| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:41 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz |
| StartedAt: 2024-06-26 23:27:34 -0400 (Wed, 26 Jun 2024) |
| EndedAt: 2024-06-26 23:33:00 -0400 (Wed, 26 Jun 2024) |
| EllapsedTime: 326.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.4.0 (2024-04-24 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 3.98 2.38 93.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
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
'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log'
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library 'F:/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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 [2024-06-26 23:30:55.015][biodb::testContext]
biodb.INFO [2024-06-26 23:30:55.020][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:30:55.023][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-26 23:30:55.025][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:30:55.027][biodb::testContext]
biodb.INFO [2024-06-26 23:30:55.037][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:30:55.040][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 23:30:55.050][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:30:55.052][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 23:30:55.054][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.060][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 23:30:55.099][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.105][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 23:30:55.107][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.111][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 23:30:55.113][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 23:30:55.114][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 23:30:55.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.119][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 23:30:55.120][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 23:30:55.121][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.126][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 23:30:55.127][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 23:30:55.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.132][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 23:30:55.133][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 23:30:55.135][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 23:30:55.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.139][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 23:30:55.140][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.145][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 23:30:55.147][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 23:30:55.148][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 23:30:55.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.153][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:30:55.155][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 23:30:55.156][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 23:30:55.157][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 23:30:55.159][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 23:30:55.162][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 23:30:55.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.167][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 23:30:55.168][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 23:30:55.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.173][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 23:30:55.174][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 23:30:55.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.177][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[2024-06-26 23:30:55.179][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 23:30:55.180][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 23:30:55.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.185][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 23:30:55.186][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 23:30:55.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.190][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 23:30:55.192][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 23:30:55.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.201][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:30:55.202][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 23:30:55.207][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 23:30:55.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.215][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 23:30:55.217][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 23:30:55.219][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 23:30:55.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.230][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 23:30:55.283][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.309][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-26 23:30:55.311][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:30:55.316][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.318][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.324][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:30:55.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:30:55.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.330][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 23:30:55.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:30:55.334][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.338][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:30:55.338][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:30:55.338][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:30:55.338][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:30:55.338][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:30:55.340][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:30:55.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:30:55.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.363][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.365][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.367][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:30:55.368][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:30:55.370][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.372][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.374][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 23:30:55.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.379][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:30:55.381][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:30:55.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.393][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:30:55.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:30:55.397][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.398][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 23:30:55.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:30:55.401][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.403][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:30:55.403][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:30:55.403][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:30:55.403][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:30:55.403][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:30:55.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:30:55.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:30:55.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.414][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:30:55.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:30:55.418][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.419][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.420][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 23:30:55.422][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.424][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-26 23:30:55.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:30:55.427][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.429][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.430][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.433][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:30:55.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:30:55.435][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.436][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 23:30:55.438][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:30:55.439][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.440][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.442][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:30:55.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:30:55.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.452][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:30:55.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:30:55.455][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.457][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.458][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 23:30:55.460][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.461][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:30:55.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:30:55.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.470][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:30:55.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:30:55.473][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.474][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 23:30:55.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:30:55.477][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.478][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:55.479][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.481][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:30:55.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:30:55.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:55.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:55.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:30:55.489][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:30:55.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:30:55.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:55.495][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:55.498][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:30:55.499][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.648][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 23:30:55.653][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 23:30:55.654][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 23:30:55.656][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 23:30:55.658][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 23:30:55.660][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 23:30:55.663][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 23:30:55.665][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 23:30:55.668][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 23:30:55.670][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 23:30:55.673][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 23:30:55.676][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 23:30:55.679][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 23:30:55.681][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 23:30:55.684][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 23:30:55.687][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:30:55.689][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 23:30:55.693][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 23:30:55.695][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 23:30:55.698][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 23:30:55.701][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 23:30:55.704][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 23:30:55.706][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 23:30:55.708][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 23:30:55.709][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 23:30:55.711][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 23:30:55.712][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 23:30:55.714][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 23:30:55.716][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 23:30:55.718][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 23:30:55.719][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 23:30:55.721][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 23:30:55.722][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 23:30:55.724][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 23:30:55.726][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 23:30:55.728][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 23:30:55.730][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 23:30:55.732][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 23:30:55.734][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 23:30:55.736][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 23:30:55.738][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 23:30:55.740][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 23:30:55.743][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 23:30:55.746][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 23:30:55.749][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 23:30:55.751][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 23:30:55.754][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 23:30:55.757][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 23:30:55.760][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 23:30:55.762][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 23:30:55.765][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 23:30:55.768][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 23:30:55.770][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 23:30:55.772][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 23:30:55.774][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 23:30:55.776][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 23:30:55.777][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 23:30:55.779][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 23:30:55.781][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 23:30:55.782][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 23:30:55.784][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 23:30:55.785][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 23:30:55.787][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 23:30:55.789][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 23:30:55.790][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 23:30:55.793][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 23:30:55.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 23:30:55.797][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 23:30:55.798][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 23:30:55.800][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 23:30:55.802][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 23:30:55.803][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 23:30:55.805][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 23:30:55.806][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 23:30:55.808][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 23:30:55.810][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 23:30:55.811][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 23:30:55.813][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 23:30:55.814][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 23:30:55.816][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 23:30:55.818][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 23:30:55.819][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 23:30:55.821][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 23:30:55.860][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 23:30:55.864][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:30:55.869][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:30:55.871][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.873][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.874][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[2024-06-26 23:30:55.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.886][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[2024-06-26 23:30:55.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.893][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[2024-06-26 23:30:55.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.941][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[2024-06-26 23:30:55.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.966][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[2024-06-26 23:30:55.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:55.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:55.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:55.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:55.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:55.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:55.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:55.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:56.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:56.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:56.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:56.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:56.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:56.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:56.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:56.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:56.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:56.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:56.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:56.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:56.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:56.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:56.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:56.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:56.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:56.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:56.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:30:56.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:56.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:56.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:56.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:56.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:30:56.036][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 23:30:56.046][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:30:56.049][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:56.050][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 23:30:56.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:56.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:30:56.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:56.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:30:56.058][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:56.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:30:56.062][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:30:56.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:30:56.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:56.069][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 23:30:56.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 23:30:56.072][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 23:30:56.073][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 23:30:56.074][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:30:56.074][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:30:56.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:30:56.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:56.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:56.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:30:56.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:30:56.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:30:56.083][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:30:56.084][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:30:56.084][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 23:30:56.085][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:30:56.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:30:56.087][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 23:30:56.089][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:30:56.094][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 23:30:56.096][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:30:56.119][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:30:56.120][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 23:30:56.124][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:30:56.128][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 23:30:56.134][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:30:56.136][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:30:56.139][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 23:30:56.142][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 23:30:56.153][biodb::testThat]
biodb.INFO [2024-06-26 23:30:56.154][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-26 23:30:56.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:56.157][biodb::testThat]
biodb.TRACE[2024-06-26 23:30:56.165][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-26 23:30:56.168][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 23:30:56.185][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:30:56.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:30:56.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:56.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:56.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:56.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:56.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:56.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:30:56.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:30:56.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:30:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.305][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:30:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:30:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:30:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:30:56.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.322][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:56.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:56.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:56.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:30:56.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:56.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:30:56.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:56.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:56.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:56.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:56.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:30:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 23:30:56.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.520][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:30:56.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.638][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:30:56.698][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-26 23:30:56.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:56.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:56.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:56.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:56.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.858][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.864][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.869][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:56.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.901][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:56.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:56.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.962][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:56.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:56.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.988][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.994][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:56.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.004][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.006][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.054][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.060][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.063][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.105][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.124][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.129][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.135][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.140][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.143][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.145][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.164][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.165][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.177][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.179][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.190][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.192][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.213][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.222][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.223][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.226][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.233][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.235][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.237][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 23:30:57.252][biodb::testThat]
biodb.INFO [2024-06-26 23:30:57.254][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-26 23:30:57.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:57.256][biodb::testThat]
biodb.DEBUG[2024-06-26 23:30:57.270][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-26 23:30:57.277][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 23:30:57.284][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-26 23:30:57.286][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:30:57.290][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-26 23:30:57.292][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 23:30:57.317][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 23:30:57.319][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:30:57.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:30:57.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:30:57.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:30:57.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:30:57.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:30:57.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:30:57.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:30:57.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:30:57.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:30:57.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:30:57.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:30:57.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.365][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:30:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:30:57.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:30:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:30:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:30:57.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:30:57.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.404][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:30:57.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:30:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:30:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:30:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.439][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:30:57.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.444][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 23:30:57.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.460][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:30:57.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.516][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:30:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:30:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:30:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:30:57.554][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-26 23:30:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-26 23:30:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-26 23:30:57.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-26 23:30:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-26 23:30:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-26 23:30:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-26 23:30:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:30:57.595][biodb::testThat]
biodb.INFO [2024-06-26 23:30:57.596][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-26 23:30:57.598][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:57.599][biodb::testThat]
biodb.TRACE[2024-06-26 23:30:57.608][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.612][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:30:57.614][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-26 23:30:57.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:57.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:57.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:57.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:30:57.678][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 23:30:57.683][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 23:30:57.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:30:57.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:30:57.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-26 23:30:58.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-06-26 23:30:58.310][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:30:58.312][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:30:58.314][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-26 23:30:58.905][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:30:58.909][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-26 23:30:58.935][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-26 23:30:58.939][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-26 23:30:58.975][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:58.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:30:58.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:58.979][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 23:30:58.993][biodb::testThat]
biodb.INFO [2024-06-26 23:30:58.995][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-26 23:30:59.004][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:59.006][biodb::testThat]
biodb.TRACE[2024-06-26 23:30:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:59.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:59.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:30:59.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:30:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:30:59.189][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 23:30:59.193][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:30:59.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 23:30:59.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:30:59.213][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-26 23:30:59.271][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.273][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-26 23:30:59.274][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:59.275][biodb::testThat]
biodb.TRACE[2024-06-26 23:30:59.311][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.321][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:59.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:59.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:59.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:59.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.403][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 23:30:59.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 23:30:59.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:30:59.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 23:30:59.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:30:59.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:30:59.450][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.452][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-26 23:30:59.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:59.454][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.467][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.469][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-26 23:30:59.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:59.471][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.493][biodb::testThat]
biodb.INFO [2024-06-26 23:30:59.495][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-26 23:30:59.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:30:59.498][biodb::testThat]
biodb.DEBUG[2024-06-26 23:30:59.505][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-26 23:30:59.797][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-26 23:31:00.628][biodb::testThat]
biodb.INFO [2024-06-26 23:31:00.630][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-26 23:31:00.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:00.634][biodb::testThat]
biodb.TRACE[2024-06-26 23:31:00.661][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:00.663][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:00.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:00.665][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:00.666][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:00.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:00.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:00.670][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 23:31:00.673][biodb::testThat]
biodb.INFO [2024-06-26 23:31:00.674][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-06-26 23:31:00.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:00.676][biodb::testThat]
biodb.TRACE[2024-06-26 23:31:00.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:00.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:00.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:00.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:00.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:00.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:00.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:00.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:00.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:00.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:00.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:00.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:00.878][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 23:31:00.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:31:00.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 23:31:00.886][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:31:00.888][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-26 23:31:00.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 23:31:00.970][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:31:00.972][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 23:31:00.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:31:00.977][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-26 23:31:01.023][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 23:31:01.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 23:31:01.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:01.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:01.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:01.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:01.125][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-26 23:31:01.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:01.147][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:01.167][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-26 23:31:01.456][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-26 23:31:01.458][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:01.460][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:01.462][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-26 23:31:07.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:07.162][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-26 23:31:07.304][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-26 23:31:09.782][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-26 23:31:09.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:09.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:09.794][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-26 23:31:10.096][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-26 23:31:10.098][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:10.102][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:10.105][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-26 23:31:10.696][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:10.701][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-26 23:31:10.713][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-26 23:31:10.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-26 23:31:10.782][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:10.785][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:10.787][rule$waitAsNeeded] Wait 0.006706 second(s).
biodb.TRACE[2024-06-26 23:31:10.806][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-26 23:31:11.100][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06 does not exist.
biodb.TRACE[2024-06-26 23:31:11.103][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:11.106][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:11.109][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-26 23:31:11.698][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:11.703][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-26 23:31:11.711][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-26 23:31:11.778][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:11.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:11.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:31:11.811][biodb::testThat]
biodb.INFO [2024-06-26 23:31:11.812][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-26 23:31:11.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:11.815][biodb::testThat]
biodb.TRACE[2024-06-26 23:31:11.820][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 23:31:11.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 23:31:11.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:11.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:11.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:11.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:11.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:11.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:11.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:11.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:11.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:11.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:11.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:11.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:11.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:11.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:11.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:11.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-26 23:31:11.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:11.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:11.919][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-26 23:31:12.216][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2024-06-26 23:31:12.218][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:12.220][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:12.222][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-26 23:31:17.732][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:17.737][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-26 23:31:17.841][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-26 23:31:19.509][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-26 23:31:19.561][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 23:31:19.563][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-26 23:31:19.565][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-06-26 23:31:19.577][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-26 23:31:19.579][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 23:31:19.580][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:31:19.581][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 23:31:19.583][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 23:31:19.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:19.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:19.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:19.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:19.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:19.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:19.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:19.607][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-26 23:31:19.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:19.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:19.613][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-26 23:31:19.909][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:19.911][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:19.913][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:19.916][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-26 23:31:20.538][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:20.543][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-26 23:31:20.550][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-26 23:31:20.556][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-26 23:31:20.560][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 23:31:20.563][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 23:31:20.566][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:31:20.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:20.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:20.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:20.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:20.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:20.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:20.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:20.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:31:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:31:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.633][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:31:20.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:31:20.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.646][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.669][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:31:20.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:20.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.676][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:31:20.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:20.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:31:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:31:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:31:20.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:31:20.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.719][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:31:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.725][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 23:31:20.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:31:20.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:20.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:20.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:20.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:20.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:20.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:20.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:20.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 23:31:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.836][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:31:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 23:31:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:31:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 23:31:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.848][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 23:31:20.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 23:31:20.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.875][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:31:20.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:20.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 23:31:20.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:20.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.889][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:31:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:31:20.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 23:31:20.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 23:31:20.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.915][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:31:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 23:31:20.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:31:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.959][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 23:31:20.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:31:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.964][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:20.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:20.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:20.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:20.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:20.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:21.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:21.064][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-26 23:31:21.077][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 23:31:21.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:21.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:21.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:21.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:21.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:21.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:21.104][FUN] Functions in observer BiodbConfig: [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[2024-06-26 23:31:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.119][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.120][private$selectFields]
biodb.TRACE[2024-06-26 23:31:21.121][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:21.122][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:21.123][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.125][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.126][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.130][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.131][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.134][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.135][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.136][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.137][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.139][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.142][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.149][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.173][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 23:31:21.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:21.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:21.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:21.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:21.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:21.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:21.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:21.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.249][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.256][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.257][private$selectFields]
biodb.TRACE[2024-06-26 23:31:21.258][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:21.259][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:21.261][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.262][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.264][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.266][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.267][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.269][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.271][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.273][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.274][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.275][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.277][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.280][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:21.281][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.292][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.297][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 23:31:21.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:21.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:21.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:21.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:21.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:21.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:21.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:21.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.668][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.670][private$selectFields]
biodb.TRACE[2024-06-26 23:31:21.672][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:21.674][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:21.676][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.678][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.680][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.684][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.686][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.692][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.694][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.696][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:21.698][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.700][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.704][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.705][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:21.708][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:21.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.734][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 23:31:21.736][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 23:31:21.738][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 23:31:21.756][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:21.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:21.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:31:21.798][biodb::testThat]
biodb.INFO [2024-06-26 23:31:21.800][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-26 23:31:21.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:21.803][biodb::testThat]
biodb.TRACE[2024-06-26 23:31:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 23:31:21.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 23:31:21.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:21.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:21.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:21.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:21.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:21.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:21.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:21.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:21.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:21.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:21.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:21.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:21.959][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-26 23:31:21.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:21.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:21.967][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-26 23:31:22.267][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2024-06-26 23:31:22.269][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:22.273][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:22.276][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-26 23:31:27.635][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:31:27.640][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-26 23:31:27.743][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-26 23:31:29.514][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 23:31:29.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:29.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:29.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:29.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:29.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:29.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:29.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.608][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.610][private$selectFields]
biodb.TRACE[2024-06-26 23:31:29.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:29.612][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:29.613][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.615][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.616][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.619][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.620][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.621][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.624][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.625][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.636][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.638][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.639][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.642][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.643][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.654][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.660][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 23:31:29.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:29.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:29.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:29.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:29.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:29.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:29.690][FUN] Functions in observer BiodbConfig: [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[2024-06-26 23:31:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.702][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.703][private$selectFields]
biodb.TRACE[2024-06-26 23:31:29.704][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:29.705][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:29.707][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.708][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.709][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.713][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.714][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.718][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.719][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.720][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.722][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.725][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:29.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.742][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 23:31:29.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:29.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:29.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:29.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:29.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:29.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:29.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.782][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.783][private$selectFields]
biodb.TRACE[2024-06-26 23:31:29.785][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:29.786][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:29.787][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.788][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.790][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.792][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.793][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.799][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.800][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:29.801][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.802][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.805][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.806][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.818][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:29.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.823][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 23:31:29.825][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 23:31:29.826][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 23:31:29.849][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:29.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:31:29.862][biodb::testThat]
biodb.INFO [2024-06-26 23:31:29.864][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-26 23:31:29.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:29.868][biodb::testThat]
biodb.TRACE[2024-06-26 23:31:29.874][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 23:31:29.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 23:31:29.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:29.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 23:31:29.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:29.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:31:29.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:29.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:29.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:29.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:29.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:29.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:29.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:29.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:29.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:29.987][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-26 23:31:29.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:31:29.993][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-26 23:31:29.995][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:31:30.135][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-26 23:31:31.893][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 23:31:31.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:31.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:31.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:31.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:31.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:31.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:31.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:31.927][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.944][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:31.946][private$selectFields]
biodb.TRACE[2024-06-26 23:31:31.948][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:31.950][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:31.952][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:31.954][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.956][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.962][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.965][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.971][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:31.973][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:31.975][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.977][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.983][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:31.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:31.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:31.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:31.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.010][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 23:31:32.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:32.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:32.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:32.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:32.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:32.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:32.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:32.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.039][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.044][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.045][private$selectFields]
biodb.TRACE[2024-06-26 23:31:32.046][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:32.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:32.049][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.050][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.051][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.054][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.055][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.056][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.060][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.061][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.062][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.064][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.068][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:32.070][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.085][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 23:31:32.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:32.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:32.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:32.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:32.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:32.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:32.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:32.104][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.120][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.122][private$selectFields]
biodb.TRACE[2024-06-26 23:31:32.124][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 23:31:32.126][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 23:31:32.128][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.130][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.132][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.138][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.141][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.144][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.145][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.147][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 23:31:32.148][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.150][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.152][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.154][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 23:31:32.155][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.165][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:32.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:32.171][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 23:31:32.172][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 23:31:32.173][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 23:31:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:32.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 23:31:32.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:32.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 23:31:32.248][biodb::testThat]
biodb.INFO [2024-06-26 23:31:32.250][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-06-26 23:31:32.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:32.254][biodb::testThat]
biodb.DEBUG[2024-06-26 23:31:32.257][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-26 23:31:32.259][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 23:31:32.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.INFO [2024-06-26 23:31:32.265][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-26 23:31:32.268][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 23:31:32.270][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 23:31:32.272][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 23:31:32.275][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:31:32.277][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 23:31:32.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 23:31:32.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:32.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:32.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:32.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:32.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:32.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:32.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:32.346][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-26 23:31:32.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:32.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:32.356][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:32.649][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:32.650][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:32.652][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[2024-06-26 23:31:32.653][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:33.246][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:33.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:33.249][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:33.251][rule$waitAsNeeded] Wait 0.104423 second(s).
biodb.TRACE[2024-06-26 23:31:33.370][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:33.667][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:33.669][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:33.670][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:33.672][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:34.264][private$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[2024-06-26 23:31:34.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:34.269][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:34.271][rule$waitAsNeeded] Wait 0.0989959 second(s).
biodb.TRACE[2024-06-26 23:31:34.388][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:34.689][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:34.691][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:34.693][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[2024-06-26 23:31:34.696][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:35.297][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:35.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:35.302][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:35.304][rule$waitAsNeeded] Wait 0.083715 second(s).
biodb.TRACE[2024-06-26 23:31:35.405][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:35.708][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:35.710][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:35.712][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:35.715][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:36.518][private$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[2024-06-26 23:31:36.521][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:36.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:36.526][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:36.823][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:36.825][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:36.827][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:36.829][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:37.426][private$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[2024-06-26 23:31:37.429][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:37.431][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:37.433][rule$waitAsNeeded] Wait 0.092387 second(s).
biodb.TRACE[2024-06-26 23:31:37.534][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:37.840][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:37.842][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:37.845][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[2024-06-26 23:31:37.847][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:38.444][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:38.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:38.447][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:38.449][rule$waitAsNeeded] Wait 0.084861 second(s).
biodb.TRACE[2024-06-26 23:31:38.552][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:38.855][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:38.857][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:38.859][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:38.862][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:39.449][private$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[2024-06-26 23:31:39.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:39.454][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:39.457][rule$waitAsNeeded] Wait 0.093976 second(s).
biodb.TRACE[2024-06-26 23:31:39.556][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:39.857][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:39.881][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:39.885][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[2024-06-26 23:31:39.886][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:40.485][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:40.487][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:40.489][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:40.491][rule$waitAsNeeded] Wait 0.0641451 second(s).
biodb.TRACE[2024-06-26 23:31:40.562][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:40.850][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:40.852][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:40.853][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:40.854][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:41.442][private$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[2024-06-26 23:31:41.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:41.445][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:41.446][rule$waitAsNeeded] Wait 0.114355 second(s).
biodb.TRACE[2024-06-26 23:31:41.567][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 23:31:41.863][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:41.865][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:41.867][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[2024-06-26 23:31:41.869][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 23:31:42.463][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.INFO [2024-06-26 23:31:42.467][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-26 23:31:42.471][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-26 23:31:42.474][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 23:31:42.477][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 23:31:42.480][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:31:42.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:42.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:42.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:42.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:42.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:42.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:42.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:31:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:42.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:31:42.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:31:42.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:31:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:31:42.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:31:42.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:31:42.558][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-26 23:31:42.559][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-26 23:31:42.587][biodb::testThat]
biodb.INFO [2024-06-26 23:31:42.588][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-26 23:31:42.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:31:42.591][biodb::testThat]
biodb.DEBUG[2024-06-26 23:31:42.606][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-26 23:31:42.608][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-26 23:31:42.609][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 23:31:42.611][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-26 23:31:42.613][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-26 23:31:42.615][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 23:31:42.616][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 23:31:42.618][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:31:42.619][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 23:31:42.620][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 23:31:42.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:42.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:42.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:42.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:42.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:42.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:42.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:42.652][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-26 23:31:42.655][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:42.657][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:31:42.658][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:42.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:42.946][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:42.947][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[2024-06-26 23:31:42.949][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:43.542][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:43.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:43.545][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:43.546][rule$waitAsNeeded] Wait 0.11183 second(s).
biodb.TRACE[2024-06-26 23:31:43.667][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:43.964][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:43.965][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:43.967][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:43.968][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:44.561][private$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[2024-06-26 23:31:44.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:44.566][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:44.568][rule$waitAsNeeded] Wait 0.0985229 second(s).
biodb.TRACE[2024-06-26 23:31:44.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:45.009][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:45.011][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:45.013][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[2024-06-26 23:31:45.015][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:45.642][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:45.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:45.647][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:45.649][rule$waitAsNeeded] Wait 0.0356908 second(s).
biodb.TRACE[2024-06-26 23:31:45.687][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:46.020][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:46.022][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:46.024][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:46.026][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:46.661][private$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[2024-06-26 23:31:46.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:46.665][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:46.667][rule$waitAsNeeded] Wait 0.0196109 second(s).
biodb.TRACE[2024-06-26 23:31:46.691][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:47.030][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:47.032][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:47.034][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[2024-06-26 23:31:47.037][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:47.659][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:47.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:47.662][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:47.664][rule$waitAsNeeded] Wait 0.0258429 second(s).
biodb.TRACE[2024-06-26 23:31:47.695][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:47.996][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:47.997][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:47.999][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:48.000][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:48.590][private$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[2024-06-26 23:31:48.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:48.595][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:48.597][rule$waitAsNeeded] Wait 0.0973909 second(s).
biodb.TRACE[2024-06-26 23:31:48.698][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:49.014][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:49.016][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:49.017][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:49.019][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:49.608][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:49.609][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:49.610][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:49.612][rule$waitAsNeeded] Wait 0.0856702 second(s).
biodb.TRACE[2024-06-26 23:31:49.701][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:50.001][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:50.003][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:50.004][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:50.006][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:50.594][private$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[2024-06-26 23:31:50.597][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:50.599][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:50.601][rule$waitAsNeeded] Wait 0.099448 second(s).
biodb.TRACE[2024-06-26 23:31:50.702][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:50.990][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:50.992][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:50.995][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[2024-06-26 23:31:50.997][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:51.599][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:51.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:51.603][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:51.605][rule$waitAsNeeded] Wait 0.096452 second(s).
biodb.TRACE[2024-06-26 23:31:51.705][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 23:31:52.000][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:52.002][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:52.004][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:52.006][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 23:31:52.599][private$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[2024-06-26 23:31:52.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:31:52.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:31:52.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:31:52.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:31:52.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:31:52.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:31:52.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:31:52.629][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-26 23:31:52.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:52.634][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:52.635][rule$waitAsNeeded] Wait 0.0686238 second(s).
biodb.TRACE[2024-06-26 23:31:52.707][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:52.996][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:52.997][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:52.999][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:53.000][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:53.602][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:53.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:53.606][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:53.609][rule$waitAsNeeded] Wait 0.098434 second(s).
biodb.TRACE[2024-06-26 23:31:53.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:54.005][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:54.007][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:54.008][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:54.010][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:54.604][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:54.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:54.608][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:54.611][rule$waitAsNeeded] Wait 0.0987041 second(s).
biodb.TRACE[2024-06-26 23:31:54.728][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:55.023][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:55.024][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:55.026][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:55.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:55.622][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:55.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:55.627][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:55.629][rule$waitAsNeeded] Wait 0.0985899 second(s).
biodb.TRACE[2024-06-26 23:31:55.746][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:56.039][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:56.041][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:56.044][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:56.046][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:56.641][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:56.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:56.645][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:56.648][rule$waitAsNeeded] Wait 0.097677 second(s).
biodb.TRACE[2024-06-26 23:31:56.764][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:57.063][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:57.065][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:57.067][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:57.070][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:57.659][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:57.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:57.663][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:57.665][rule$waitAsNeeded] Wait 0.0980899 second(s).
biodb.TRACE[2024-06-26 23:31:57.766][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:58.064][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:58.067][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:58.069][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:58.071][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:58.668][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:58.671][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:58.674][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:58.677][rule$waitAsNeeded] Wait 0.089247 second(s).
biodb.TRACE[2024-06-26 23:31:58.773][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:31:59.064][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:31:59.066][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:31:59.067][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:31:59.069][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:31:59.668][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:31:59.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:31:59.672][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:31:59.675][rule$waitAsNeeded] Wait 0.0979309 second(s).
biodb.TRACE[2024-06-26 23:31:59.791][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:32:00.094][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:00.096][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:00.098][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:00.101][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:32:00.905][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:00.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:00.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:00.913][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:32:01.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:01.233][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:01.235][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:01.236][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:32:01.830][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:01.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:01.834][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:01.837][rule$waitAsNeeded] Wait 0.076273 second(s).
biodb.TRACE[2024-06-26 23:32:01.922][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 23:32:02.221][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:02.223][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:02.226][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:02.228][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 23:32:02.832][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-26 23:32:02.836][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-26 23:32:02.840][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 23:32:02.843][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 23:32:02.844][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:32:02.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:02.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:02.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:02.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:02.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:02.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:02.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:02.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:32:02.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:02.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:02.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:02.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:02.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:02.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:02.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:02.922][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.930][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:02.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:02.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:02.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:02.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:03.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:03.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:03.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:03.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:03.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:03.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:32:03.009][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-26 23:32:03.010][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-26 23:32:03.012][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-26 23:32:03.381][biodb::testThat]
biodb.INFO [2024-06-26 23:32:03.383][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-06-26 23:32:03.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:03.387][biodb::testThat]
biodb.INFO [2024-06-26 23:32:03.476][biodb::testThat]
biodb.INFO [2024-06-26 23:32:03.478][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-06-26 23:32:03.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:03.482][biodb::testThat]
biodb.INFO [2024-06-26 23:32:03.513][biodb::testThat]
biodb.INFO [2024-06-26 23:32:03.515][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-06-26 23:32:03.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:03.519][biodb::testThat]
biodb.DEBUG[2024-06-26 23:32:03.525][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[2024-06-26 23:32:03.531][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:03.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:03.537][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-26 23:32:03.837][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-06-26 23:32:03.839][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:03.842][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:03.845][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-26 23:32:09.672][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:09.675][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-26 23:32:10.062][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-26 23:32:11.979][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 23:32:11.982][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 23:32:11.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:11.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:11.987][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:32:11.990][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 23:32:11.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:11.993][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 23:32:11.997][biodb::testThat]
biodb.INFO [2024-06-26 23:32:11.999][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-26 23:32:12.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:12.003][biodb::testThat]
biodb.ERROR[2024-06-26 23:32:12.039][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-26 23:32:12.067][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-26 23:32:12.102][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 23:32:12.103][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 23:32:12.105][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 23:32:12.106][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 23:32:12.108][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.110][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.112][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 23:32:12.124][biodb::testContext]
biodb.INFO [2024-06-26 23:32:12.126][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:32:12.127][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-26 23:32:12.128][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:32:12.129][biodb::testContext]
biodb.INFO [2024-06-26 23:32:12.132][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:32:12.137][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 23:32:12.143][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:12.144][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 23:32:12.146][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.150][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[2024-06-26 23:32:12.151][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 23:32:12.153][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.157][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 23:32:12.159][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.164][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 23:32:12.165][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 23:32:12.166][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 23:32:12.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.171][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 23:32:12.172][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 23:32:12.173][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.177][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[2024-06-26 23:32:12.178][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 23:32:12.180][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 23:32:12.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.184][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 23:32:12.185][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 23:32:12.187][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 23:32:12.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.191][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 23:32:12.192][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.197][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 23:32:12.198][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 23:32:12.200][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 23:32:12.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.204][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:32:12.206][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 23:32:12.207][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 23:32:12.208][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 23:32:12.209][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 23:32:12.211][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 23:32:12.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.215][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 23:32:12.217][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 23:32:12.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.221][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 23:32:12.223][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 23:32:12.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.229][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 23:32:12.230][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 23:32:12.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.234][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[2024-06-26 23:32:12.235][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 23:32:12.236][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 23:32:12.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.241][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 23:32:12.242][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 23:32:12.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.247][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:32:12.248][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 23:32:12.252][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 23:32:12.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.257][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 23:32:12.259][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 23:32:12.260][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 23:32:12.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.265][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 23:32:12.267][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.268][self$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[2024-06-26 23:32:12.269][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.270][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:12.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.277][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:12.278][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:12.279][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.280][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 23:32:12.282][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:12.283][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.284][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.285][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:12.285][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:12.285][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:32:12.285][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:32:12.285][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:32:12.287][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:12.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:12.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.295][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.297][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:12.298][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:12.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.300][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.302][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 23:32:12.305][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.306][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:32:12.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:12.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.313][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.315][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:32:12.316][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:12.318][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.319][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 23:32:12.320][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:12.321][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.323][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.324][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:12.324][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:12.324][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:32:12.324][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:32:12.324][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:32:12.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:12.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.329][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:12.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.332][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.333][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.335][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:12.336][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:12.337][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.338][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.340][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 23:32:12.342][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.343][self$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[2024-06-26 23:32:12.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:12.346][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.352][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:12.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:12.354][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.355][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 23:32:12.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:12.358][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.359][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.360][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.361][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:12.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:12.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.370][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:12.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:12.373][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.388][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.390][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 23:32:12.392][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.394][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:32:12.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:12.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.399][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.403][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:32:12.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:12.405][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.406][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 23:32:12.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:12.409][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.410][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.411][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.412][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:12.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:12.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.423][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.424][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:12.425][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:12.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.428][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.430][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:12.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.473][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[2024-06-26 23:32:12.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.497][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[2024-06-26 23:32:12.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.534][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 23:32:12.536][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 23:32:12.538][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 23:32:12.540][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 23:32:12.542][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 23:32:12.544][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 23:32:12.545][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 23:32:12.547][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 23:32:12.549][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 23:32:12.551][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 23:32:12.552][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 23:32:12.554][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 23:32:12.556][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 23:32:12.558][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 23:32:12.559][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 23:32:12.561][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:32:12.563][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 23:32:12.565][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 23:32:12.566][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 23:32:12.568][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 23:32:12.570][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 23:32:12.572][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 23:32:12.574][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 23:32:12.575][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 23:32:12.577][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 23:32:12.579][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 23:32:12.580][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 23:32:12.582][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 23:32:12.584][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 23:32:12.586][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 23:32:12.587][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 23:32:12.589][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 23:32:12.591][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 23:32:12.592][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 23:32:12.594][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 23:32:12.596][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 23:32:12.597][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 23:32:12.599][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 23:32:12.601][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 23:32:12.602][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 23:32:12.604][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 23:32:12.606][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 23:32:12.608][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 23:32:12.609][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 23:32:12.611][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 23:32:12.613][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 23:32:12.614][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 23:32:12.616][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 23:32:12.618][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 23:32:12.619][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 23:32:12.621][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 23:32:12.623][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 23:32:12.624][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 23:32:12.626][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 23:32:12.628][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 23:32:12.629][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 23:32:12.631][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 23:32:12.633][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 23:32:12.634][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 23:32:12.636][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 23:32:12.638][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 23:32:12.639][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 23:32:12.641][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 23:32:12.643][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 23:32:12.644][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 23:32:12.646][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 23:32:12.648][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 23:32:12.649][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 23:32:12.651][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 23:32:12.653][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 23:32:12.654][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 23:32:12.656][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 23:32:12.658][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 23:32:12.659][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 23:32:12.661][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 23:32:12.663][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 23:32:12.664][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 23:32:12.666][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 23:32:12.668][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 23:32:12.669][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 23:32:12.671][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 23:32:12.673][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 23:32:12.674][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 23:32:12.676][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 23:32:12.679][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:32:12.680][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:12.681][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.684][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:12.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:12.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:12.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:12.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:12.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:12.877][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 23:32:12.881][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:12.884][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.887][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:12.894][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.898][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.900][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.902][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:12.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:12.906][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.909][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 23:32:12.911][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 23:32:12.913][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 23:32:12.915][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:12.917][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:12.917][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:12.919][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:12.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.925][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:12.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:12.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:12.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:12.934][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:32:12.934][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 23:32:12.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:12.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:12.941][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:12.943][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:12.945][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 23:32:12.948][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:32:12.954][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:12.956][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 23:32:12.959][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:12.962][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 23:32:12.964][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:32:12.967][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:32:12.970][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 23:32:12.972][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 23:32:12.975][biodb::testThat]
biodb.INFO [2024-06-26 23:32:12.978][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-26 23:32:12.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:12.982][biodb::testThat]
biodb.DEBUG[2024-06-26 23:32:12.989][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-26 23:32:12.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:13.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:13.004][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-26 23:32:13.306][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-06-26 23:32:13.308][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:13.312][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:13.315][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-26 23:32:13.899][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:13.904][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-26 23:32:13.912][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-26 23:32:14.464][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[2024-06-26 23:32:14.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:14.470][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:14.473][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-26 23:32:14.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2024-06-26 23:32:14.774][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:14.777][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:14.781][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-26 23:32:15.571][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:15.577][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-26 23:32:15.587][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-26 23:32:15.622][biodb::testThat]
biodb.INFO [2024-06-26 23:32:15.623][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-26 23:32:15.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:15.626][biodb::testThat]
biodb.INFO [2024-06-26 23:32:15.660][biodb::testThat]
biodb.INFO [2024-06-26 23:32:15.661][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-26 23:32:15.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:15.664][biodb::testThat]
biodb.DEBUG[2024-06-26 23:32:15.667][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-26 23:32:15.671][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:15.672][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:15.674][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-26 23:32:15.969][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-26 23:32:15.971][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:15.973][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:15.976][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-26 23:32:16.387][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:16.391][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-26 23:32:16.399][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-26 23:32:16.410][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[2024-06-26 23:32:16.417][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:32:16.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-26 23:32:16.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:32:16.431][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-26 23:32:16.442][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[2024-06-26 23:32:16.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:16.451][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:16.453][rule$waitAsNeeded] Wait 0.220872 second(s).
biodb.TRACE[2024-06-26 23:32:16.682][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-26 23:32:16.982][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-26 23:32:16.983][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:16.985][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:16.987][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-26 23:32:17.402][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:17.405][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-26 23:32:17.424][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-26 23:32:17.438][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[2024-06-26 23:32:17.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:17.444][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:17.445][rule$waitAsNeeded] Wait 0.234829 second(s).
biodb.TRACE[2024-06-26 23:32:17.683][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-26 23:32:17.977][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-06-26 23:32:17.978][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:17.980][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:17.982][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-26 23:32:19.449][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:19.452][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-26 23:32:19.471][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-26 23:32:19.674][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[2024-06-26 23:32:19.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:19.679][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:19.682][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-26 23:32:19.975][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-06-26 23:32:19.977][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:19.980][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:19.983][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-26 23:32:21.488][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 23:32:21.492][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-26 23:32:21.515][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-26 23:32:21.722][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 23:32:21.724][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 23:32:21.726][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 23:32:21.727][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 23:32:21.729][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:21.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:21.731][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:21.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:21.733][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 23:32:21.740][biodb::testContext]
biodb.INFO [2024-06-26 23:32:21.742][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:32:21.744][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-26 23:32:21.745][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 23:32:21.746][biodb::testContext]
biodb.INFO [2024-06-26 23:32:21.749][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:32:21.752][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 23:32:21.759][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:21.761][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 23:32:21.762][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.766][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[2024-06-26 23:32:21.767][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 23:32:21.769][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.775][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 23:32:21.777][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.782][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 23:32:21.784][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 23:32:21.785][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 23:32:21.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.789][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 23:32:21.791][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 23:32:21.792][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.796][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 23:32:21.798][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 23:32:21.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.802][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 23:32:21.804][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 23:32:21.805][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 23:32:21.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.809][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 23:32:21.811][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.815][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 23:32:21.817][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 23:32:21.818][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 23:32:21.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.821][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[2024-06-26 23:32:21.822][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:32:21.824][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 23:32:21.825][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 23:32:21.826][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 23:32:21.828][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 23:32:21.829][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 23:32:21.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.834][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 23:32:21.835][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 23:32:21.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.839][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[2024-06-26 23:32:21.840][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 23:32:21.841][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 23:32:21.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.846][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 23:32:21.847][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 23:32:21.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.852][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 23:32:21.853][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 23:32:21.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.858][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 23:32:21.860][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 23:32:21.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.864][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 23:32:21.866][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 23:32:21.870][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 23:32:21.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.875][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 23:32:21.876][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 23:32:21.877][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 23:32:21.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:21.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:21.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:21.882][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 23:32:21.884][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.886][self$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[2024-06-26 23:32:21.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:21.891][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.896][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:21.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:21.898][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.899][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 23:32:21.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:21.902][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.905][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:21.905][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:21.905][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:32:21.905][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:32:21.905][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:32:21.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:21.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:21.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.915][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:21.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:21.919][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.920][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.922][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 23:32:21.924][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.925][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:32:21.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:21.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.931][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.934][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:32:21.936][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:21.937][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.938][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 23:32:21.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:21.941][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:21.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:21.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 23:32:21.943][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 23:32:21.943][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 23:32:21.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:21.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:21.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.952][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.953][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.955][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:21.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:21.957][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.959][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.960][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 23:32:21.963][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.965][self$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[2024-06-26 23:32:21.966][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.968][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:21.969][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.972][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:21.974][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:21.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:21.977][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:21.978][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 23:32:21.981][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:21.984][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.987][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:21.988][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:21.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:21.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:21.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:21.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:21.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.001][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.003][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:22.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:22.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.009][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.010][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 23:32:22.012][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.013][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 23:32:22.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:22.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.041][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.043][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.044][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 23:32:22.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:22.047][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.048][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 23:32:22.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:22.050][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.052][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.053][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:22.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:22.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:22.059][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:22.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:22.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:22.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.064][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:22.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:22.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.069][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:22.072][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.133][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[2024-06-26 23:32:22.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.201][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 23:32:22.204][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 23:32:22.206][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 23:32:22.209][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 23:32:22.212][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 23:32:22.214][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 23:32:22.217][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 23:32:22.220][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 23:32:22.222][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 23:32:22.225][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 23:32:22.227][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 23:32:22.230][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 23:32:22.233][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 23:32:22.235][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 23:32:22.238][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 23:32:22.240][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:32:22.243][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 23:32:22.245][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 23:32:22.248][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 23:32:22.251][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 23:32:22.253][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 23:32:22.256][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 23:32:22.258][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 23:32:22.261][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 23:32:22.264][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 23:32:22.266][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 23:32:22.269][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 23:32:22.272][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 23:32:22.274][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 23:32:22.277][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 23:32:22.280][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 23:32:22.282][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 23:32:22.285][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 23:32:22.288][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 23:32:22.290][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 23:32:22.293][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 23:32:22.295][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 23:32:22.298][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 23:32:22.301][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 23:32:22.304][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 23:32:22.306][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 23:32:22.309][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 23:32:22.311][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 23:32:22.314][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 23:32:22.317][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 23:32:22.319][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 23:32:22.322][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 23:32:22.325][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 23:32:22.327][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 23:32:22.330][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 23:32:22.333][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 23:32:22.335][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 23:32:22.338][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 23:32:22.340][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 23:32:22.343][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 23:32:22.346][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 23:32:22.348][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 23:32:22.351][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 23:32:22.353][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 23:32:22.356][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 23:32:22.359][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 23:32:22.361][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 23:32:22.364][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 23:32:22.366][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 23:32:22.369][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 23:32:22.372][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 23:32:22.374][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 23:32:22.377][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 23:32:22.379][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 23:32:22.382][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 23:32:22.385][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 23:32:22.387][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 23:32:22.390][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 23:32:22.393][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 23:32:22.395][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 23:32:22.398][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 23:32:22.401][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 23:32:22.403][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 23:32:22.406][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 23:32:22.409][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 23:32:22.411][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 23:32:22.414][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 23:32:22.416][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 23:32:22.419][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 23:32:22.423][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 23:32:22.425][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 23:32:22.427][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.433][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[2024-06-26 23:32:22.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:22.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 23:32:22.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:22.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:22.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:22.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:22.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:22.665][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[2024-06-26 23:32:22.670][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 23:32:22.673][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:22.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.678][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.682][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 23:32:22.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.687][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.691][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 23:32:22.693][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 23:32:22.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.697][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 23:32:22.699][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 23:32:22.701][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 23:32:22.703][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 23:32:22.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 23:32:22.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 23:32:22.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 23:32:22.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:22.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:22.712][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 23:32:22.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 23:32:22.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 23:32:22.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 23:32:22.720][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:32:22.720][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 23:32:22.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 23:32:22.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 23:32:22.725][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 23:32:22.727][self$setPropertyValue]
biodb.DEBUG[2024-06-26 23:32:22.730][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 23:32:22.732][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 23:32:22.738][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:22.740][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 23:32:22.742][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 23:32:22.745][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 23:32:22.748][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:32:22.750][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 23:32:22.753][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 23:32:22.755][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 23:32:22.758][biodb::testThat]
biodb.INFO [2024-06-26 23:32:22.760][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-06-26 23:32:22.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 23:32:22.764][biodb::testThat]
biodb.DEBUG[2024-06-26 23:32:22.771][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-26 23:32:22.779][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 23:32:22.782][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-26 23:32:22.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 23:32:22.916][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-26 23:32:24.823][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-26 23:32:24.825][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 23:32:24.829][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-26 23:32:24.831][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-26 23:32:24.834][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 23:32:24.836][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 23:32:24.838][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 23:32:24.840][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 23:32:24.842][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 23:32:24.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:24.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:24.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:24.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:24.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:24.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:24.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:24.876][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-06-26 23:32:24.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:24.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:24.882][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:25.172][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:25.174][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:25.176][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:25.177][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:25.765][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:25.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:25.769][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:25.772][rule$waitAsNeeded] Wait 0.110798 second(s).
biodb.TRACE[2024-06-26 23:32:25.888][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:26.185][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:26.187][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:26.190][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:26.192][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:26.783][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:26.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:26.788][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:26.790][rule$waitAsNeeded] Wait 0.0977511 second(s).
biodb.TRACE[2024-06-26 23:32:26.906][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:27.205][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:27.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:27.208][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:27.209][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:27.816][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:27.818][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:27.820][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:27.822][rule$waitAsNeeded] Wait 0.0837479 second(s).
biodb.TRACE[2024-06-26 23:32:27.923][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:28.225][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:28.227][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:28.229][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:28.232][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:28.835][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:28.838][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:28.840][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:28.842][rule$waitAsNeeded] Wait 0.0807252 second(s).
biodb.TRACE[2024-06-26 23:32:28.942][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:29.235][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:29.238][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:29.240][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:29.242][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:29.835][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:29.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:29.838][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:29.839][rule$waitAsNeeded] Wait 0.101676 second(s).
biodb.TRACE[2024-06-26 23:32:29.944][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:30.246][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:30.248][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:30.251][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:30.253][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:31.041][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:31.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:31.045][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 23:32:31.048][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:31.344][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:31.346][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:31.348][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:31.351][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:31.947][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:31.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:31.952][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:31.955][rule$waitAsNeeded] Wait 0.0937409 second(s).
biodb.TRACE[2024-06-26 23:32:32.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:32.358][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:32.361][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:32.363][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:32.365][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:32.940][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:32.942][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:32.944][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:32.945][rule$waitAsNeeded] Wait 0.111932 second(s).
biodb.TRACE[2024-06-26 23:32:33.061][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:33.356][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:33.358][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:33.361][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:33.363][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:33.962][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:33.966][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:33.968][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:33.971][rule$waitAsNeeded] Wait 0.0898912 second(s).
biodb.TRACE[2024-06-26 23:32:34.069][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-26 23:32:34.364][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:34.366][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:34.369][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:34.371][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-26 23:32:34.964][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:34.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:34.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:34.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:34.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:34.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:34.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:34.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 23:32:35.000][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-26 23:32:35.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:35.008][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:35.011][rule$waitAsNeeded] Wait 0.058048 second(s).
biodb.TRACE[2024-06-26 23:32:35.088][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:35.379][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:35.380][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:35.382][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:35.383][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:35.942][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:35.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:35.946][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:35.948][rule$waitAsNeeded] Wait 0.138634 second(s).
biodb.TRACE[2024-06-26 23:32:36.106][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:36.408][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:36.410][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:36.413][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:36.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:37.016][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:37.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:37.020][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:37.023][rule$waitAsNeeded] Wait 0.0823019 second(s).
biodb.TRACE[2024-06-26 23:32:37.109][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:37.409][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:37.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:37.413][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:37.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:38.017][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:38.019][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:38.025][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:38.027][rule$waitAsNeeded] Wait 0.0809689 second(s).
biodb.TRACE[2024-06-26 23:32:38.110][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:38.404][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:38.406][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:38.408][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:38.410][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:39.005][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:39.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:39.009][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:39.012][rule$waitAsNeeded] Wait 0.0981669 second(s).
biodb.TRACE[2024-06-26 23:32:39.116][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:39.406][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:39.408][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:39.411][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:39.413][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:40.008][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:40.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:40.012][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:40.014][rule$waitAsNeeded] Wait 0.09812 second(s).
biodb.TRACE[2024-06-26 23:32:40.115][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:40.415][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:40.417][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:40.419][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:40.421][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:41.010][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:41.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:41.014][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:41.016][rule$waitAsNeeded] Wait 0.0982981 second(s).
biodb.TRACE[2024-06-26 23:32:41.118][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:41.411][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:41.412][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:41.414][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:41.416][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:42.012][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:42.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:42.017][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:42.019][rule$waitAsNeeded] Wait 0.0977931 second(s).
biodb.TRACE[2024-06-26 23:32:42.135][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:42.440][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:42.443][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:42.445][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:42.448][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:43.046][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:43.048][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:43.050][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:43.052][rule$waitAsNeeded] Wait 0.0829151 second(s).
biodb.TRACE[2024-06-26 23:32:43.138][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:43.436][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:43.438][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:43.441][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:43.443][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:44.033][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 23:32:44.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 23:32:44.037][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-26 23:32:44.039][rule$waitAsNeeded] Wait 0.098119 second(s).
biodb.TRACE[2024-06-26 23:32:44.140][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 23:32:44.442][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-26 23:32:44.444][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 23:32:44.447][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 23:32:44.449][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-26 23:32:45.051][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-26 23:32:45.055][private$doSaveContentToFile] Saving to 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[2024-06-26 23:32:45.059][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 23:32:45.061][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 23:32:45.062][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 23:32:45.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:45.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:45.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:45.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:45.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:45.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:45.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:45.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:32:45.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:45.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:45.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:45.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:45.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:45.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:45.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:45.267][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.275][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 23:32:45.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 23:32:45.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 23:32:45.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 23:32:45.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 23:32:45.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 23:32:45.373][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-26 23:32:45.375][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-26 23:32:45.380][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 23:32:45.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:45.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:45.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:45.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:45.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:45.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:45.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:45.413][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-26 23:32:45.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 23:32:45.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:45.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:45.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:45.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:45.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:45.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 23:32:45.447][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-26 23:32:45.449][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 23:32:45.451][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-26 23:32:45.463][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 23:32:45.466][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 23:32:45.469][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 23:32:45.471][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 23:32:45.472][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 23:32:45.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 23:32:45.474][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 23:32:45.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 23:32:45.477][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 23:32:45.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 3.98 | 2.38 | 93.75 | |
| LipidmapsStructureEntry | 0.80 | 0.00 | 0.87 | |