| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:04 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the biodbLipidmaps package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbLipidmaps |
| Version: 1.10.0 |
| Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz |
| StartedAt: 2024-07-21 23:55:09 -0400 (Sun, 21 Jul 2024) |
| EndedAt: 2024-07-21 23:59:21 -0400 (Sun, 21 Jul 2024) |
| EllapsedTime: 252.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbLipidmaps/DESCRIPTION' ... OK
* this is package 'biodbLipidmaps' version '1.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LipidmapsStructureConn 3.28 1.98 80.35
* 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 98 ]
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
'E:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log'
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'biodbLipidmaps' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
Package 'biodbLipidmaps' is deprecated and will be removed from
Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-07-21 23:58:36.706][biodb::testContext]
biodb.INFO [2024-07-21 23:58:36.709][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:58:36.711][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-21 23:58:36.712][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:58:36.714][biodb::testContext]
biodb.INFO [2024-07-21 23:58:36.725][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:58:36.729][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 23:58:36.759][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:58:36.760][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 23:58:36.762][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.767][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 23:58:36.798][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.802][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 23:58:36.804][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.808][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 23:58:36.809][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 23:58:36.811][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 23:58:36.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.815][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 23:58:36.816][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 23:58:36.817][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.822][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 23:58:36.823][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 23:58:36.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.828][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 23:58:36.829][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 23:58:36.830][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 23:58:36.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.834][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 23:58:36.836][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.840][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 23:58:36.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 23:58:36.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 23:58:36.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.847][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:58:36.848][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 23:58:36.849][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 23:58:36.850][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 23:58:36.852][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 23:58:36.853][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 23:58:36.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.857][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 23:58:36.859][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 23:58:36.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.863][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 23:58:36.864][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 23:58:36.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.869][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 23:58:36.870][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 23:58:36.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.875][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 23:58:36.876][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 23:58:36.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.881][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 23:58:36.882][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 23:58:36.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.887][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:58:36.889][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 23:58:36.892][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 23:58:36.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.897][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 23:58:36.898][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 23:58:36.899][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 23:58:36.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:36.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:36.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:36.906][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 23:58:36.934][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:36.948][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-21 23:58:36.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:58:36.952][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.953][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:58:36.954][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:36.955][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:58:36.957][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:58:36.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:58:36.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.960][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 23:58:36.962][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:58:36.963][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:36.964][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.965][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:58:36.965][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:58:36.965][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:58:36.965][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:58:36.965][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:58:36.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:58:36.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:36.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:36.970][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:58:36.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:36.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:36.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:58:36.981][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:36.982][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:58:36.983][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:58:36.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:36.986][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:36.987][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 23:58:36.989][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:36.990][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:58:36.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:58:36.994][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:36.995][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:58:36.996][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:36.997][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:58:36.999][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:58:37.000][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:58:37.001][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.002][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 23:58:37.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:58:37.005][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.007][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:58:37.007][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:58:37.007][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:58:37.007][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:58:37.007][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:58:37.008][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:58:37.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:58:37.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.016][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:58:37.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:58:37.020][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.021][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.022][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 23:58:37.024][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.026][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-21 23:58:37.027][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.028][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:58:37.029][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.034][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:58:37.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:58:37.036][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.038][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 23:58:37.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:58:37.040][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.041][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.042][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:58:37.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.047][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:58:37.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.051][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.053][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:58:37.054][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:58:37.055][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.056][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.057][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 23:58:37.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.061][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:58:37.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:58:37.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.067][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.069][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:58:37.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:58:37.071][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.073][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 23:58:37.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:58:37.075][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.077][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.079][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:58:37.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:58:37.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.085][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.086][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.088][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:58:37.089][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:58:37.090][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.091][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:58:37.095][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.167][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[2024-07-21 23:58:37.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.195][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 23:58:37.199][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 23:58:37.201][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 23:58:37.202][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 23:58:37.204][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 23:58:37.205][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 23:58:37.207][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 23:58:37.208][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 23:58:37.210][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 23:58:37.212][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 23:58:37.213][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 23:58:37.215][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 23:58:37.216][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 23:58:37.218][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 23:58:37.219][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 23:58:37.221][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:58:37.222][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 23:58:37.224][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 23:58:37.225][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 23:58:37.227][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 23:58:37.229][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 23:58:37.230][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 23:58:37.232][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 23:58:37.233][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 23:58:37.235][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 23:58:37.237][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 23:58:37.238][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 23:58:37.240][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 23:58:37.241][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 23:58:37.243][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 23:58:37.244][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 23:58:37.246][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 23:58:37.248][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 23:58:37.249][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 23:58:37.251][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 23:58:37.252][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 23:58:37.254][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 23:58:37.255][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 23:58:37.257][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 23:58:37.259][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 23:58:37.260][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 23:58:37.262][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 23:58:37.263][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 23:58:37.265][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 23:58:37.266][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 23:58:37.268][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 23:58:37.270][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 23:58:37.271][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 23:58:37.273][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 23:58:37.274][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 23:58:37.276][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 23:58:37.277][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 23:58:37.279][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 23:58:37.280][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 23:58:37.282][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 23:58:37.283][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 23:58:37.285][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 23:58:37.287][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 23:58:37.288][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 23:58:37.290][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 23:58:37.291][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 23:58:37.293][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 23:58:37.294][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 23:58:37.296][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 23:58:37.298][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 23:58:37.299][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 23:58:37.301][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 23:58:37.302][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 23:58:37.304][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 23:58:37.305][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 23:58:37.307][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 23:58:37.310][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 23:58:37.313][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 23:58:37.314][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 23:58:37.316][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 23:58:37.317][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 23:58:37.319][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 23:58:37.321][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 23:58:37.322][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 23:58:37.324][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 23:58:37.325][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 23:58:37.327][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 23:58:37.328][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 23:58:37.351][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 23:58:37.354][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:58:37.357][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:58:37.358][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.360][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.457][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[2024-07-21 23:58:37.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.481][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[2024-07-21 23:58:37.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.489][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[2024-07-21 23:58:37.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:58:37.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:37.507][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 23:58:37.516][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:58:37.518][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.520][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.521][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.522][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:58:37.523][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.526][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.527][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.528][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:58:37.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:58:37.531][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.532][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 23:58:37.533][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 23:58:37.534][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 23:58:37.536][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 23:58:37.537][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:58:37.537][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:58:37.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:58:37.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:58:37.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:58:37.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:58:37.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:58:37.546][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 23:58:37.546][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 23:58:37.548][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:58:37.549][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:58:37.550][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 23:58:37.551][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:58:37.557][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 23:58:37.559][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:58:37.584][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:58:37.586][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 23:58:37.590][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:58:37.594][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 23:58:37.598][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:58:37.599][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:58:37.601][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 23:58:37.602][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 23:58:37.616][biodb::testThat]
biodb.INFO [2024-07-21 23:58:37.618][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-21 23:58:37.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:37.620][biodb::testThat]
biodb.TRACE[2024-07-21 23:58:37.659][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-07-21 23:58:37.661][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 23:58:37.673][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 23:58:37.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:58:37.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:37.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:37.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:37.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:37.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:37.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:58:37.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:37.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:37.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 23:58:37.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 23:58:37.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:58:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:58:37.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.802][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:58:37.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:58:37.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:37.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:37.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:37.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:37.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:37.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.865][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 23:58:37.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:37.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.870][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 23:58:37.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:37.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:37.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:37.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.881][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:37.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:37.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.896][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 23:58:37.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.901][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 23:58:37.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.953][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 23:58:37.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:37.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:37.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:37.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:37.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.042][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:58:38.077][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-21 23:58:38.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 23:58:38.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 23:58:38.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.101][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-21 23:58:38.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-21 23:58:38.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-21 23:58:38.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-21 23:58:38.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.116][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-21 23:58:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-21 23:58:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.184][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.247][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.279][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.281][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.283][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.316][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.317][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.320][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.353][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.358][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.359][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.362][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.384][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.394][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.396][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.398][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.434][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.435][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.437][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.457][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.482][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.484][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.488][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.490][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.512][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.516][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.522][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.524][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:58:38.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.526][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.544][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:58:38.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:58:38.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.548][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.556][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:38.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.578][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.597][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.598][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:58:38.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.601][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 23:58:38.619][biodb::testThat]
biodb.INFO [2024-07-21 23:58:38.621][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-21 23:58:38.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:38.625][biodb::testThat]
biodb.DEBUG[2024-07-21 23:58:38.643][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-07-21 23:58:38.652][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-21 23:58:38.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-07-21 23:58:38.664][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:58:38.669][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-07-21 23:58:38.670][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 23:58:38.692][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 23:58:38.694][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 23:58:38.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:58:38.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:38.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:38.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:38.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:38.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:38.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:58:38.711][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:38.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:38.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:38.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:38.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:58:38.753][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-07-21 23:58:38.754][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-21 23:58:38.794][biodb::testThat]
biodb.INFO [2024-07-21 23:58:38.795][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-21 23:58:38.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:38.798][biodb::testThat]
biodb.TRACE[2024-07-21 23:58:38.801][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:38.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:38.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:38.805][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:58:38.807][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.INFO [2024-07-21 23:58:39.234][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.236][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-21 23:58:39.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:39.238][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.312][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.313][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-21 23:58:39.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:39.316][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.386][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.387][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-21 23:58:39.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:39.390][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.403][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.405][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-21 23:58:39.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:39.407][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.419][biodb::testThat]
biodb.INFO [2024-07-21 23:58:39.420][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-21 23:58:39.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:39.422][biodb::testThat]
biodb.DEBUG[2024-07-21 23:58:39.433][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-07-21 23:58:40.196][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-07-21 23:58:41.103][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.104][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-21 23:58:41.105][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.106][biodb::testThat]
biodb.TRACE[2024-07-21 23:58:41.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:58:41.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:58:41.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:41.131][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:41.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:41.167][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:58:41.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:41.169][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 23:58:41.172][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.173][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-21 23:58:41.174][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.175][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.244][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.246][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-21 23:58:41.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.250][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.471][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.473][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-21 23:58:41.475][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.476][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.502][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.503][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-21 23:58:41.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.506][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.532][biodb::testThat]
biodb.INFO [2024-07-21 23:58:41.534][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-21 23:58:41.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:41.537][biodb::testThat]
biodb.DEBUG[2024-07-21 23:58:41.540][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-21 23:58:41.591][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-21 23:58:41.608][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-21 23:58:41.611][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-21 23:58:41.612][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-21 23:58:41.614][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 23:58:41.616][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 23:58:41.617][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-21 23:58:41.618][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-21 23:58:41.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:58:41.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:41.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:41.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:41.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:41.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:41.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:41.644][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-07-21 23:58:41.666][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:41.668][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 23:58:41.669][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:41.966][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:41.968][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:41.971][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:41.974][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:42.579][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:42.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:42.582][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:42.600][rule$waitAsNeeded] Wait 0.0695539 second(s).
biodb.TRACE[2024-07-21 23:58:42.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:42.987][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:42.989][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:42.990][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:42.992][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:43.594][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:43.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:43.598][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:43.601][rule$waitAsNeeded] Wait 0.0838208 second(s).
biodb.TRACE[2024-07-21 23:58:43.701][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:44.000][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:44.002][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:44.004][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:44.005][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:44.609][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:44.611][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:44.612][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:44.614][rule$waitAsNeeded] Wait 0.086489 second(s).
biodb.TRACE[2024-07-21 23:58:44.717][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:45.013][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:45.014][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:45.016][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:45.017][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:45.628][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:45.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:45.633][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:45.636][rule$waitAsNeeded] Wait 0.0812881 second(s).
biodb.TRACE[2024-07-21 23:58:45.721][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:46.018][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:46.019][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:46.021][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:46.022][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:46.630][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:46.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:46.635][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:46.637][rule$waitAsNeeded] Wait 0.0837998 second(s).
biodb.TRACE[2024-07-21 23:58:46.737][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:47.032][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:47.033][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:47.034][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:47.036][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:47.645][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:47.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:47.649][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:47.650][rule$waitAsNeeded] Wait 0.086019 second(s).
biodb.TRACE[2024-07-21 23:58:47.753][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:48.050][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:48.052][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:48.054][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:48.056][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:48.661][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:48.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:48.664][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:48.666][rule$waitAsNeeded] Wait 0.086849 second(s).
biodb.TRACE[2024-07-21 23:58:48.769][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:49.072][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:49.074][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:49.075][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:49.077][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:49.678][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:49.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:49.682][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:49.685][rule$waitAsNeeded] Wait 0.0843101 second(s).
biodb.TRACE[2024-07-21 23:58:49.779][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:50.075][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:50.076][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:50.078][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:50.079][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:50.678][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:50.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:50.681][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:50.682][rule$waitAsNeeded] Wait 0.095839 second(s).
biodb.TRACE[2024-07-21 23:58:50.787][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-21 23:58:51.084][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:51.086][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:51.087][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:51.089][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-21 23:58:51.693][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-21 23:58:51.697][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-07-21 23:58:51.700][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-21 23:58:51.702][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-21 23:58:51.704][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 23:58:51.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:58:51.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:51.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:51.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:51.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:51.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:51.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:58:51.730][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:51.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:58:51.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:58:51.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:58:51.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:58:51.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:58:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:58:51.775][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-07-21 23:58:51.776][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-21 23:58:51.800][biodb::testThat]
biodb.INFO [2024-07-21 23:58:51.801][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-21 23:58:51.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:58:51.804][biodb::testThat]
biodb.DEBUG[2024-07-21 23:58:51.823][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-07-21 23:58:51.825][private$loadEntries] Creating entries from ids [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.DEBUG[2024-07-21 23:58:51.827][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-21 23:58:51.829][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.TRACE[2024-07-21 23:58:51.831][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, TRUE".
biodb.TRACE[2024-07-21 23:58:51.847][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-07-21 23:58:51.849][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 23:58:51.850][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 23:58:51.852][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-21 23:58:51.853][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-21 23:58:51.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:58:51.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:58:51.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:58:51.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:58:51.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:58:51.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:58:51.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:58:51.926][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-07-21 23:58:51.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:51.943][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-21 23:58:51.944][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:52.239][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:52.241][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:52.242][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:52.243][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:52.853][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:52.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:52.856][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:52.857][rule$waitAsNeeded] Wait 0.087291 second(s).
biodb.TRACE[2024-07-21 23:58:52.946][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:53.243][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:53.244][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:53.246][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:53.247][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:53.857][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:53.860][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:53.862][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:53.866][rule$waitAsNeeded] Wait 0.081557 second(s).
biodb.TRACE[2024-07-21 23:58:53.965][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:54.262][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:54.263][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:54.265][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:54.266][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:54.872][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:54.874][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:54.875][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:54.876][rule$waitAsNeeded] Wait 0.0878389 second(s).
biodb.TRACE[2024-07-21 23:58:54.980][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:55.275][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:55.277][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:55.278][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:55.279][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:55.888][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:55.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:55.891][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:55.892][rule$waitAsNeeded] Wait 0.0878718 second(s).
biodb.TRACE[2024-07-21 23:58:55.997][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:56.297][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:56.299][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:56.301][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:56.302][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:56.907][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:56.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:56.909][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:56.911][rule$waitAsNeeded] Wait 0.085453 second(s).
biodb.TRACE[2024-07-21 23:58:57.001][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:57.301][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:57.302][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:57.303][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:57.305][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:57.914][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:57.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:57.918][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:57.920][rule$waitAsNeeded] Wait 0.080235 second(s).
biodb.TRACE[2024-07-21 23:58:58.005][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:58.300][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:58.301][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:58.303][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:58.304][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:58.898][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:58.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:58.903][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:58.905][rule$waitAsNeeded] Wait 0.100341 second(s).
biodb.TRACE[2024-07-21 23:58:59.021][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:58:59.320][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:58:59.321][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:58:59.323][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:58:59.324][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:58:59.929][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:58:59.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:58:59.932][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:58:59.934][rule$waitAsNeeded] Wait 0.087333 second(s).
biodb.TRACE[2024-07-21 23:59:00.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:59:00.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:59:00.336][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:59:00.337][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:59:00.339][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:59:00.946][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-21 23:59:00.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-21 23:59:00.950][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-21 23:59:00.953][rule$waitAsNeeded] Wait 0.0848691 second(s).
biodb.TRACE[2024-07-21 23:59:01.054][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-21 23:59:01.352][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-21 23:59:01.353][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-21 23:59:01.355][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-21 23:59:01.356][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-21 23:59:01.983][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-21 23:59:01.997][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv"
biodb.DEBUG[2024-07-21 23:59:01.999][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-21 23:59:02.001][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s).
biodb.DEBUG[2024-07-21 23:59:02.003][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 23:59:02.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:02.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:02.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:02.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:02.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:02.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:02.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.039][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:59:02.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:02.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:02.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:02.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:02.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:02.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:02.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:02.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:59:02.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:02.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:02.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:02.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:02.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:02.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:02.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 23:59:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 23:59:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-21 23:59:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-21 23:59:02.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.159][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:59:02.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:59:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:59:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-21 23:59:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.170][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:59:02.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:59:02.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:59:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-21 23:59:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:59:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:59:02.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.186][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:59:02.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-21 23:59:02.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:59:02.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:59:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.197][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:59:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-21 23:59:02.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.203][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 23:59:02.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:59:02.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.208][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-21 23:59:02.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:59:02.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:59:02.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:59:02.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-21 23:59:02.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-21 23:59:02.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.235][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 23:59:02.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.240][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-21 23:59:02.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.256][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-21 23:59:02.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.300][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:02.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:02.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:02.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:02.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:02.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:59:02.397][self$createEntryFromContent] Accession numbers: NA, NA, LMFA08040013.
biodb.DEBUG[2024-07-21 23:59:02.398][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-21 23:59:02.400][function(conn, opt)] Entries: [4]: "NULL, NULL, NULL, <environment>"
biodb.INFO [2024-07-21 23:59:02.465][biodb::testThat]
biodb.INFO [2024-07-21 23:59:02.467][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-21 23:59:02.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:02.471][biodb::testThat]
biodb.INFO [2024-07-21 23:59:02.562][biodb::testThat]
biodb.INFO [2024-07-21 23:59:02.564][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-21 23:59:02.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:02.569][biodb::testThat]
biodb.INFO [2024-07-21 23:59:02.605][biodb::testThat]
biodb.INFO [2024-07-21 23:59:02.607][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-21 23:59:02.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:02.610][biodb::testThat]
biodb.DEBUG[2024-07-21 23:59:02.614][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-07-21 23:59:02.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:02.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-07-21 23:59:02.621][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:02.925][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-07-21 23:59:04.846][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-21 23:59:04.847][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-21 23:59:04.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:04.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:04.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:59:04.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-21 23:59:04.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:04.855][ef$get] fields variable is a list.
biodb.INFO [2024-07-21 23:59:04.857][biodb::testThat]
biodb.INFO [2024-07-21 23:59:04.858][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-21 23:59:04.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:04.861][biodb::testThat]
biodb.ERROR[2024-07-21 23:59:04.929][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-21 23:59:04.947][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-21 23:59:04.968][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 23:59:04.970][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 23:59:04.972][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 23:59:04.973][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 23:59:04.974][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:04.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:04.977][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:04.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:04.979][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:04.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-21 23:59:04.991][biodb::testContext]
biodb.INFO [2024-07-21 23:59:04.993][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:59:04.994][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-07-21 23:59:04.995][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:59:04.997][biodb::testContext]
biodb.INFO [2024-07-21 23:59:05.000][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:59:05.002][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 23:59:05.008][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:05.009][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 23:59:05.011][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.015][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.DEBUG[2024-07-21 23:59:05.016][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 23:59:05.017][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.022][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 23:59:05.023][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.028][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 23:59:05.030][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 23:59:05.031][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 23:59:05.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.036][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 23:59:05.038][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 23:59:05.039][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.044][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 23:59:05.046][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 23:59:05.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.078][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 23:59:05.079][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 23:59:05.080][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 23:59:05.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.085][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 23:59:05.087][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.091][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 23:59:05.093][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 23:59:05.094][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 23:59:05.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.099][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:59:05.100][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 23:59:05.102][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 23:59:05.103][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 23:59:05.104][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 23:59:05.106][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 23:59:05.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.110][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 23:59:05.112][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 23:59:05.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.116][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 23:59:05.118][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 23:59:05.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.122][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 23:59:05.124][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 23:59:05.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.127][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[2024-07-21 23:59:05.129][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 23:59:05.130][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 23:59:05.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.135][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 23:59:05.136][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 23:59:05.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.141][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:59:05.142][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 23:59:05.146][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 23:59:05.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.151][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 23:59:05.152][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 23:59:05.154][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 23:59:05.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.159][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 23:59:05.185][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.186][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-21 23:59:05.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:05.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.192][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.193][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.195][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:05.197][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:05.198][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.199][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 23:59:05.200][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:05.202][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.203][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.204][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:05.204][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:05.204][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:59:05.204][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:59:05.204][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:59:05.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:05.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:05.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.214][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.215][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:05.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:05.217][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.218][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.220][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 23:59:05.222][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.223][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:59:05.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:05.227][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.228][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.229][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.231][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.233][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:59:05.235][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:05.237][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.239][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 23:59:05.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:05.243][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.245][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.246][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:05.246][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:05.246][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:59:05.246][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:59:05.246][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:59:05.247][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:05.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:05.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.255][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.256][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:05.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:05.259][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.261][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.262][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 23:59:05.264][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.265][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-21 23:59:05.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:05.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.271][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.273][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.274][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:05.275][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:05.277][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.278][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 23:59:05.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:05.281][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.283][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:05.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:05.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.292][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.293][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:05.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:05.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.298][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.300][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 23:59:05.302][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.303][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:59:05.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:05.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.310][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.312][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:59:05.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:05.315][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.316][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 23:59:05.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:05.320][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.323][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:05.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.331][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:05.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.335][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.336][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:05.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:05.340][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.341][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.343][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:05.344][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.387][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[2024-07-21 23:59:05.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.423][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[2024-07-21 23:59:05.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.440][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[2024-07-21 23:59:05.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.453][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 23:59:05.455][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 23:59:05.457][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 23:59:05.458][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 23:59:05.460][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 23:59:05.462][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 23:59:05.463][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 23:59:05.465][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 23:59:05.467][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 23:59:05.468][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 23:59:05.470][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 23:59:05.471][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 23:59:05.473][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 23:59:05.474][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 23:59:05.476][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 23:59:05.478][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:59:05.479][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 23:59:05.481][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 23:59:05.483][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 23:59:05.485][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 23:59:05.487][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 23:59:05.489][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 23:59:05.491][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 23:59:05.493][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 23:59:05.495][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 23:59:05.498][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 23:59:05.501][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 23:59:05.504][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 23:59:05.507][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 23:59:05.509][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 23:59:05.511][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 23:59:05.513][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 23:59:05.515][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 23:59:05.516][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 23:59:05.518][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 23:59:05.520][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 23:59:05.522][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 23:59:05.524][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 23:59:05.526][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 23:59:05.528][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 23:59:05.531][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 23:59:05.533][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 23:59:05.535][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 23:59:05.537][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 23:59:05.539][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 23:59:05.541][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 23:59:05.543][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 23:59:05.546][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 23:59:05.548][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 23:59:05.550][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 23:59:05.552][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 23:59:05.565][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 23:59:05.566][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 23:59:05.568][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 23:59:05.570][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 23:59:05.572][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 23:59:05.573][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 23:59:05.575][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 23:59:05.577][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 23:59:05.579][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 23:59:05.580][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 23:59:05.582][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 23:59:05.584][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 23:59:05.585][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 23:59:05.587][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 23:59:05.588][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 23:59:05.590][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 23:59:05.592][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 23:59:05.595][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 23:59:05.597][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 23:59:05.600][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 23:59:05.602][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 23:59:05.605][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 23:59:05.607][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 23:59:05.610][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 23:59:05.612][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 23:59:05.615][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 23:59:05.617][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 23:59:05.620][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 23:59:05.622][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 23:59:05.625][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 23:59:05.627][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 23:59:05.630][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 23:59:05.632][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 23:59:05.636][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:59:05.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:05.640][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.643][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.741][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[2024-07-21 23:59:05.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.825][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[2024-07-21 23:59:05.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:05.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:05.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:05.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:05.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:05.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:05.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:05.843][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 23:59:05.845][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:05.847][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.849][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:05.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.854][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.857][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:05.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:05.859][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.861][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 23:59:05.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 23:59:05.863][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 23:59:05.864][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:05.866][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:05.866][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:05.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:05.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:05.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:05.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:05.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:05.875][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 23:59:05.875][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 23:59:05.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:05.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:05.878][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:05.880][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:05.885][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 23:59:05.887][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:59:05.890][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:05.892][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 23:59:05.893][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:05.895][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 23:59:05.896][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:59:05.897][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:59:05.899][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 23:59:05.900][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 23:59:05.902][biodb::testThat]
biodb.INFO [2024-07-21 23:59:05.904][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-07-21 23:59:05.905][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:05.906][biodb::testThat]
biodb.DEBUG[2024-07-21 23:59:05.910][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-07-21 23:59:05.916][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:05.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2024-07-21 23:59:05.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:05.979][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2024-07-21 23:59:06.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-07-21 23:59:06.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-07-21 23:59:06.051][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.126][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-07-21 23:59:06.157][biodb::testThat]
biodb.INFO [2024-07-21 23:59:06.158][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-07-21 23:59:06.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:06.160][biodb::testThat]
biodb.INFO [2024-07-21 23:59:06.231][biodb::testThat]
biodb.INFO [2024-07-21 23:59:06.233][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-07-21 23:59:06.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:06.238][biodb::testThat]
biodb.DEBUG[2024-07-21 23:59:06.244][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-21 23:59:06.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-07-21 23:59:06.267][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.404][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-07-21 23:59:06.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-21 23:59:06.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-07-21 23:59:06.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.429][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-07-21 23:59:06.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-07-21 23:59:06.441][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.443][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2024-07-21 23:59:06.445][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.515][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2024-07-21 23:59:06.527][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-07-21 23:59:06.533][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.536][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2024-07-21 23:59:06.539][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.660][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2024-07-21 23:59:06.918][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-07-21 23:59:06.924][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:06.927][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2024-07-21 23:59:06.929][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:06.996][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2024-07-21 23:59:07.197][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 23:59:07.199][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 23:59:07.200][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 23:59:07.201][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 23:59:07.202][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.205][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.207][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-21 23:59:07.213][biodb::testContext]
biodb.INFO [2024-07-21 23:59:07.214][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:59:07.215][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-07-21 23:59:07.216][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-21 23:59:07.217][biodb::testContext]
biodb.INFO [2024-07-21 23:59:07.220][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:59:07.223][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-21 23:59:07.228][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:07.230][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-21 23:59:07.231][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.235][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-21 23:59:07.237][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.241][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-21 23:59:07.242][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.248][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-21 23:59:07.250][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-21 23:59:07.251][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-21 23:59:07.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.255][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-21 23:59:07.257][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-21 23:59:07.258][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.262][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-21 23:59:07.264][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-21 23:59:07.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.268][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-21 23:59:07.269][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-21 23:59:07.270][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-21 23:59:07.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.275][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-21 23:59:07.276][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.281][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-21 23:59:07.282][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-21 23:59:07.283][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-21 23:59:07.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.288][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:59:07.289][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-21 23:59:07.290][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-21 23:59:07.291][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-21 23:59:07.292][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-21 23:59:07.294][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-21 23:59:07.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.298][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-21 23:59:07.299][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-21 23:59:07.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.304][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-21 23:59:07.305][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-21 23:59:07.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.310][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-21 23:59:07.311][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-21 23:59:07.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.316][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-21 23:59:07.317][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-21 23:59:07.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.322][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-21 23:59:07.323][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-21 23:59:07.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.327][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-21 23:59:07.329][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-21 23:59:07.335][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-21 23:59:07.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.341][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-21 23:59:07.342][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-21 23:59:07.343][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-21 23:59:07.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.348][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-21 23:59:07.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.373][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-21 23:59:07.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.376][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:07.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.382][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:07.383][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:07.384][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.385][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-21 23:59:07.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:07.388][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.389][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.390][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:07.390][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:07.390][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:59:07.390][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:59:07.390][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:59:07.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:07.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:07.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.399][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.400][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.401][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:07.403][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:07.404][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.406][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.407][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-21 23:59:07.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.410][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:59:07.412][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.413][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:07.414][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.415][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.416][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.419][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:59:07.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:07.423][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.425][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-21 23:59:07.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:07.428][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.430][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.432][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:07.432][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:07.432][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-21 23:59:07.432][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-21 23:59:07.432][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-21 23:59:07.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:07.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:07.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.447][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:07.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:07.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.455][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.457][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-21 23:59:07.460][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.462][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-21 23:59:07.464][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:07.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.476][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:07.478][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:07.480][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.482][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-21 23:59:07.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:07.485][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.487][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.489][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:07.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.497][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:07.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.504][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:07.508][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:07.510][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.512][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.514][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-21 23:59:07.517][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.519][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-21 23:59:07.521][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.523][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:07.525][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.527][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.528][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.532][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-21 23:59:07.534][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:07.536][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.538][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-21 23:59:07.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:07.542][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:07.546][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.548][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:07.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:07.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:07.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:07.559][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:07.561][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.563][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:07.565][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:07.567][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:07.569][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:07.571][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:07.573][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.676][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[2024-07-21 23:59:07.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.688][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-21 23:59:07.690][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-21 23:59:07.691][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-21 23:59:07.693][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-21 23:59:07.695][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-21 23:59:07.698][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-21 23:59:07.701][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-21 23:59:07.704][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-21 23:59:07.707][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-21 23:59:07.709][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-21 23:59:07.712][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-21 23:59:07.715][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-21 23:59:07.718][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-21 23:59:07.721][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-21 23:59:07.723][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-21 23:59:07.726][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:59:07.729][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-21 23:59:07.731][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-21 23:59:07.734][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-21 23:59:07.737][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-21 23:59:07.739][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-21 23:59:07.742][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-21 23:59:07.745][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-21 23:59:07.747][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-21 23:59:07.750][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-21 23:59:07.752][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-21 23:59:07.755][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-21 23:59:07.758][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-21 23:59:07.760][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-21 23:59:07.763][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-21 23:59:07.765][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-21 23:59:07.768][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-21 23:59:07.770][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-21 23:59:07.771][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-21 23:59:07.773][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-21 23:59:07.774][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-21 23:59:07.776][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-21 23:59:07.778][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-21 23:59:07.779][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-21 23:59:07.781][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-21 23:59:07.782][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-21 23:59:07.784][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-21 23:59:07.786][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-21 23:59:07.787][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-21 23:59:07.789][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-21 23:59:07.790][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-21 23:59:07.792][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-21 23:59:07.794][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-21 23:59:07.795][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-21 23:59:07.797][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-21 23:59:07.799][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-21 23:59:07.800][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-21 23:59:07.802][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-21 23:59:07.804][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-21 23:59:07.805][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-21 23:59:07.807][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-21 23:59:07.808][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-21 23:59:07.810][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-21 23:59:07.812][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-21 23:59:07.813][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-21 23:59:07.815][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-21 23:59:07.816][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-21 23:59:07.818][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-21 23:59:07.819][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-21 23:59:07.821][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-21 23:59:07.823][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-21 23:59:07.824][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-21 23:59:07.826][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-21 23:59:07.828][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-21 23:59:07.829][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-21 23:59:07.831][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-21 23:59:07.833][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-21 23:59:07.834][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-21 23:59:07.836][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-21 23:59:07.837][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-21 23:59:07.839][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-21 23:59:07.840][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-21 23:59:07.842][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-21 23:59:07.844][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-21 23:59:07.845][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-21 23:59:07.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-21 23:59:07.848][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-21 23:59:07.850][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-21 23:59:07.852][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-21 23:59:07.854][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-21 23:59:07.856][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-21 23:59:07.857][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.859][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.893][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[2024-07-21 23:59:07.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:07.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-21 23:59:07.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:07.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:07.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:07.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:07.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:07.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-21 23:59:08.002][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-21 23:59:08.004][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:08.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:08.007][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-21 23:59:08.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:08.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-21 23:59:08.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:08.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-21 23:59:08.014][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:08.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-21 23:59:08.017][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-21 23:59:08.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-21 23:59:08.019][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:08.021][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-21 23:59:08.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-21 23:59:08.023][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-21 23:59:08.025][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-21 23:59:08.026][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-21 23:59:08.026][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-21 23:59:08.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-21 23:59:08.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:08.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:08.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-21 23:59:08.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-21 23:59:08.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-21 23:59:08.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-21 23:59:08.036][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-21 23:59:08.036][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-21 23:59:08.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-21 23:59:08.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-21 23:59:08.039][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-21 23:59:08.041][self$setPropertyValue]
biodb.DEBUG[2024-07-21 23:59:08.047][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-21 23:59:08.048][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-21 23:59:08.052][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:08.054][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-21 23:59:08.055][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-21 23:59:08.057][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-21 23:59:08.059][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:59:08.060][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-21 23:59:08.062][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-21 23:59:08.063][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-21 23:59:08.065][biodb::testThat]
biodb.INFO [2024-07-21 23:59:08.067][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-07-21 23:59:08.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-21 23:59:08.070][biodb::testThat]
biodb.DEBUG[2024-07-21 23:59:08.076][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-07-21 23:59:08.084][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-21 23:59:08.086][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-07-21 23:59:08.088][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-21 23:59:08.214][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-07-21 23:59:09.904][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-07-21 23:59:09.907][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-21 23:59:09.910][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-07-21 23:59:09.913][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-21 23:59:09.920][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-07-21 23:59:09.922][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-21 23:59:09.924][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-21 23:59:09.927][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-21 23:59:09.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:09.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:09.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:09.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:09.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:09.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:09.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:09.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:09.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:09.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:09.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:09.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:09.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:09.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:09.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:09.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:09.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:09.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:59:09.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:09.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:09.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:09.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:09.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:09.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:09.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:10.000][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:10.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:10.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.005][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:10.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-21 23:59:10.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-21 23:59:10.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-21 23:59:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-21 23:59:10.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-21 23:59:10.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-21 23:59:10.070][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-07-21 23:59:10.071][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-21 23:59:10.074][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-21 23:59:10.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:10.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:10.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:10.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:10.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:10.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:10.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:10.109][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-07-21 23:59:10.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-21 23:59:10.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:10.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:10.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:10.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:10.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:10.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-21 23:59:10.154][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-07-21 23:59:10.155][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-07-21 23:59:10.156][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-07-21 23:59:10.191][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-21 23:59:10.192][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-21 23:59:10.194][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-21 23:59:10.195][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-21 23:59:10.196][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-21 23:59:10.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-21 23:59:10.199][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-21 23:59:10.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-21 23:59:10.201][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-21 23:59:10.202][FUN] Functions in observer 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 98 ]
══ 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 98 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 3.28 | 1.98 | 80.35 | |
| LipidmapsStructureEntry | 0.56 | 0.00 | 0.56 | |