| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-25 11:40:28 -0400 (Mon, 25 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4694 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4433 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4457 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4365 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 203/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.9.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the biodbLipidmaps package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbLipidmaps |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings biodbLipidmaps_1.9.0.tar.gz |
| StartedAt: 2024-03-25 02:49:00 -0000 (Mon, 25 Mar 2024) |
| EndedAt: 2024-03-25 02:50:39 -0000 (Mon, 25 Mar 2024) |
| EllapsedTime: 98.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings biodbLipidmaps_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 96 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘biodbLipidmaps’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-03-25 02:50:07.713][biodb::testContext]
biodb.INFO [2024-03-25 02:50:07.716][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:07.717][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-25 02:50:07.718][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:07.720][biodb::testContext]
biodb.INFO [2024-03-25 02:50:07.728][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:07.731][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:07.740][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:07.741][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-25 02:50:07.743][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.749][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-25 02:50:07.777][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.782][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-25 02:50:07.784][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.789][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-25 02:50:07.790][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-25 02:50:07.792][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-25 02:50:07.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.797][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-25 02:50:07.799][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-25 02:50:07.800][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.805][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-25 02:50:07.807][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-25 02:50:07.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.810][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[2024-03-25 02:50:07.812][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-25 02:50:07.813][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-25 02:50:07.815][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-25 02:50:07.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.820][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-25 02:50:07.822][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.827][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-25 02:50:07.828][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-25 02:50:07.830][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-25 02:50:07.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.835][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:07.837][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-25 02:50:07.838][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-25 02:50:07.840][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-25 02:50:07.841][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-25 02:50:07.843][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-25 02:50:07.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.847][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[2024-03-25 02:50:07.848][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-25 02:50:07.849][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-25 02:50:07.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.855][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-25 02:50:07.856][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-25 02:50:07.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.862][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-25 02:50:07.863][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-25 02:50:07.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.868][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-25 02:50:07.870][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-25 02:50:07.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.875][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-25 02:50:07.877][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-25 02:50:07.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.882][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:07.884][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-25 02:50:07.889][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-25 02:50:07.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.895][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-25 02:50:07.897][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-25 02:50:07.898][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-25 02:50:07.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:07.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:07.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:07.907][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-25 02:50:07.957][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:07.992][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-25 02:50:07.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:07.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:07.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:07.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:07.999][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.002][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:08.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:08.005][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.006][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-25 02:50:08.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:08.009][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.012][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:08.012][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:08.012][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:08.012][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:08.012][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:08.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:08.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:08.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.021][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.022][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:08.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:08.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.028][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.030][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-25 02:50:08.032][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.034][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:08.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:08.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.041][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.042][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.043][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:08.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:08.046][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.048][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-25 02:50:08.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:08.050][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.052][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.053][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:08.053][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:08.053][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:08.053][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:08.053][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:08.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:08.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:08.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.064][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:08.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:08.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.069][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.071][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-25 02:50:08.073][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.075][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-25 02:50:08.076][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.078][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:08.079][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.080][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.082][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.085][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:08.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:08.087][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.089][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-25 02:50:08.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:08.091][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.093][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.094][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:08.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.100][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:08.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.105][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:08.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:08.109][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.110][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.112][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-25 02:50:08.114][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.116][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:08.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.119][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:08.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.122][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.123][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.124][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.126][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:08.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:08.129][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.130][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-25 02:50:08.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:08.133][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.134][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.136][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.137][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:08.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.141][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:08.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.147][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:08.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:08.151][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.152][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.157][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:08.159][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.249][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[2024-03-25 02:50:08.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.269][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[2024-03-25 02:50:08.270][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-25 02:50:08.276][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-25 02:50:08.278][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-25 02:50:08.280][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-25 02:50:08.282][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-25 02:50:08.284][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-25 02:50:08.286][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:08.288][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:08.291][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-25 02:50:08.293][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-25 02:50:08.295][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-25 02:50:08.297][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-25 02:50:08.299][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:08.301][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:08.303][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-25 02:50:08.305][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:08.307][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-25 02:50:08.309][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-25 02:50:08.311][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-25 02:50:08.313][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-25 02:50:08.315][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-25 02:50:08.317][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-25 02:50:08.319][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-25 02:50:08.321][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-25 02:50:08.323][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-25 02:50:08.325][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-25 02:50:08.327][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-25 02:50:08.329][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-25 02:50:08.331][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-25 02:50:08.333][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-25 02:50:08.335][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-25 02:50:08.337][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-25 02:50:08.339][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-25 02:50:08.341][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-25 02:50:08.343][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-25 02:50:08.345][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-25 02:50:08.347][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-25 02:50:08.349][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-25 02:50:08.351][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-25 02:50:08.353][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-25 02:50:08.354][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-25 02:50:08.364][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-25 02:50:08.366][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-25 02:50:08.368][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-25 02:50:08.370][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-25 02:50:08.372][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-25 02:50:08.374][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-25 02:50:08.376][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-25 02:50:08.378][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-25 02:50:08.380][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-25 02:50:08.382][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-25 02:50:08.384][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-25 02:50:08.386][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-25 02:50:08.388][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-25 02:50:08.390][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-25 02:50:08.392][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-25 02:50:08.394][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-25 02:50:08.396][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-25 02:50:08.398][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-25 02:50:08.400][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-25 02:50:08.402][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-25 02:50:08.404][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-25 02:50:08.406][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-25 02:50:08.409][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-25 02:50:08.411][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-25 02:50:08.413][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-25 02:50:08.415][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-25 02:50:08.417][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-25 02:50:08.419][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-25 02:50:08.421][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-25 02:50:08.423][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-25 02:50:08.425][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-25 02:50:08.427][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-25 02:50:08.429][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-25 02:50:08.431][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-25 02:50:08.433][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-25 02:50:08.435][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-25 02:50:08.437][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-25 02:50:08.439][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-25 02:50:08.441][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-25 02:50:08.443][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-25 02:50:08.445][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-25 02:50:08.447][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-25 02:50:08.455][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-25 02:50:08.457][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:08.461][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:08.462][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.465][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.585][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[2024-03-25 02:50:08.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:08.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:08.622][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:08.635][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:08.638][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.639][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:08.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.647][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.649][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:08.651][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:08.652][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.654][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-25 02:50:08.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-25 02:50:08.657][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-25 02:50:08.658][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:08.660][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:08.660][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:08.661][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:08.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:08.667][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:08.668][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:08.669][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:08.671][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-25 02:50:08.671][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-25 02:50:08.672][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:08.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:08.675][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:08.676][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:08.684][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-25 02:50:08.686][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:08.716][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:08.718][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-25 02:50:08.723][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:08.738][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-25 02:50:08.744][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:08.745][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:08.747][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-25 02:50:08.749][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-25 02:50:08.760][biodb::testThat]
biodb.INFO [2024-03-25 02:50:08.762][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-25 02:50:08.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:08.765][biodb::testThat]
biodb.TRACE[2024-03-25 02:50:08.770][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-25 02:50:08.772][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-25 02:50:08.777][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-25 02:50:08.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:08.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:08.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:08.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:08.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:08.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:08.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:08.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:08.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:08.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:08.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:08.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:08.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.859][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:08.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:08.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.864][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:08.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:08.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.870][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:08.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:08.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:08.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:08.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.918][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:08.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:08.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.924][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:08.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:08.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.929][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:08.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:08.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.935][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:08.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:08.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:08.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:08.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:08.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:08.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:08.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:08.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.964][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:08.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.970][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-25 02:50:08.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:08.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:08.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:08.987][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:08.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:08.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:08.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:09.166][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-25 02:50:09.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-25 02:50:09.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-25 02:50:09.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-25 02:50:09.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-25 02:50:09.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-25 02:50:09.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-25 02:50:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-25 02:50:09.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-25 02:50:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.236][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.332][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.334][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.336][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.372][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.376][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.448][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.449][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.452][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.487][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.489][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.491][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.528][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.532][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.550][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.556][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.561][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.567][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.569][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.571][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.573][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.590][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.591][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.594][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.600][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.602][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:09.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.605][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.611][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:09.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:09.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.615][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.621][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.623][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:09.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.626][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.632][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.634][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.636][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.643][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.644][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:09.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.647][ef$get] fields variable is a list.
biodb.INFO [2024-03-25 02:50:09.657][biodb::testThat]
biodb.INFO [2024-03-25 02:50:09.658][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-25 02:50:09.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:09.661][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:09.680][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-25 02:50:09.689][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-25 02:50:09.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-25 02:50:09.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:09.697][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-25 02:50:09.699][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-25 02:50:09.733][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-25 02:50:09.735][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-25 02:50:09.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:09.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:09.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:09.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:09.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:09.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:09.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.768][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:09.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:09.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:09.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:09.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:09.808][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-25 02:50:09.810][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-25 02:50:09.836][biodb::testThat]
biodb.INFO [2024-03-25 02:50:09.838][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-25 02:50:09.839][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:09.840][biodb::testThat]
biodb.TRACE[2024-03-25 02:50:09.845][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:09.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:09.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:09.849][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:09.851][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.INFO [2024-03-25 02:50:10.126][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.128][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-25 02:50:10.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:10.130][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.195][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.196][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-25 02:50:10.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:10.199][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.277][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.278][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-25 02:50:10.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:10.281][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.293][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.294][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-25 02:50:10.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:10.297][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.309][biodb::testThat]
biodb.INFO [2024-03-25 02:50:10.310][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-25 02:50:10.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:10.313][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:10.318][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-25 02:50:18.938][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-25 02:50:27.656][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.658][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-25 02:50:27.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.660][biodb::testThat]
biodb.TRACE[2024-03-25 02:50:27.687][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:27.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:27.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:27.692][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:27.693][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:27.694][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:27.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:27.697][ef$get] fields variable is a list.
biodb.INFO [2024-03-25 02:50:27.699][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.701][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-25 02:50:27.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.703][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.783][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.784][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-25 02:50:27.786][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.787][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.826][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.828][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-25 02:50:27.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.830][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.854][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.856][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-25 02:50:27.857][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.858][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.882][biodb::testThat]
biodb.INFO [2024-03-25 02:50:27.884][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-25 02:50:27.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:27.887][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:27.889][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-25 02:50:27.957][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-25 02:50:27.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-25 02:50:27.992][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:27.995][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv".
biodb.DEBUG[2024-03-25 02:50:27.997][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-25 02:50:27.998][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-25 02:50:28.000][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-25 02:50:28.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:28.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:28.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:28.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:28.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:28.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:28.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:28.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.023][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:28.060][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-25 02:50:28.061][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-25 02:50:28.083][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.085][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-25 02:50:28.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:28.088][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:28.100][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-25 02:50:28.101][private$loadEntries] Creating entries from ids [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.DEBUG[2024-03-25 02:50:28.103][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)...
biodb.TRACE[2024-03-25 02:50:28.105][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.TRACE[2024-03-25 02:50:28.107][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-03-25 02:50:28.111][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-03-25 02:50:28.113][conn$getEntryContent] 3 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-25 02:50:28.114][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s).
biodb.DEBUG[2024-03-25 02:50:28.116][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-25 02:50:28.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:28.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:28.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:28.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:28.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:28.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:28.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:28.133][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.138][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:28.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:28.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:28.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:28.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:28.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:28.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:28.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:28.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:28.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:28.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:28.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:28.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.201][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:28.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:28.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.207][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:28.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:28.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:28.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:28.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.218][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:28.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:28.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:28.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.229][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:28.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:28.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.234][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:28.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.239][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:28.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:28.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:28.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:28.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:28.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.266][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.272][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-25 02:50:28.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:28.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:28.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.288][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:28.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:28.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.309][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:28.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:28.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:28.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:28.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:28.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:28.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:28.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:28.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:28.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:28.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:28.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:28.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:28.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:28.465][self$createEntryFromContent] Accession numbers: NA, LMFA00000002, NA.
biodb.DEBUG[2024-03-25 02:50:28.467][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-25 02:50:28.470][function(conn, opt)] Entries: [4]: "NULL, NULL, <environment>, NULL"
biodb.INFO [2024-03-25 02:50:28.581][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.583][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-25 02:50:28.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:28.588][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.687][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.689][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-25 02:50:28.691][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:28.692][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.709][biodb::testThat]
biodb.INFO [2024-03-25 02:50:28.711][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-25 02:50:28.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:28.715][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:28.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-25 02:50:28.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:28.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-25 02:50:28.816][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:28.934][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-03-25 02:50:30.425][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:30.426][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:30.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:30.429][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:30.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:30.432][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:30.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:30.434][ef$get] fields variable is a list.
biodb.INFO [2024-03-25 02:50:30.437][biodb::testThat]
biodb.INFO [2024-03-25 02:50:30.438][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-25 02:50:30.439][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:30.441][biodb::testThat]
biodb.ERROR[2024-03-25 02:50:30.535][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-25 02:50:30.558][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-25 02:50:30.577][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-25 02:50:30.578][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-25 02:50:30.580][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-25 02:50:30.581][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-25 02:50:30.582][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:30.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:30.584][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:30.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:30.587][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-25 02:50:30.601][biodb::testContext]
biodb.INFO [2024-03-25 02:50:30.603][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:30.604][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-25 02:50:30.605][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:30.607][biodb::testContext]
biodb.INFO [2024-03-25 02:50:30.609][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:30.612][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:30.616][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:30.618][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-25 02:50:30.619][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.624][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-25 02:50:30.625][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.630][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-25 02:50:30.631][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.636][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-25 02:50:30.637][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-25 02:50:30.638][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-25 02:50:30.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.643][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-25 02:50:30.644][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-25 02:50:30.645][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.649][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[2024-03-25 02:50:30.650][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-25 02:50:30.651][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-25 02:50:30.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.656][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-25 02:50:30.657][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-25 02:50:30.659][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-25 02:50:30.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.662][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[2024-03-25 02:50:30.663][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-25 02:50:30.665][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.669][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-25 02:50:30.671][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-25 02:50:30.672][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-25 02:50:30.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.677][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:30.679][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-25 02:50:30.680][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-25 02:50:30.682][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-25 02:50:30.683][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-25 02:50:30.685][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-25 02:50:30.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.690][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-25 02:50:30.691][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-25 02:50:30.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.696][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-25 02:50:30.698][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-25 02:50:30.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.703][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-25 02:50:30.705][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-25 02:50:30.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.710][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-25 02:50:30.711][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-25 02:50:30.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.717][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-25 02:50:30.718][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-25 02:50:30.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.723][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:30.725][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-25 02:50:30.729][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-25 02:50:30.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.735][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-25 02:50:30.736][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-25 02:50:30.738][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-25 02:50:30.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.743][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-25 02:50:30.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.747][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-25 02:50:30.749][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.750][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:30.751][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.757][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:30.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:30.760][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.761][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-25 02:50:30.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:30.764][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.767][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:30.767][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:30.767][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:30.767][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:30.767][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:30.768][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:30.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.772][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:30.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.776][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.778][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.779][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:30.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:30.782][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.783][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-25 02:50:30.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.789][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:30.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.792][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:30.793][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.794][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.799][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:30.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:30.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.803][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-25 02:50:30.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:30.806][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:30.809][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:30.809][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:30.809][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:30.809][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:30.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:30.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.815][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:30.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.820][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:30.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:30.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.826][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.827][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-25 02:50:30.830][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.832][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-25 02:50:30.833][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.834][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:30.836][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.837][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.840][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.841][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:30.843][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:30.844][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.867][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-25 02:50:30.870][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:30.871][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.873][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.874][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.875][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:30.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.879][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:30.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.884][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:30.887][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:30.888][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.889][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.891][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-25 02:50:30.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.895][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:30.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.898][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:30.900][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.901][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.902][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.919][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.924][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:30.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:30.930][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.932][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-25 02:50:30.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:30.937][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.940][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:30.942][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:30.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.951][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:30.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:30.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:30.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:30.960][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:30.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:30.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:30.968][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:30.972][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:30.974][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:30.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:30.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:30.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:30.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:30.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:30.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:30.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.030][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[2024-03-25 02:50:31.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.109][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[2024-03-25 02:50:31.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.146][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-25 02:50:31.149][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-25 02:50:31.151][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-25 02:50:31.153][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-25 02:50:31.156][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-25 02:50:31.159][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-25 02:50:31.161][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:31.164][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:31.167][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-25 02:50:31.170][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-25 02:50:31.173][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-25 02:50:31.176][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-25 02:50:31.180][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:31.183][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:31.186][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-25 02:50:31.188][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:31.190][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-25 02:50:31.193][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-25 02:50:31.195][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-25 02:50:31.197][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-25 02:50:31.199][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-25 02:50:31.201][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-25 02:50:31.204][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-25 02:50:31.206][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-25 02:50:31.208][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-25 02:50:31.210][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-25 02:50:31.212][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-25 02:50:31.214][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-25 02:50:31.217][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-25 02:50:31.219][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-25 02:50:31.221][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-25 02:50:31.223][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-25 02:50:31.225][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-25 02:50:31.227][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-25 02:50:31.229][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-25 02:50:31.232][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-25 02:50:31.234][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-25 02:50:31.236][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-25 02:50:31.239][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-25 02:50:31.241][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-25 02:50:31.243][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-25 02:50:31.245][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-25 02:50:31.247][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-25 02:50:31.249][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-25 02:50:31.251][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-25 02:50:31.253][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-25 02:50:31.256][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-25 02:50:31.258][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-25 02:50:31.260][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-25 02:50:31.262][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-25 02:50:31.264][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-25 02:50:31.267][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-25 02:50:31.269][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-25 02:50:31.271][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-25 02:50:31.273][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-25 02:50:31.275][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-25 02:50:31.277][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-25 02:50:31.279][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-25 02:50:31.282][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-25 02:50:31.284][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-25 02:50:31.286][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-25 02:50:31.288][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-25 02:50:31.290][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-25 02:50:31.292][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-25 02:50:31.295][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-25 02:50:31.297][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-25 02:50:31.299][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-25 02:50:31.301][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-25 02:50:31.304][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-25 02:50:31.306][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-25 02:50:31.308][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-25 02:50:31.311][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-25 02:50:31.313][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-25 02:50:31.315][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-25 02:50:31.317][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-25 02:50:31.319][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-25 02:50:31.322][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-25 02:50:31.324][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-25 02:50:31.326][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-25 02:50:31.328][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-25 02:50:31.331][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-25 02:50:31.333][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-25 02:50:31.335][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-25 02:50:31.338][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-25 02:50:31.341][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:31.343][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:31.344][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.347][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.585][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[2024-03-25 02:50:31.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:31.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:31.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:31.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:31.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:31.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:31.596][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:31.598][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:31.600][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:31.602][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-25 02:50:31.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:31.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:31.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:31.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:31.609][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:31.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:31.611][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:31.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:31.614][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:31.616][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-25 02:50:31.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-25 02:50:31.618][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-25 02:50:31.620][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:31.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:31.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:31.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:31.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:31.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:31.627][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:31.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:31.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:31.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:31.632][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-25 02:50:31.632][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-25 02:50:31.634][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:31.635][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:31.636][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:31.638][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:31.639][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-25 02:50:31.641][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:31.646][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:31.648][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-25 02:50:31.650][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:31.652][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-25 02:50:31.654][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:31.655][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:31.657][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-25 02:50:31.658][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-25 02:50:31.661][biodb::testThat]
biodb.INFO [2024-03-25 02:50:31.662][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-25 02:50:31.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:31.665][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:31.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-25 02:50:31.677][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.679][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2024-03-25 02:50:31.681][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.683][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2024-03-25 02:50:31.790][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-03-25 02:50:31.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-03-25 02:50:31.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.801][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-03-25 02:50:31.814][biodb::testThat]
biodb.INFO [2024-03-25 02:50:31.815][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-25 02:50:31.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:31.818][biodb::testThat]
biodb.INFO [2024-03-25 02:50:31.887][biodb::testThat]
biodb.INFO [2024-03-25 02:50:31.888][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-25 02:50:31.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:31.891][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:31.895][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-25 02:50:31.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-25 02:50:31.904][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.906][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-25 02:50:31.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-25 02:50:31.917][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-25 02:50:31.921][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.923][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-25 02:50:31.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-03-25 02:50:31.936][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2024-03-25 02:50:31.939][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.942][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2024-03-25 02:50:31.951][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-25 02:50:31.955][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:31.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2024-03-25 02:50:31.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:31.978][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2024-03-25 02:50:32.137][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-03-25 02:50:32.164][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:32.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2024-03-25 02:50:32.168][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:32.188][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2024-03-25 02:50:32.345][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-25 02:50:32.347][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-25 02:50:32.349][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-25 02:50:32.350][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-25 02:50:32.352][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:32.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:32.354][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.358][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-25 02:50:32.364][biodb::testContext]
biodb.INFO [2024-03-25 02:50:32.365][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:32.367][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-25 02:50:32.368][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-25 02:50:32.370][biodb::testContext]
biodb.INFO [2024-03-25 02:50:32.373][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:32.375][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:32.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:32.382][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-25 02:50:32.383][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.389][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-25 02:50:32.390][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.395][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-25 02:50:32.397][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.402][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-25 02:50:32.403][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-25 02:50:32.405][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-25 02:50:32.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.410][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-25 02:50:32.411][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-25 02:50:32.413][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.418][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-25 02:50:32.419][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-25 02:50:32.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.424][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-25 02:50:32.425][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-25 02:50:32.427][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-25 02:50:32.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.432][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-25 02:50:32.433][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.438][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-25 02:50:32.440][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-25 02:50:32.441][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-25 02:50:32.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.445][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[2024-03-25 02:50:32.446][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:32.448][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-25 02:50:32.449][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-25 02:50:32.450][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-25 02:50:32.452][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-25 02:50:32.453][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-25 02:50:32.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.458][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-25 02:50:32.460][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-25 02:50:32.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.465][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-25 02:50:32.466][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-25 02:50:32.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.471][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-25 02:50:32.473][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-25 02:50:32.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.478][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-25 02:50:32.479][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-25 02:50:32.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.484][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-25 02:50:32.486][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-25 02:50:32.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.491][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-25 02:50:32.492][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-25 02:50:32.497][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-25 02:50:32.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.502][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-25 02:50:32.504][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-25 02:50:32.505][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-25 02:50:32.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.510][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-25 02:50:32.513][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.514][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-25 02:50:32.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.517][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:32.518][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.520][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.521][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.524][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:32.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:32.527][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.528][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-25 02:50:32.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:32.531][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.532][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.533][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:32.533][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:32.533][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:32.533][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:32.533][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:32.535][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:32.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:32.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.544][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:32.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:32.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.549][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.551][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-25 02:50:32.554][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.555][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:32.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:32.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.560][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.562][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.565][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:32.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:32.567][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.569][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-25 02:50:32.570][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:32.571][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.573][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.574][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:32.574][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:32.574][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-25 02:50:32.574][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-25 02:50:32.574][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-25 02:50:32.576][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:32.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:32.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.585][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:32.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:32.589][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.590][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.592][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-25 02:50:32.594][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.596][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-25 02:50:32.597][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.598][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:32.600][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.601][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.602][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.604][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.605][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:32.607][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:32.608][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.609][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-25 02:50:32.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:32.612][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.614][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.615][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.616][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:32.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:32.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.624][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.625][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:32.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:32.629][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.631][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.632][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-25 02:50:32.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-25 02:50:32.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:32.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.646][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-25 02:50:32.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:32.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.650][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-25 02:50:32.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:32.653][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:32.656][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:32.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:32.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:32.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:32.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:32.667][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:32.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:32.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:32.672][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:32.674][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:32.675][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.733][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[2024-03-25 02:50:32.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.753][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[2024-03-25 02:50:32.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.759][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[2024-03-25 02:50:32.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.766][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[2024-03-25 02:50:32.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.793][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[2024-03-25 02:50:32.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.799][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[2024-03-25 02:50:32.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.805][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[2024-03-25 02:50:32.806][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-25 02:50:32.808][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-25 02:50:32.810][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-25 02:50:32.812][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-25 02:50:32.814][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-25 02:50:32.816][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-25 02:50:32.818][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:32.820][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:32.822][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-25 02:50:32.824][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-25 02:50:32.826][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-25 02:50:32.828][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-25 02:50:32.830][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-25 02:50:32.832][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-25 02:50:32.833][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-25 02:50:32.835][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:32.837][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-25 02:50:32.839][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-25 02:50:32.841][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-25 02:50:32.843][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-25 02:50:32.845][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-25 02:50:32.847][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-25 02:50:32.849][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-25 02:50:32.851][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-25 02:50:32.853][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-25 02:50:32.855][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-25 02:50:32.857][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-25 02:50:32.859][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-25 02:50:32.861][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-25 02:50:32.862][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-25 02:50:32.864][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-25 02:50:32.866][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-25 02:50:32.868][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-25 02:50:32.870][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-25 02:50:32.872][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-25 02:50:32.874][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-25 02:50:32.876][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-25 02:50:32.878][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-25 02:50:32.880][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-25 02:50:32.882][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-25 02:50:32.884][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-25 02:50:32.886][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-25 02:50:32.888][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-25 02:50:32.890][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-25 02:50:32.892][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-25 02:50:32.894][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-25 02:50:32.895][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-25 02:50:32.897][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-25 02:50:32.899][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-25 02:50:32.901][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-25 02:50:32.903][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-25 02:50:32.905][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-25 02:50:32.907][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-25 02:50:32.909][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-25 02:50:32.911][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-25 02:50:32.913][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-25 02:50:32.915][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-25 02:50:32.917][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-25 02:50:32.919][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-25 02:50:32.921][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-25 02:50:32.923][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-25 02:50:32.925][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-25 02:50:32.927][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-25 02:50:32.929][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-25 02:50:32.931][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-25 02:50:32.933][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-25 02:50:32.935][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-25 02:50:32.937][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-25 02:50:32.939][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-25 02:50:32.941][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-25 02:50:32.943][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-25 02:50:32.945][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-25 02:50:32.947][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-25 02:50:32.949][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-25 02:50:32.951][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-25 02:50:32.953][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-25 02:50:32.955][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-25 02:50:32.957][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-25 02:50:32.959][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-25 02:50:32.961][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-25 02:50:32.963][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-25 02:50:32.965][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-25 02:50:32.967][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-25 02:50:32.969][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-25 02:50:32.971][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-25 02:50:32.972][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-25 02:50:32.974][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.976][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:32.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:32.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:32.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.986][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[2024-03-25 02:50:32.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:32.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:32.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:32.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:32.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:32.995][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[2024-03-25 02:50:32.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:32.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:32.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.004][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[2024-03-25 02:50:33.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.030][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[2024-03-25 02:50:33.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.092][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[2024-03-25 02:50:33.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.109][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[2024-03-25 02:50:33.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.118][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[2024-03-25 02:50:33.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-25 02:50:33.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:33.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:33.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:33.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:33.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:33.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-25 02:50:33.129][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-25 02:50:33.131][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:33.133][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:33.135][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-25 02:50:33.136][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:33.138][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-25 02:50:33.139][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:33.140][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-25 02:50:33.142][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:33.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-25 02:50:33.145][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-25 02:50:33.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-25 02:50:33.147][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:33.149][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-25 02:50:33.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-25 02:50:33.152][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-25 02:50:33.153][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-25 02:50:33.154][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-25 02:50:33.154][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-25 02:50:33.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-25 02:50:33.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:33.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:33.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-25 02:50:33.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-25 02:50:33.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-25 02:50:33.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-25 02:50:33.165][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-25 02:50:33.165][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-25 02:50:33.167][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-25 02:50:33.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-25 02:50:33.169][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-25 02:50:33.170][self$setPropertyValue]
biodb.DEBUG[2024-03-25 02:50:33.172][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-25 02:50:33.174][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-25 02:50:33.179][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:33.180][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-25 02:50:33.182][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-25 02:50:33.184][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-25 02:50:33.186][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:33.187][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-25 02:50:33.189][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-25 02:50:33.190][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-25 02:50:33.192][biodb::testThat]
biodb.INFO [2024-03-25 02:50:33.194][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-03-25 02:50:33.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-25 02:50:33.196][biodb::testThat]
biodb.DEBUG[2024-03-25 02:50:33.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-25 02:50:33.206][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-25 02:50:33.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-25 02:50:33.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-25 02:50:33.303][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-25 02:50:34.480][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-25 02:50:34.482][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-25 02:50:34.484][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-25 02:50:34.486][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-25 02:50:34.488][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-25 02:50:34.489][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-25 02:50:34.491][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-25 02:50:34.493][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-25 02:50:34.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:34.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:34.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:34.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:34.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:34.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:34.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:34.512][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.518][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:34.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:34.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:34.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:34.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:34.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:34.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:34.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:34.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.572][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:34.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-25 02:50:34.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.578][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:34.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-25 02:50:34.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.590][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.613][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-25 02:50:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:34.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:34.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:34.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-25 02:50:34.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.665][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-25 02:50:34.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.671][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.677][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.689][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-25 02:50:34.759][self$createEntryFromContent] Accession numbers: NA, LMFA00000002.
biodb.DEBUG[2024-03-25 02:50:34.760][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-25 02:50:34.764][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-25 02:50:34.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:34.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:34.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:34.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:34.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:34.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:34.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:34.781][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-03-25 02:50:34.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-25 02:50:34.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:34.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:34.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:34.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:34.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:34.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-25 02:50:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-25 02:50:34.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-25 02:50:34.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-25 02:50:34.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-25 02:50:34.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-25 02:50:34.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-25 02:50:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-25 02:50:34.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-25 02:50:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.820][private$selectFields] Fields none
biodb.TRACE[2024-03-25 02:50:34.821][private$selectFields]
biodb.TRACE[2024-03-25 02:50:34.822][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-25 02:50:34.824][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-25 02:50:34.825][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-25 02:50:34.826][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.828][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.830][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.838][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.839][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.842][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.843][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.845][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.848][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.851][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.853][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.855][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:34.856][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:34.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.859][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.861][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.865][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.866][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.868][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.871][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.872][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.876][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.878][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.879][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.882][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.883][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.885][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.887][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.889][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.890][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.894][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.895][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.899][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:34.901][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:34.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.903][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.905][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.906][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.909][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.910][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.912][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.914][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.916][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-25 02:50:34.917][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-25 02:50:34.918][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.922][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:34.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.928][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.959][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.961][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:34.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.964][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.966][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.967][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:34.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.969][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:34.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.975][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.976][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:34.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:34.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.980][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.981][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:34.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:34.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.985][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.986][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.988][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:34.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.990][ef$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.992][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-25 02:50:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:34.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:35.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:35.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-25 02:50:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-25 02:50:35.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-25 02:50:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.025][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.036][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-25 02:50:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-25 02:50:35.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-25 02:50:35.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:35.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:35.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-25 02:50:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-25 02:50:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:35.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:35.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:35.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:35.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-25 02:50:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-25 02:50:35.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-25 02:50:35.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-25 02:50:35.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-25 02:50:35.144][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-25 02:50:35.146][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-25 02:50:35.147][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-25 02:50:35.155][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-25 02:50:35.156][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-25 02:50:35.158][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-25 02:50:35.159][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-25 02:50:35.160][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-25 02:50:35.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-25 02:50:35.162][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-25 02:50:35.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-25 02:50:35.165][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-25 02:50:35.166][FUN] Functions in observer 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 14 | WARN 0 | SKIP 0 | PASS 96 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(...)
4. └─testthat::quasi_label(enquo(object), label, arg = "object")
5. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by name. ──────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─opt$refEntries$getRealEntry(id)
4. └─self$getRealEntries(ids = id)
5. └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── 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 14 | WARN 0 | SKIP 0 | PASS 96 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 0.680 | 0.042 | 0.728 | |
| LipidmapsStructureEntry | 0.162 | 0.003 | 0.164 | |