09:55.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:09:55.978][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:55.979][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:55.984][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:09:55.985][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.986][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[2024-07-21 22:09:55.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:55.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:55.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.991][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[2024-07-21 22:09:55.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:55.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:55.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:55.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:55.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:55.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:55.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:55.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.004][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[2024-07-21 22:09:56.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.008][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[2024-07-21 22:09:56.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.038][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[2024-07-21 22:09:56.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.043][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[2024-07-21 22:09:56.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.062][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 22:09:56.067][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 22:09:56.068][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 22:09:56.070][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 22:09:56.071][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 22:09:56.072][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 22:09:56.074][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 22:09:56.075][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 22:09:56.076][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 22:09:56.077][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 22:09:56.079][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 22:09:56.080][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 22:09:56.081][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 22:09:56.083][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 22:09:56.084][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 22:09:56.085][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:09:56.087][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 22:09:56.088][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 22:09:56.089][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 22:09:56.091][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 22:09:56.092][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 22:09:56.093][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 22:09:56.094][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 22:09:56.096][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 22:09:56.097][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 22:09:56.098][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 22:09:56.100][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 22:09:56.101][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 22:09:56.102][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 22:09:56.104][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 22:09:56.105][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 22:09:56.106][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 22:09:56.108][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 22:09:56.109][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 22:09:56.110][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 22:09:56.112][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 22:09:56.113][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 22:09:56.119][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 22:09:56.121][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 22:09:56.122][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 22:09:56.124][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 22:09:56.125][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 22:09:56.126][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 22:09:56.128][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 22:09:56.129][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 22:09:56.130][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 22:09:56.132][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 22:09:56.133][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 22:09:56.134][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 22:09:56.136][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 22:09:56.137][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 22:09:56.138][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 22:09:56.139][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 22:09:56.141][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 22:09:56.142][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 22:09:56.143][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 22:09:56.145][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 22:09:56.146][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 22:09:56.147][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 22:09:56.149][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 22:09:56.150][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 22:09:56.151][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 22:09:56.153][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 22:09:56.154][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 22:09:56.155][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 22:09:56.157][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 22:09:56.158][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 22:09:56.159][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 22:09:56.161][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 22:09:56.162][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 22:09:56.163][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 22:09:56.165][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 22:09:56.166][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 22:09:56.167][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 22:09:56.169][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 22:09:56.170][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 22:09:56.171][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 22:09:56.173][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 22:09:56.174][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 22:09:56.175][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 22:09:56.176][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 22:09:56.178][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 22:09:56.179][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 22:09:56.185][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 22:09:56.187][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:09:56.190][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:09:56.191][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.193][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:09:56.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:09:56.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.299][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[2024-07-21 22:09:56.301][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 22:09:56.310][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:09:56.312][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:56.314][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 22:09:56.315][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:56.316][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:09:56.317][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:56.318][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:09:56.319][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:56.320][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:09:56.321][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:09:56.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:09:56.322][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:56.323][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 22:09:56.324][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 22:09:56.325][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 22:09:56.326][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 22:09:56.327][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:09:56.327][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:09:56.328][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:09:56.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:56.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:56.331][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:09:56.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:09:56.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:09:56.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:09:56.335][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:09:56.335][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 22:09:56.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:09:56.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:09:56.338][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 22:09:56.339][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:09:56.344][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 22:09:56.346][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:09:56.378][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:09:56.379][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 22:09:56.384][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:09:56.388][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 22:09:56.392][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:09:56.394][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:09:56.395][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 22:09:56.396][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 22:09:56.406][biodb::testThat]
biodb.INFO [2024-07-21 22:09:56.407][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-21 22:09:56.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:56.409][biodb::testThat]
biodb.TRACE[2024-07-21 22:09:56.413][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[2024-07-21 22:09:56.415][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 22:09:56.418][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:09:56.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:09:56.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:56.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:56.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:56.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:56.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:56.444][FUN] Functions in observer BiodbConfig: [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[2024-07-21 22:09:56.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:09:56.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:09:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.479][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:09:56.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:09:56.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.483][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:09:56.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:09:56.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.526][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:09:56.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.530][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:09:56.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:09:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:09:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.564][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:09:56.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.642][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.646][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:09:56.679][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-21 22:09:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:56.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:56.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:56.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.759][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:56.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.789][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.790][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.792][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.816][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:56.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.875][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.876][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.878][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.902][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.903][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.905][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.928][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.929][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.931][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.947][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.951][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.955][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.956][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.957][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:56.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.969][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:56.970][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:56.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.972][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.976][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.977][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:56.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.979][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.983][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:56.984][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:56.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.986][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.990][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.992][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:56.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:56.994][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:56.998][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:56.999][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.001][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.005][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.006][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.008][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 22:09:57.015][biodb::testThat]
biodb.INFO [2024-07-21 22:09:57.016][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-21 22:09:57.017][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:57.018][biodb::testThat]
biodb.DEBUG[2024-07-21 22:09:57.031][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-07-21 22:09:57.038][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-21 22:09:57.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-07-21 22:09:57.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:09:57.046][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-07-21 22:09:57.047][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 22:09:57.070][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 22:09:57.071][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:09:57.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:09:57.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:09:57.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:09:57.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:09:57.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:09:57.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:09:57.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:09:57.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:09:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:09:57.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:09:57.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:09:57.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.107][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:09:57.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:09:57.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.110][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:09:57.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:09:57.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:09:57.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:57.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:57.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:57.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:09:57.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:09:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:09:57.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:57.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:57.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:57.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:09:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:09:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.154][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:09:57.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:09:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.169][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:09:57.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.192][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.196][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:09:57.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:09:57.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:09:57.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:09:57.230][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-21 22:09:57.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-21 22:09:57.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-21 22:09:57.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-21 22:09:57.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-21 22:09:57.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-21 22:09:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-21 22:09:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:09:57.249][biodb::testThat]
biodb.INFO [2024-07-21 22:09:57.250][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-21 22:09:57.251][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:57.252][biodb::testThat]
biodb.TRACE[2024-07-21 22:09:57.255][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.258][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:09:57.259][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-07-21 22:09:57.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:57.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:57.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:57.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:57.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:09:57.302][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-21 22:09:57.308][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[2024-07-21 22:09:57.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:09:57.330][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:09:57.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-07-21 22:09:58.056][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-07-21 22:09:58.689][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:09:58.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-07-21 22:09:58.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-07-21 22:09:58.712][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-07-21 22:09:58.726][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:58.728][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:09:58.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.730][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 22:09:58.735][biodb::testThat]
biodb.INFO [2024-07-21 22:09:58.736][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-21 22:09:58.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:58.738][biodb::testThat]
biodb.TRACE[2024-07-21 22:09:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:58.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:58.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:58.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:09:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:09:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:09:58.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-21 22:09:58.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:09:58.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-21 22:09:58.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:09:58.936][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-07-21 22:09:58.961][biodb::testThat]
biodb.INFO [2024-07-21 22:09:58.963][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-21 22:09:58.964][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:58.965][biodb::testThat]
biodb.TRACE[2024-07-21 22:09:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:58.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:58.997][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:58.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:58.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:59.001][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:59.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:59.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:59.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:09:59.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:09:59.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:59.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 22:09:59.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:09:59.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:59.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 22:09:59.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:09:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:09:59.075][biodb::testThat]
biodb.INFO [2024-07-21 22:09:59.076][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-21 22:09:59.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:59.078][biodb::testThat]
biodb.INFO [2024-07-21 22:09:59.086][biodb::testThat]
biodb.INFO [2024-07-21 22:09:59.087][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-21 22:09:59.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:59.089][biodb::testThat]
biodb.INFO [2024-07-21 22:09:59.097][biodb::testThat]
biodb.INFO [2024-07-21 22:09:59.098][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-21 22:09:59.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:09:59.100][biodb::testThat]
biodb.DEBUG[2024-07-21 22:09:59.104][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-07-21 22:09:59.878][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-07-21 22:10:00.294][biodb::testThat]
biodb.INFO [2024-07-21 22:10:00.296][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-21 22:10:00.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:00.298][biodb::testThat]
biodb.TRACE[2024-07-21 22:10:00.303][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:00.304][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:00.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.306][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.307][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.310][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 22:10:00.312][biodb::testThat]
biodb.INFO [2024-07-21 22:10:00.313][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-21 22:10:00.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:00.315][biodb::testThat]
biodb.TRACE[2024-07-21 22:10:00.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:00.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:00.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:00.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:00.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:00.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:00.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-21 22:10:00.438][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:10:00.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-21 22:10:00.441][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:10:00.442][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-07-21 22:10:00.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-21 22:10:00.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:10:00.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-21 22:10:00.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:10:00.514][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-07-21 22:10:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-21 22:10:00.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-21 22:10:00.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:00.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:00.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:00.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:00.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:00.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:00.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-07-21 22:10:00.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:00.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:00.616][private$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[2024-07-21 22:10:05.057][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[2024-07-21 22:10:15.033][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:15.036][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-07-21 22:10:15.048][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-07-21 22:10:16.148][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[2024-07-21 22:10:16.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:16.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:16.156][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-07-21 22:10:16.785][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-07-21 22:10:17.443][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:17.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-07-21 22:10:17.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-07-21 22:10:17.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-07-21 22:10:17.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:17.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:17.484][private$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[2024-07-21 22:10:18.122][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[2024-07-21 22:10:18.752][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:18.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-07-21 22:10:18.765][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-07-21 22:10:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:10:18.803][biodb::testThat]
biodb.INFO [2024-07-21 22:10:18.804][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-21 22:10:18.805][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:18.806][biodb::testThat]
biodb.TRACE[2024-07-21 22:10:18.809][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-21 22:10:18.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-21 22:10:18.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:18.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:18.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:18.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:18.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:18.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:18.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:18.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:18.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:18.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:18.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:18.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:10:18.850][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[2024-07-21 22:10:18.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:18.855][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:18.857][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-07-21 22:10:23.455][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-07-21 22:10:33.422][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:33.431][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-07-21 22:10:33.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-07-21 22:10:35.087][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-07-21 22:10:35.166][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-21 22:10:35.170][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-07-21 22:10:35.172][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-21 22:10:35.174][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-21 22:10:35.176][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 22:10:35.178][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:10:35.180][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-21 22:10:35.182][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-21 22:10:35.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:35.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:35.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:35.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:35.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:35.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:35.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:10:35.223][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-07-21 22:10:35.228][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:35.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:35.232][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-21 22:10:35.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-07-21 22:10:36.588][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:36.594][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-07-21 22:10:36.602][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-07-21 22:10:36.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:36.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:36.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:36.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:36.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:36.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:36.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:10:36.632][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-07-21 22:10:36.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:36.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:36.643][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-07-21 22:10:37.315][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-07-21 22:10:37.963][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:37.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-07-21 22:10:37.972][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-07-21 22:10:37.976][private$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[2024-07-21 22:10:37.979][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-21 22:10:37.980][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-21 22:10:37.982][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:10:37.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:37.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:37.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:37.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:38.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.049][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:10:38.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:10:38.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.057][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:10:38.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:10:38.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.064][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.093][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:10:38.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.101][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:10:38.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.109][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:10:38.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:10:38.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:10:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:10:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.139][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:10:38.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.147][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:10:38.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.176][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:10:38.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.194][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:38.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:38.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:38.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:38.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:38.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:10:38.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:10:38.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:10:38.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:10:38.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:10:38.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.312][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:10:38.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:10:38.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.335][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:10:38.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.341][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:10:38.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:10:38.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:10:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:10:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:10:38.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.380][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:10:38.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.387][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:10:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:10:38.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.451][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:10:38.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:10:38.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.476][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:10:38.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:10:38.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:38.524][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-07-21 22:10:38.541][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-21 22:10:38.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:38.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:38.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:38.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:38.568][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.573][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.579][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.581][private$selectFields]
biodb.TRACE[2024-07-21 22:10:38.582][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:38.583][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:38.584][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.585][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.586][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.588][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.589][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.590][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.592][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.593][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.594][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.595][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.597][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.600][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.602][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:38.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.609][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.614][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-21 22:10:38.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:38.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:38.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:38.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.660][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.661][private$selectFields]
biodb.TRACE[2024-07-21 22:10:38.662][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:38.663][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:38.664][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.665][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.666][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.668][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.669][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.670][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.673][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.675][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.677][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.678][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.680][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.683][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.685][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:38.687][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.700][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.707][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-21 22:10:38.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:38.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:38.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:38.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.721][FUN] Functions in observer BiodbConfig: [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[2024-07-21 22:10:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.728][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.735][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.736][private$selectFields]
biodb.TRACE[2024-07-21 22:10:38.738][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:38.739][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:38.741][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.743][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.745][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.748][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.749][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.751][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.754][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.756][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.758][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:38.759][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.761][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.764][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.765][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:38.767][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.772][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.777][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:38.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.784][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-21 22:10:38.786][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-21 22:10:38.787][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-21 22:10:38.803][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:10:38.817][biodb::testThat]
biodb.INFO [2024-07-21 22:10:38.819][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-21 22:10:38.820][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:38.822][biodb::testThat]
biodb.TRACE[2024-07-21 22:10:38.827][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-21 22:10:38.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-21 22:10:38.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:38.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:38.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:38.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:38.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:38.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:38.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:38.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:38.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:38.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:38.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:38.987][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[2024-07-21 22:10:38.991][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[2024-07-21 22:10:38.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:38.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:38.999][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-07-21 22:10:43.417][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-07-21 22:10:53.018][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:10:53.020][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-07-21 22:10:53.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-07-21 22:10:54.170][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-21 22:10:54.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:54.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:54.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:54.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:54.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:54.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:54.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:54.216][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.220][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.242][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.243][private$selectFields]
biodb.TRACE[2024-07-21 22:10:54.244][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:54.245][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:54.246][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.247][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.248][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.250][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.251][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.252][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.254][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.255][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.265][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.266][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.267][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.269][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.270][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.275][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.283][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-21 22:10:54.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:54.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:54.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:54.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:54.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:54.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:54.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:54.294][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.301][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.302][private$selectFields]
biodb.TRACE[2024-07-21 22:10:54.304][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:54.305][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:54.306][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.308][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.309][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.311][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.312][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.313][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.315][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.316][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.317][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.319][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.321][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.322][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.331][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.335][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-21 22:10:54.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:54.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:54.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:54.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:54.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:54.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:54.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:54.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.350][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.353][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.354][private$selectFields]
biodb.TRACE[2024-07-21 22:10:54.355][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:54.356][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:54.357][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.358][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.359][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.361][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.362][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.363][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.365][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.366][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:54.367][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.368][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.370][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.371][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.376][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.384][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-21 22:10:54.385][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-21 22:10:54.386][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-21 22:10:54.393][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:54.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:54.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:10:54.401][biodb::testThat]
biodb.INFO [2024-07-21 22:10:54.402][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-21 22:10:54.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:54.403][biodb::testThat]
biodb.TRACE[2024-07-21 22:10:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-21 22:10:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-21 22:10:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-21 22:10:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:54.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:10:54.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:54.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:10:54.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:54.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:54.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:54.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:54.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:54.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:54.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:10:54.448][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-07-21 22:10:54.451][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:10:54.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-07-21 22:10:54.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:10:54.499][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-07-21 22:10:55.524][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-21 22:10:55.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:55.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:55.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:55.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:55.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:55.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:55.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:55.536][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.543][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.544][private$selectFields]
biodb.TRACE[2024-07-21 22:10:55.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:55.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:55.547][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.547][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.548][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.550][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.551][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.552][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.554][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.555][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.556][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.557][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.558][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.559][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.560][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.565][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.573][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-21 22:10:55.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:55.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:55.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:55.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:55.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:55.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:55.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.587][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.590][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.591][private$selectFields]
biodb.TRACE[2024-07-21 22:10:55.592][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:55.593][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:55.594][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.595][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.596][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.598][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.599][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.600][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.601][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.602][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.603][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.604][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.605][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.607][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.608][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.620][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-21 22:10:55.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:55.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:55.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:55.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:55.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:55.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:55.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:10:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.638][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.639][private$selectFields]
biodb.TRACE[2024-07-21 22:10:55.640][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-21 22:10:55.641][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:10:55.642][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.643][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.644][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.646][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.646][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.647][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.649][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.650][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.651][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:10:55.652][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.653][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.655][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.656][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-21 22:10:55.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:10:55.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:10:55.668][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-21 22:10:55.669][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-21 22:10:55.670][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-21 22:10:55.687][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:55.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-21 22:10:55.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:10:55.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-21 22:10:55.694][biodb::testThat]
biodb.INFO [2024-07-21 22:10:55.694][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-21 22:10:55.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:10:55.696][biodb::testThat]
biodb.DEBUG[2024-07-21 22:10:55.698][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-21 22:10:55.699][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-21 22:10:55.700][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-21 22:10:55.701][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-21 22:10:55.702][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-21 22:10:55.703][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 22:10:55.704][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:10:55.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-21 22:10:55.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-21 22:10:55.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:10:55.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:10:55.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:10:55.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:10:55.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:10:55.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:10:55.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:10:55.729][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-07-21 22:10:55.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:55.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:55.734][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:10:56.354][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:10:56.356][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:10:56.357][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:10:56.359][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:10:57.052][private$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[2024-07-21 22:10:57.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:57.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:57.055][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:10:57.660][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:10:57.662][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:10:57.664][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:10:57.666][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:10:58.459][private$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[2024-07-21 22:10:58.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:58.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:58.470][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:10:59.114][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:10:59.117][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:10:59.120][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:10:59.123][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:10:59.821][private$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[2024-07-21 22:10:59.823][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:10:59.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:10:59.826][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:00.416][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:00.417][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:00.419][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:00.420][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:01.114][private$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[2024-07-21 22:11:01.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:01.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:01.123][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:01.765][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:01.767][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:01.769][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:01.770][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:02.522][private$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[2024-07-21 22:11:02.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:02.525][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:02.526][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:03.136][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:03.138][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:03.140][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:03.142][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:03.834][private$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[2024-07-21 22:11:03.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:03.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:03.839][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:04.435][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:04.436][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:04.438][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:04.439][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:05.266][private$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[2024-07-21 22:11:05.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:05.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:05.275][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:05.890][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:05.893][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:05.896][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:05.898][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:06.646][private$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[2024-07-21 22:11:06.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:06.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:06.650][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:07.225][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:07.227][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:07.229][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:07.231][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:07.923][private$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[2024-07-21 22:11:07.926][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:07.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:07.931][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 22:11:08.539][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:08.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:08.545][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:08.548][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 22:11:09.300][private$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[2024-07-21 22:11:09.304][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-07-21 22:11:09.306][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-21 22:11:09.308][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 22:11:09.310][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:11:09.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:11:09.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:09.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:09.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:09.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:09.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:09.325][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.TRACE[2024-07-21 22:11:09.328][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:09.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:09.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.332][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:09.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:09.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:09.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:09.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:09.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:09.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:11:09.457][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-07-21 22:11:09.458][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-21 22:11:09.467][biodb::testThat]
biodb.INFO [2024-07-21 22:11:09.469][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-21 22:11:09.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:09.471][biodb::testThat]
biodb.DEBUG[2024-07-21 22:11:09.480][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-07-21 22:11:09.481][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-07-21 22:11:09.482][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-21 22:11:09.484][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-07-21 22:11:09.486][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-21 22:11:09.487][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-21 22:11:09.488][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 22:11:09.489][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:11:09.490][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-21 22:11:09.491][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-21 22:11:09.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:11:09.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:09.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:09.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:09.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:09.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:09.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:09.508][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-07-21 22:11:09.511][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:09.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:09.514][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:10.110][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:10.111][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:10.112][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[2024-07-21 22:11:10.114][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:10.804][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:10.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:10.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:10.808][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:11.373][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:11.374][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:11.376][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[2024-07-21 22:11:11.378][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:12.071][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:12.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:12.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:12.076][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:12.644][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:12.645][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:12.647][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[2024-07-21 22:11:12.648][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:13.340][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:13.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:13.342][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:13.344][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:13.922][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:13.923][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:13.925][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[2024-07-21 22:11:13.926][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:14.618][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:14.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:14.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:14.623][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:15.203][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:15.204][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:15.205][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[2024-07-21 22:11:15.206][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:15.896][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:15.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:15.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:15.900][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:16.461][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:16.463][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:16.465][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[2024-07-21 22:11:16.467][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:17.213][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:17.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:17.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:17.217][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:17.792][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:17.794][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:17.796][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[2024-07-21 22:11:17.797][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:18.496][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:18.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:18.500][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:18.503][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:19.064][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:19.065][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:19.067][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[2024-07-21 22:11:19.068][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:19.858][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:19.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:19.863][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:19.867][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:20.479][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:20.481][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:20.482][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[2024-07-21 22:11:20.483][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:21.176][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:21.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:21.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:21.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 22:11:21.745][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:21.747][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:21.750][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[2024-07-21 22:11:21.753][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 22:11:22.445][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 22:11:22.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:11:22.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:22.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:22.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:22.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:22.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:22.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:22.459][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-07-21 22:11:22.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:22.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:22.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:23.019][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:23.021][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:23.023][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:23.024][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:23.716][private$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[2024-07-21 22:11:23.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:23.718][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:23.720][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:24.285][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:24.287][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:24.288][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:24.290][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:24.982][private$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[2024-07-21 22:11:24.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:24.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:24.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:25.543][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:25.545][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:25.546][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:25.547][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:26.293][private$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[2024-07-21 22:11:26.295][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:26.296][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:26.298][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:26.867][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:26.872][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:26.874][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:26.875][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:27.570][private$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[2024-07-21 22:11:27.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:27.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:27.576][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:28.139][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:28.140][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:28.142][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:28.143][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:28.837][private$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[2024-07-21 22:11:28.839][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:28.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:28.844][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:29.426][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:29.428][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:29.429][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:29.430][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:30.123][private$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[2024-07-21 22:11:30.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:30.125][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:30.127][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:30.691][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:30.693][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:30.695][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:30.697][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:31.389][private$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[2024-07-21 22:11:31.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:31.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:31.393][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:31.954][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:31.955][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:31.957][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:31.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:32.649][private$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[2024-07-21 22:11:32.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:32.652][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:32.653][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:33.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:33.233][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:33.235][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:33.236][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:33.928][private$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[2024-07-21 22:11:33.930][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:33.931][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:33.933][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-21 22:11:34.500][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-21 22:11:34.502][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 22:11:34.505][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 22:11:34.507][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-21 22:11:35.204][private$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[2024-07-21 22:11:35.214][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-07-21 22:11:35.218][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-21 22:11:35.222][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-21 22:11:35.226][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:11:35.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:11:35.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:35.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:35.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:35.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:35.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:35.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:11:35.259][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.266][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:11:35.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:11:35.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:35.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:35.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:35.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:35.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:35.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:11:35.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:11:35.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:35.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:11:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:11:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:11:35.348][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-07-21 22:11:35.349][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-21 22:11:35.350][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-07-21 22:11:35.581][biodb::testThat]
biodb.INFO [2024-07-21 22:11:35.583][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-21 22:11:35.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:35.585][biodb::testThat]
biodb.INFO [2024-07-21 22:11:35.627][biodb::testThat]
biodb.INFO [2024-07-21 22:11:35.628][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-21 22:11:35.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:35.630][biodb::testThat]
biodb.INFO [2024-07-21 22:11:35.638][biodb::testThat]
biodb.INFO [2024-07-21 22:11:35.639][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-21 22:11:35.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:35.641][biodb::testThat]
biodb.DEBUG[2024-07-21 22:11:35.645][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[2024-07-21 22:11:35.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:35.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:35.651][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-07-21 22:11:39.736][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-07-21 22:11:49.714][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:11:49.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-07-21 22:11:49.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-07-21 22:11:50.654][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:11:50.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:11:50.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:50.659][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:11:50.660][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:11:50.661][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:11:50.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:11:50.663][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 22:11:50.666][biodb::testThat]
biodb.INFO [2024-07-21 22:11:50.667][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-21 22:11:50.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:50.669][biodb::testThat]
biodb.ERROR[2024-07-21 22:11:50.687][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-21 22:11:50.710][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-21 22:11:50.726][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 22:11:50.727][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 22:11:50.729][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 22:11:50.730][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 22:11:50.731][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:50.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:50.733][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:50.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:50.734][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-21 22:11:50.747][biodb::testContext]
biodb.INFO [2024-07-21 22:11:50.748][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:11:50.750][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-07-21 22:11:50.751][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:11:50.752][biodb::testContext]
biodb.INFO [2024-07-21 22:11:50.754][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:11:50.756][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 22:11:50.761][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:11:50.762][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 22:11:50.763][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.767][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 22:11:50.768][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.772][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 22:11:50.773][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.777][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 22:11:50.778][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 22:11:50.779][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 22:11:50.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.783][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 22:11:50.784][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 22:11:50.785][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.789][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 22:11:50.790][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 22:11:50.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.794][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 22:11:50.795][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 22:11:50.796][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 22:11:50.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.799][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[2024-07-21 22:11:50.800][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 22:11:50.801][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.805][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 22:11:50.806][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 22:11:50.807][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 22:11:50.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.811][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:11:50.812][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 22:11:50.813][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 22:11:50.814][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 22:11:50.815][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 22:11:50.816][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 22:11:50.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.820][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 22:11:50.821][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 22:11:50.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.825][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 22:11:50.826][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 22:11:50.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.830][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 22:11:50.831][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 22:11:50.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.835][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 22:11:50.836][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 22:11:50.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.840][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 22:11:50.842][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 22:11:50.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.846][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:11:50.847][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 22:11:50.850][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 22:11:50.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.854][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 22:11:50.855][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 22:11:50.856][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 22:11:50.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.860][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 22:11:50.863][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.864][self$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[2024-07-21 22:11:50.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:11:50.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.871][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:11:50.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:11:50.873][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.874][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 22:11:50.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:11:50.877][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:11:50.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:11:50.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:11:50.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:11:50.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:11:50.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:11:50.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:11:50.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.887][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:11:50.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:11:50.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.891][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.892][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 22:11:50.894][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.896][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:11:50.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.898][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:11:50.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.903][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:11:50.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:11:50.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.906][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 22:11:50.907][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:11:50.908][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.909][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.910][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:11:50.910][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:11:50.910][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:11:50.910][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:11:50.910][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:11:50.911][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:11:50.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:11:50.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.918][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:11:50.920][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:11:50.921][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.922][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.924][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 22:11:50.926][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.927][self$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[2024-07-21 22:11:50.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:11:50.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.934][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:11:50.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:11:50.936][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.937][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 22:11:50.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:11:50.939][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.940][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.942][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.943][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:11:50.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:11:50.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.949][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.950][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.951][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:11:50.952][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:11:50.953][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.954][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.955][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 22:11:50.957][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.958][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:11:50.960][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:11:50.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.964][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.966][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:11:50.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:11:50.968][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.969][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 22:11:50.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:11:50.972][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:50.974][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:11:50.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:11:50.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:50.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:50.981][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:11:50.982][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:11:50.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:11:50.985][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:50.986][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:50.988][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:11:50.989][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:50.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:50.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:50.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:50.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:50.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:50.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.144][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 22:11:51.145][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 22:11:51.147][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 22:11:51.148][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 22:11:51.149][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 22:11:51.151][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 22:11:51.152][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 22:11:51.153][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 22:11:51.155][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 22:11:51.156][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 22:11:51.157][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 22:11:51.158][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 22:11:51.160][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 22:11:51.161][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 22:11:51.162][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 22:11:51.164][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:11:51.165][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 22:11:51.166][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 22:11:51.168][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 22:11:51.169][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 22:11:51.171][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 22:11:51.172][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 22:11:51.173][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 22:11:51.175][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 22:11:51.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 22:11:51.177][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 22:11:51.179][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 22:11:51.180][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 22:11:51.181][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 22:11:51.183][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 22:11:51.184][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 22:11:51.185][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 22:11:51.186][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 22:11:51.188][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 22:11:51.189][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 22:11:51.190][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 22:11:51.192][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 22:11:51.193][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 22:11:51.194][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 22:11:51.196][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 22:11:51.197][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 22:11:51.198][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 22:11:51.199][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 22:11:51.201][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 22:11:51.202][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 22:11:51.203][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 22:11:51.205][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 22:11:51.206][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 22:11:51.207][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 22:11:51.209][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 22:11:51.210][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 22:11:51.211][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 22:11:51.213][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 22:11:51.214][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 22:11:51.215][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 22:11:51.217][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 22:11:51.218][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 22:11:51.219][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 22:11:51.221][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 22:11:51.222][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 22:11:51.224][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 22:11:51.225][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 22:11:51.226][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 22:11:51.228][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 22:11:51.229][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 22:11:51.230][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 22:11:51.232][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 22:11:51.233][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 22:11:51.235][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 22:11:51.236][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 22:11:51.237][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 22:11:51.239][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 22:11:51.240][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 22:11:51.241][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 22:11:51.243][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 22:11:51.244][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 22:11:51.245][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 22:11:51.247][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 22:11:51.248][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 22:11:51.249][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 22:11:51.251][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 22:11:51.252][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 22:11:51.253][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 22:11:51.255][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 22:11:51.257][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:11:51.258][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:11:51.258][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.260][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.317][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[2024-07-21 22:11:51.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.323][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[2024-07-21 22:11:51.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:11:51.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:11:51.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:11:51.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:11:51.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:11:51.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:11:51.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:11:51.368][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 22:11:51.369][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:11:51.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:51.372][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 22:11:51.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:51.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:11:51.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:51.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:11:51.377][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:51.378][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:11:51.379][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:11:51.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:11:51.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:51.382][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 22:11:51.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 22:11:51.384][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 22:11:51.386][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 22:11:51.387][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:11:51.387][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:11:51.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:11:51.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:51.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:51.403][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:11:51.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:11:51.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:11:51.406][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:11:51.407][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:11:51.407][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 22:11:51.408][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:11:51.408][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:11:51.409][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 22:11:51.410][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:11:51.411][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 22:11:51.413][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:11:51.416][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:11:51.417][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 22:11:51.418][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:11:51.420][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 22:11:51.421][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:11:51.422][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:11:51.423][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 22:11:51.424][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 22:11:51.426][biodb::testThat]
biodb.INFO [2024-07-21 22:11:51.427][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-07-21 22:11:51.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:51.428][biodb::testThat]
biodb.DEBUG[2024-07-21 22:11:51.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-07-21 22:11:51.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:51.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:51.439][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-07-21 22:11:52.064][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[2024-07-21 22:11:52.952][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:11:52.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-07-21 22:11:52.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-07-21 22:11:52.970][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[2024-07-21 22:11:52.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:52.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:52.977][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-07-21 22:11:53.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-07-21 22:11:54.236][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:11:54.240][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-07-21 22:11:54.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-07-21 22:11:54.255][biodb::testThat]
biodb.INFO [2024-07-21 22:11:54.257][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-07-21 22:11:54.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:54.259][biodb::testThat]
biodb.INFO [2024-07-21 22:11:54.285][biodb::testThat]
biodb.INFO [2024-07-21 22:11:54.286][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-07-21 22:11:54.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:11:54.288][biodb::testThat]
biodb.DEBUG[2024-07-21 22:11:54.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-21 22:11:54.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:54.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:54.297][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-07-21 22:11:54.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-07-21 22:11:55.479][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:11:55.481][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-07-21 22:11:55.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-07-21 22:11:55.492][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[2024-07-21 22:11:55.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:11:55.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-07-21 22:11:55.498][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:11:55.500][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-07-21 22:11:55.506][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[2024-07-21 22:11:55.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:55.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:11:55.512][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-07-21 22:11:55.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-07-21 22:11:56.429][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:11:56.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-07-21 22:11:56.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-07-21 22:11:56.453][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-07-21 22:11:56.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:11:56.461][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 22:11:56.464][rule$waitAsNeeded] Wait 0.0483637 second(s).
biodb.TRACE[2024-07-21 22:11:56.515][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-07-21 22:11:57.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-07-21 22:12:00.756][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:12:00.761][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-07-21 22:12:00.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-07-21 22:12:00.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-07-21 22:12:00.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 22:12:00.919][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 22:12:00.922][private$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[2024-07-21 22:12:02.264][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[2024-07-21 22:12:05.066][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-21 22:12:05.070][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-07-21 22:12:05.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-07-21 22:12:05.210][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 22:12:05.212][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 22:12:05.214][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 22:12:05.215][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 22:12:05.216][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.219][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.221][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.222][FUN] Functions in observer BiodbConfig: [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 [2024-07-21 22:12:05.228][biodb::testContext]
biodb.INFO [2024-07-21 22:12:05.229][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:12:05.230][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-07-21 22:12:05.231][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 22:12:05.232][biodb::testContext]
biodb.INFO [2024-07-21 22:12:05.235][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:12:05.237][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 22:12:05.243][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:12:05.244][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 22:12:05.245][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.250][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 22:12:05.251][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.256][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 22:12:05.257][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.261][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 22:12:05.263][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 22:12:05.264][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 22:12:05.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.269][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 22:12:05.270][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 22:12:05.272][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.276][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 22:12:05.277][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 22:12:05.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.282][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 22:12:05.283][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 22:12:05.284][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 22:12:05.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.289][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 22:12:05.290][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.294][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 22:12:05.295][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 22:12:05.297][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 22:12:05.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.301][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:12:05.302][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 22:12:05.304][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 22:12:05.305][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 22:12:05.306][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 22:12:05.307][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 22:12:05.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.311][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 22:12:05.313][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 22:12:05.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.317][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 22:12:05.318][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 22:12:05.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.323][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 22:12:05.324][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 22:12:05.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.328][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 22:12:05.330][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 22:12:05.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.334][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 22:12:05.335][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 22:12:05.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.339][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 22:12:05.341][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 22:12:05.345][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 22:12:05.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.349][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 22:12:05.415][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 22:12:05.416][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 22:12:05.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.422][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 22:12:05.425][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.427][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-21 22:12:05.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:12:05.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.433][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.435][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.436][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:12:05.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:12:05.439][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.440][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 22:12:05.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:12:05.442][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.443][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.445][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:12:05.445][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:12:05.445][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:12:05.445][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:12:05.445][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:12:05.446][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:12:05.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:12:05.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.454][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.455][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:12:05.456][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:12:05.457][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.458][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.460][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 22:12:05.462][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.463][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:12:05.464][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:12:05.467][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.468][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.469][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.470][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.471][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:12:05.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:12:05.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.475][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 22:12:05.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:12:05.477][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.478][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.480][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:12:05.480][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:12:05.480][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 22:12:05.480][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 22:12:05.480][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 22:12:05.481][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:12:05.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:12:05.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.487][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.488][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.489][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:12:05.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:12:05.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.493][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.495][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 22:12:05.497][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.498][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-21 22:12:05.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:12:05.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.506][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.507][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:12:05.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:12:05.510][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.511][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 22:12:05.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:12:05.513][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.515][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.516][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:12:05.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:12:05.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.526][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.527][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:12:05.528][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:12:05.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.530][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.532][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 22:12:05.535][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.536][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 22:12:05.537][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:12:05.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.543][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.544][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.545][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 22:12:05.546][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:12:05.548][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.549][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 22:12:05.550][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:12:05.552][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.553][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.554][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.555][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:12:05.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:12:05.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.563][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.564][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.565][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:12:05.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:12:05.568][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.569][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.571][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:12:05.572][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.585][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[2024-07-21 22:12:05.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.608][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[2024-07-21 22:12:05.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.624][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[2024-07-21 22:12:05.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.649][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[2024-07-21 22:12:05.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.653][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[2024-07-21 22:12:05.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.657][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[2024-07-21 22:12:05.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.663][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 22:12:05.664][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 22:12:05.666][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 22:12:05.667][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 22:12:05.669][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 22:12:05.670][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 22:12:05.671][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 22:12:05.673][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 22:12:05.674][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 22:12:05.675][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 22:12:05.677][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 22:12:05.678][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 22:12:05.679][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 22:12:05.681][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 22:12:05.682][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 22:12:05.684][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:12:05.685][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 22:12:05.686][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 22:12:05.688][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 22:12:05.689][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 22:12:05.690][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 22:12:05.692][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 22:12:05.693][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 22:12:05.694][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 22:12:05.696][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 22:12:05.697][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 22:12:05.698][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 22:12:05.700][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 22:12:05.701][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 22:12:05.702][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 22:12:05.704][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 22:12:05.705][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 22:12:05.706][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 22:12:05.708][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 22:12:05.709][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 22:12:05.710][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 22:12:05.712][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 22:12:05.713][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 22:12:05.715][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 22:12:05.716][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 22:12:05.717][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 22:12:05.719][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 22:12:05.720][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 22:12:05.721][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 22:12:05.723][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 22:12:05.724][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 22:12:05.726][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 22:12:05.727][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 22:12:05.728][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 22:12:05.730][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 22:12:05.731][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 22:12:05.732][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 22:12:05.734][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 22:12:05.735][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 22:12:05.737][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 22:12:05.738][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 22:12:05.740][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 22:12:05.741][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 22:12:05.742][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 22:12:05.744][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 22:12:05.745][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 22:12:05.747][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 22:12:05.748][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 22:12:05.750][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 22:12:05.751][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 22:12:05.752][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 22:12:05.754][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 22:12:05.755][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 22:12:05.756][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 22:12:05.758][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 22:12:05.759][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 22:12:05.761][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 22:12:05.762][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 22:12:05.764][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 22:12:05.765][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 22:12:05.767][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 22:12:05.768][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 22:12:05.783][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 22:12:05.785][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 22:12:05.786][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 22:12:05.787][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 22:12:05.789][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 22:12:05.790][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 22:12:05.792][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 22:12:05.794][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 22:12:05.795][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 22:12:05.796][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.797][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.829][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.DEBUG[2024-07-21 22:12:05.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 22:12:05.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:05.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:05.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:05.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:05.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:05.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 22:12:05.901][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 22:12:05.903][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:12:05.905][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.906][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.907][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 22:12:05.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.910][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.912][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 22:12:05.913][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 22:12:05.914][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.915][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 22:12:05.916][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 22:12:05.917][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 22:12:05.918][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 22:12:05.919][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 22:12:05.919][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 22:12:05.920][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 22:12:05.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.922][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.923][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 22:12:05.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 22:12:05.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 22:12:05.926][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 22:12:05.927][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 22:12:05.927][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 22:12:05.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 22:12:05.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 22:12:05.930][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 22:12:05.931][self$setPropertyValue]
biodb.DEBUG[2024-07-21 22:12:05.932][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 22:12:05.933][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 22:12:05.937][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:12:05.938][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 22:12:05.939][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 22:12:05.941][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 22:12:05.942][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:12:05.943][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 22:12:05.945][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 22:12:05.946][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 22:12:05.947][biodb::testThat]
biodb.INFO [2024-07-21 22:12:05.948][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-07-21 22:12:05.949][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 22:12:05.950][biodb::testThat]
biodb.DEBUG[2024-07-21 22:12:05.954][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[2024-07-21 22:12:05.958][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 22:12:05.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-07-21 22:12:05.961][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 22:12:06.018][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-07-21 22:12:06.936][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-07-21 22:12:06.938][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-21 22:12:06.940][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-07-21 22:12:06.942][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-21 22:12:06.945][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[2024-07-21 22:12:06.946][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 22:12:06.947][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-21 22:12:06.949][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 22:12:06.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:12:06.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:06.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:06.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:06.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:06.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:06.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:12:06.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:06.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:06.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:06.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:06.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:06.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:06.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:06.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.987][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:12:06.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:12:06.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:12:06.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:12:06.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:06.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:06.997][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:06.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.016][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:12:07.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.021][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:12:07.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:12:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.047][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:12:07.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:12:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:12:07.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:12:07.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:07.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:07.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:07.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:07.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:07.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:12:07.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.148][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:12:07.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 22:12:07.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.152][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:12:07.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 22:12:07.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.157][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.175][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:12:07.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 22:12:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.204][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:12:07.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 22:12:07.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.223][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 22:12:07.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.227][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 22:12:07.314][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-07-21 22:12:07.317][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-21 22:12:07.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:12:07.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:07.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:07.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:07.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:07.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:07.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:12:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 22:12:07.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 22:12:07.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.346][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 22:12:07.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 22:12:07.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.349][private$selectFields] Fields none
biodb.TRACE[2024-07-21 22:12:07.350][private$selectFields]
biodb.TRACE[2024-07-21 22:12:07.351][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-07-21 22:12:07.352][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:12:07.353][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.354][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.355][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.357][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.360][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.361][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.362][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.365][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.366][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.368][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.369][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.370][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.372][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.373][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.375][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.376][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.379][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.380][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.381][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.383][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.384][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.385][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.387][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.390][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.391][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.392][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.394][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.395][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.396][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.398][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.399][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.400][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.401][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.402][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.405][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.406][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.409][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.410][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.411][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.413][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.413][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.414][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.415][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.416][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.418][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.420][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.422][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.423][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.424][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.426][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.426][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.427][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.429][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.433][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.434][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.437][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.437][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.438][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.440][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.441][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.442][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.444][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.445][private$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[2024-07-21 22:12:07.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.479][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.533][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.537][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.551][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-07-21 22:12:07.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 22:12:07.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:07.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:07.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:07.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:07.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:07.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 22:12:07.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 22:12:07.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 22:12:07.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 22:12:07.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 22:12:07.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 22:12:07.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.578][private$selectFields] Fields none
biodb.TRACE[2024-07-21 22:12:07.579][private$selectFields]
biodb.TRACE[2024-07-21 22:12:07.580][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-07-21 22:12:07.581][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-21 22:12:07.582][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.583][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.586][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.587][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.588][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.590][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.591][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.592][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.593][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.594][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.595][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.597][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.598][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.599][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.601][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.605][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.606][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.609][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.610][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.611][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.613][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.614][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.617][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.620][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.636][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.638][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.640][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.641][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.642][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.644][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.645][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.646][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.648][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.649][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.650][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.651][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.652][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.655][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.656][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.657][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.659][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.660][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.661][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-21 22:12:07.662][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.663][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.665][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.666][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.668][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.669][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.670][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.672][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.673][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.674][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.676][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.677][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.680][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.681][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.682][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.683][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.684][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.685][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.687][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.688][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.689][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.691][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.692][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-07-21 22:12:07.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 22:12:07.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 22:12:07.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 22:12:07.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 22:12:07.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.735][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 22:12:07.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 22:12:07.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.751][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 22:12:07.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 22:12:07.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 22:12:07.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 22:12:07.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.777][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.781][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 22:12:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 22:12:07.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 22:12:07.789][private$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[2024-07-21 22:12:07.790][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-07-21 22:12:07.791][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-07-21 22:12:07.797][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 22:12:07.798][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 22:12:07.800][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 22:12:07.800][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 22:12:07.801][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 22:12:07.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 22:12:07.803][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 22:12:07.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 22:12:07.805][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 22:12:07.806][FUN] Functions in observer 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 | 0.954 | 0.070 | 3.481 | |
| LipidmapsStructureEntry | 0.144 | 0.005 | 0.149 | |