| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:23 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 203/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.9.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2024-03-27 23:48:41 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:54:15 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 333.8 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 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 4.08 2.19 156.78
* 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-03-27 23:52:05.852][biodb::testContext]
biodb.INFO [2024-03-27 23:52:05.856][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:52:05.857][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-27 23:52:05.859][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:52:05.860][biodb::testContext]
biodb.INFO [2024-03-27 23:52:05.868][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:52:05.871][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:52:05.881][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:52:05.884][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:52:05.886][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.895][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:52:05.926][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.934][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:52:05.936][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.941][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:52:05.942][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:52:05.944][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:52:05.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.949][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:52:05.951][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:52:05.966][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.971][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:52:05.972][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:52:05.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.975][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[2024-03-27 23:52:05.977][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:52:05.978][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:52:05.979][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:52:05.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.985][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:52:05.987][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:05.992][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:52:05.993][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:52:05.994][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:52:05.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:05.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:05.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.000][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:52:06.001][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:52:06.002][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:52:06.004][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:52:06.005][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:52:06.006][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:52:06.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.011][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:52:06.012][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:52:06.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.017][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:52:06.018][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:52:06.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.023][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:52:06.024][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:52:06.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.029][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:52:06.030][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:52:06.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.035][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:52:06.036][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:52:06.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.041][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:52:06.042][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:52:06.046][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:52:06.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.052][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:52:06.054][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:52:06.055][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:52:06.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.062][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:52:06.091][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.106][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:52:06.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:52:06.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.113][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.115][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.116][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.118][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:52:06.119][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:52:06.121][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.122][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:52:06.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:52:06.125][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.127][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:52:06.127][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:52:06.127][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:52:06.127][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:52:06.127][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:52:06.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:52:06.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.132][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:52:06.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.136][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.138][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.139][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:52:06.140][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:52:06.142][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.143][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.144][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:52:06.146][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.148][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:52:06.149][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:52:06.152][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.153][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.155][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.159][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:52:06.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:52:06.162][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.164][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:52:06.166][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:52:06.168][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.170][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:52:06.171][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:52:06.171][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:52:06.171][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:52:06.171][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:52:06.173][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:52:06.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:52:06.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.184][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.186][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:52:06.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:52:06.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.193][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.196][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:52:06.199][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.201][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:52:06.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.205][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:52:06.207][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.211][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.213][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.215][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:52:06.217][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:52:06.219][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.221][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:52:06.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:52:06.226][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.229][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.242][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:52:06.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:52:06.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.262][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:52:06.266][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:52:06.268][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.271][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.274][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:52:06.278][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.280][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:52:06.283][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:52:06.287][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.290][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.296][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:52:06.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:52:06.301][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.304][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:52:06.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:52:06.308][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:06.313][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:52:06.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.322][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:52:06.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:06.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:06.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:52:06.326][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:52:06.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:52:06.330][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:06.331][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:06.335][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:52:06.336][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.337][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.DEBUG[2024-03-27 23:52:06.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:06.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.343][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[2024-03-27 23:52:06.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:06.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:06.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:06.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:06.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:06.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:06.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:06.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:06.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.795][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[2024-03-27 23:52:07.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.801][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[2024-03-27 23:52:07.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:07.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:07.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:07.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:07.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:07.820][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:52:07.825][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:52:07.827][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:52:07.828][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:52:07.830][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:52:07.832][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:52:07.834][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:52:07.836][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:52:07.837][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:52:07.839][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:52:07.841][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:52:07.842][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:52:07.844][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:52:07.846][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:52:07.848][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:52:07.849][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:52:07.851][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:52:07.853][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:52:07.855][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:52:07.857][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:52:07.858][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:52:07.860][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:52:07.861][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:52:07.863][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:52:07.865][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:52:07.867][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:52:07.868][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:52:07.870][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:52:07.872][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:52:07.873][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:52:07.875][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:52:07.877][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:52:07.878][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:52:07.880][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:52:07.882][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:52:07.883][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:52:07.885][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:52:07.886][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:52:07.888][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:52:07.890][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:52:07.891][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:52:07.893][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:52:07.895][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:52:07.897][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:52:07.898][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:52:07.900][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:52:07.902][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:52:07.903][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:52:07.905][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:52:07.907][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:52:07.915][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:52:07.917][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:52:07.919][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:52:07.920][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:52:07.922][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:52:07.924][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:52:07.926][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:52:07.927][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:52:07.929][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:52:07.931][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:52:07.932][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:52:07.934][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:52:07.936][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:52:07.937][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:52:07.939][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:52:07.941][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:52:07.943][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:52:07.944][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:52:07.946][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:52:07.948][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:52:07.949][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:52:07.951][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:52:07.953][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:52:07.954][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:52:07.956][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:52:07.958][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:52:07.960][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:52:07.962][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:52:07.963][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:52:07.965][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:52:07.967][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:52:07.969][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:52:07.970][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:52:08.011][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:52:08.015][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:52:08.019][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:52:08.020][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.022][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.024][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[2024-03-27 23:52:08.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.104][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[2024-03-27 23:52:08.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.117][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[2024-03-27 23:52:08.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.171][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[2024-03-27 23:52:08.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:52:08.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:08.183][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:52:08.196][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:52:08.200][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:08.202][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:52:08.204][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:08.207][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:52:08.209][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:08.211][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:52:08.213][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:08.221][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:52:08.223][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:52:08.225][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:52:08.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:08.227][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:52:08.229][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:52:08.230][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:52:08.232][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:52:08.233][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:52:08.233][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:52:08.234][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:52:08.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:08.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:08.238][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:52:08.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:52:08.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:52:08.241][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:52:08.243][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:52:08.243][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:52:08.244][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:52:08.245][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:52:08.246][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:52:08.248][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:52:08.253][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:52:08.256][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:52:08.281][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:52:08.282][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:52:08.286][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:52:08.291][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:52:08.295][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:52:08.296][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:52:08.298][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:52:08.299][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:52:08.309][biodb::testThat]
biodb.INFO [2024-03-27 23:52:08.311][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-27 23:52:08.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:08.313][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:08.320][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[2024-03-27 23:52:08.323][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:52:08.326][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:52:08.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:08.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:08.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:08.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:08.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:08.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:08.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:08.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:08.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:08.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:08.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:08.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:08.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:08.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:08.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:08.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:08.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:08.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:08.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:08.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:08.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:08.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.590][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:08.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:52:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.730][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:08.842][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 23:52:08.863][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:08.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:08.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:08.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:08.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:08.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:08.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:08.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:08.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:08.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:08.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:08.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:08.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:08.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.030][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:09.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.097][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.101][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.158][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.163][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.212][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.213][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.216][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.260][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.261][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.264][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.331][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.334][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.368][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.385][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.387][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.390][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.391][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.409][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.415][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.446][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.449][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.453][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.489][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.491][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.495][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.509][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.533][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.536][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.540][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.557][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.559][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.564][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:09.579][biodb::testThat]
biodb.INFO [2024-03-27 23:52:09.581][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-27 23:52:09.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:09.584][biodb::testThat]
biodb.DEBUG[2024-03-27 23:52:09.603][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-27 23:52:09.610][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 23:52:09.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 23:52:09.619][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:52:09.623][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-27 23:52:09.625][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:52:09.653][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:52:09.656][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:52:09.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:09.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:09.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:09.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:09.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:09.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:09.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:09.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:09.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:09.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:09.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:09.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:09.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:09.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:09.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:09.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:09.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.840][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.848][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.865][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:09.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.882][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:09.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:09.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:09.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:09.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.924][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:09.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.932][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:52:09.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.940][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.957][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:09.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:09.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:09.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:09.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:10.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:10.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:10.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:10.101][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 23:52:10.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-27 23:52:10.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-27 23:52:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-27 23:52:10.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-27 23:52:10.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-27 23:52:10.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-27 23:52:10.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:10.156][biodb::testThat]
biodb.INFO [2024-03-27 23:52:10.158][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-27 23:52:10.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:10.161][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:10.167][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.173][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:10.175][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-27 23:52:10.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:10.260][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:52:10.268][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[2024-03-27 23:52:10.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:10.305][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:10.309][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-03-27 23:52:11.147][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-03-27 23:52:11.149][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:11.152][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:11.156][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-03-27 23:52:11.754][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:11.757][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-03-27 23:52:11.777][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-03-27 23:52:11.781][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 23:52:11.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:11.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:11.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:11.827][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:11.853][biodb::testThat]
biodb.INFO [2024-03-27 23:52:11.855][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-27 23:52:11.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:11.858][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:11.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:11.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:11.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:11.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:11.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:11.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:11.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:11.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:12.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:52:12.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:52:12.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:52:12.066][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:52:12.069][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-27 23:52:12.107][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.108][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-27 23:52:12.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:12.111][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:12.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:12.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:12.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.165][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:12.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:12.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.229][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 23:52:12.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:12.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 23:52:12.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:12.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:12.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 23:52:12.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:12.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:12.341][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.343][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-27 23:52:12.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:12.347][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.373][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.376][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-27 23:52:12.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:12.380][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.408][biodb::testThat]
biodb.INFO [2024-03-27 23:52:12.411][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-27 23:52:12.413][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:12.415][biodb::testThat]
biodb.DEBUG[2024-03-27 23:52:12.423][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-27 23:52:12.732][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-27 23:52:13.528][biodb::testThat]
biodb.INFO [2024-03-27 23:52:13.529][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-27 23:52:13.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:13.533][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:13.558][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:13.560][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:13.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.564][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.573][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:13.577][biodb::testThat]
biodb.INFO [2024-03-27 23:52:13.579][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-27 23:52:13.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:13.583][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:13.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:13.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:13.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:13.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:13.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:13.739][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:52:13.743][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:52:13.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:52:13.747][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:52:13.749][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-27 23:52:13.825][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 23:52:13.829][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:52:13.831][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 23:52:13.833][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:52:13.836][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-27 23:52:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:52:13.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:52:13.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:13.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:13.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:13.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:13.976][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-27 23:52:13.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:13.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:14.015][private$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[2024-03-27 23:52:14.328][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[2024-03-27 23:52:14.330][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:14.333][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[2024-03-27 23:52:14.336][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[2024-03-27 23:52:19.771][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:19.774][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-03-27 23:52:19.925][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-03-27 23:52:21.905][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[2024-03-27 23:52:21.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:21.912][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:21.914][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-27 23:52:22.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-03-27 23:52:22.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:22.224][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:22.226][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 23:52:22.818][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:22.822][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-03-27 23:52:22.830][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-03-27 23:52:22.899][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-03-27 23:52:22.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:22.908][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:22.910][rule$waitAsNeeded] Wait 0.00367308 second(s).
biodb.TRACE[2024-03-27 23:52:22.927][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-03-27 23:52:23.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06 does not exist.
biodb.TRACE[2024-03-27 23:52:23.233][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:23.235][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:23.237][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-03-27 23:52:23.834][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:23.839][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-03-27 23:52:23.845][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-03-27 23:52:23.901][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:23.933][biodb::testThat]
biodb.INFO [2024-03-27 23:52:23.936][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-27 23:52:23.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:23.938][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:52:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:52:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:23.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:23.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:23.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:23.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:23.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:23.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:23.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:23.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:23.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:23.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:23.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:24.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:24.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:24.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:24.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:24.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-27 23:52:24.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:24.035][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:24.039][private$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[2024-03-27 23:52:24.347][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[2024-03-27 23:52:24.349][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:24.352][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[2024-03-27 23:52:24.354][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[2024-03-27 23:52:29.827][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:29.830][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-27 23:52:29.948][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-27 23:52:31.739][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-27 23:52:31.801][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:52:31.804][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-03-27 23:52:31.808][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-03-27 23:52:31.820][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-27 23:52:31.823][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:52:31.825][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:52:31.827][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:52:31.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:52:31.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:31.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:31.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:31.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:31.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:31.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:31.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:31.848][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-27 23:52:31.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:31.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:31.855][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-27 23:52:32.171][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:32.173][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:32.174][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[2024-03-27 23:52:32.176][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-27 23:52:32.774][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:32.778][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-27 23:52:32.786][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-27 23:52:32.792][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-03-27 23:52:32.796][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:52:32.799][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:52:32.801][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:52:32.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:32.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:32.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:32.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:32.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:32.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:32.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:32.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:32.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:32.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:32.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:32.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:32.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:32.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:32.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.877][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:32.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:32.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.886][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:32.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:32.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:32.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.901][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:32.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:32.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:32.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:32.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:32.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:32.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.924][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:32.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:32.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.933][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:32.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:32.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:32.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.951][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:32.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:32.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.977][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:32.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.983][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:52:32.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:32.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:32.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:32.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.002][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:33.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.008][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.014][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.028][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:33.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:33.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:33.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:33.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:33.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:33.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:33.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:33.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 23:52:33.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 23:52:33.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.138][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:33.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 23:52:33.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:33.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 23:52:33.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:33.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:33.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:33.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 23:52:33.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:33.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:33.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 23:52:33.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.188][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:33.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:33.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.195][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 23:52:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 23:52:33.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 23:52:33.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.252][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.258][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 23:52:33.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:33.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:52:33.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.275][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 23:52:33.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:52:33.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:52:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:52:33.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:33.364][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-27 23:52:33.381][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:52:33.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:33.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:33.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:33.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:33.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:33.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:33.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:33.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.430][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.432][private$selectFields]
biodb.TRACE[2024-03-27 23:52:33.434][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:33.435][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:33.436][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.438][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.440][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.442][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.444][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.446][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.449][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.450][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.452][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.453][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.454][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.457][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.459][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.473][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.496][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:52:33.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:33.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:33.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:33.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:33.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:33.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:33.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.694][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.696][private$selectFields]
biodb.TRACE[2024-03-27 23:52:33.698][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:33.700][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:33.701][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.703][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.706][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.709][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.711][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.714][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.718][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.720][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.722][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.724][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.726][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.730][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.732][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:33.734][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.742][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:52:33.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:33.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:33.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:33.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:33.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:33.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:33.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.803][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.804][private$selectFields]
biodb.TRACE[2024-03-27 23:52:33.806][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:33.807][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:33.808][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.810][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.811][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.814][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.815][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.816][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.819][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.820][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.821][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:33.823][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.824][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.828][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.830][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:33.832][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:33.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:33.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:33.857][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:52:33.859][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:52:33.861][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:52:35.274][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:35.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:35.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:35.293][biodb::testThat]
biodb.INFO [2024-03-27 23:52:35.296][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-27 23:52:35.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:35.300][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:35.306][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:52:35.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:52:35.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:35.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:35.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:35.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:35.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:35.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:35.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:35.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:35.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:35.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:35.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:35.491][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[2024-03-27 23:52:35.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:35.497][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:35.499][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-27 23:52:35.809][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2024-03-27 23:52:35.810][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:35.812][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:35.814][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-27 23:52:41.563][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:52:41.566][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-27 23:52:41.667][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-27 23:52:43.356][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:52:43.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:43.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:43.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:43.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:43.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:43.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:43.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:43.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.428][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.466][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.468][private$selectFields]
biodb.TRACE[2024-03-27 23:52:43.470][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:43.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:43.474][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.476][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.478][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.482][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.484][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.486][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.490][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.492][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.509][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.511][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.513][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.517][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.519][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:43.522][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.546][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:52:43.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:43.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:43.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:43.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:43.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:43.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:43.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:43.573][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.584][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.585][private$selectFields]
biodb.TRACE[2024-03-27 23:52:43.587][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:43.588][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:43.589][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.591][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.592][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.596][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.598][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.600][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.604][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.606][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.609][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.611][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.613][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.615][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.617][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:43.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.642][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:52:43.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:43.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:43.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:43.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:43.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:43.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:43.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.675][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.681][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.682][private$selectFields]
biodb.TRACE[2024-03-27 23:52:43.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:43.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:43.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.689][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.692][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.694][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.696][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.700][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.702][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.705][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:43.707][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.709][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.713][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.715][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.741][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:52:43.742][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:52:43.744][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:52:43.767][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:43.785][biodb::testThat]
biodb.INFO [2024-03-27 23:52:43.787][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-27 23:52:43.788][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:43.790][biodb::testThat]
biodb.TRACE[2024-03-27 23:52:43.794][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 23:52:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 23:52:43.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:43.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 23:52:43.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:52:43.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:43.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:52:43.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:43.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:43.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:43.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:43.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:43.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:43.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:43.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.INFO [2024-03-27 23:52:43.901][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2024-03-27 23:52:43.903][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:43.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:43.907][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-03-27 23:52:44.219][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2024-03-27 23:52:44.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:44.223][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:44.225][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-03-27 23:52:49.520][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-03-27 23:52:49.522][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-03-27 23:52:49.525][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-27 23:52:49.623][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-27 23:52:51.131][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:52:51.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:51.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:51.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:51.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:51.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:51.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:51.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.173][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.174][private$selectFields]
biodb.TRACE[2024-03-27 23:52:51.175][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:51.176][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:51.178][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.179][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.180][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.183][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.184][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.185][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.188][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.189][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.190][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.191][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.193][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.195][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.196][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.214][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 23:52:51.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:51.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:51.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:51.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:51.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:51.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:51.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.235][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.306][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.307][private$selectFields]
biodb.TRACE[2024-03-27 23:52:51.309][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:51.310][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:51.311][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.313][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.314][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.317][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.318][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.320][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.322][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.324][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.325][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.327][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.328][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.331][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.332][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:51.334][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.339][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.351][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 23:52:51.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:51.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:51.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:51.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:51.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:51.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:51.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:52:51.367][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.378][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.379][private$selectFields]
biodb.TRACE[2024-03-27 23:52:51.380][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 23:52:51.381][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 23:52:51.383][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.384][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.385][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.388][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.389][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.390][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.393][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.394][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.396][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 23:52:51.397][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.398][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.401][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.402][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 23:52:51.403][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.408][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.414][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:52:51.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:52:51.419][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 23:52:51.422][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:52:51.424][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 23:52:51.511][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:51.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 23:52:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:52:51.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 23:52:51.533][biodb::testThat]
biodb.INFO [2024-03-27 23:52:51.535][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-27 23:52:51.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:52:51.540][biodb::testThat]
biodb.DEBUG[2024-03-27 23:52:51.544][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-27 23:52:51.546][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 23:52:51.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-27 23:52:51.552][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 23:52:51.554][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:52:51.556][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:52:51.558][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:52:51.561][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:52:51.562][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:52:51.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:52:51.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:52:51.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:52:51.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:52:51.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:52:51.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:52:51.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:52:51.637][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-27 23:52:51.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:51.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:52:51.643][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:51.941][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:51.943][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:51.944][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[2024-03-27 23:52:51.946][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:52.538][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:52:52.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:52.543][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:52.545][rule$waitAsNeeded] Wait 0.0980501 second(s).
biodb.TRACE[2024-03-27 23:52:52.661][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:52.978][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:52.981][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:52.983][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:52.985][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:53.569][private$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[2024-03-27 23:52:53.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:53.572][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:53.574][rule$waitAsNeeded] Wait 0.086767 second(s).
biodb.TRACE[2024-03-27 23:52:53.677][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:53.983][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:53.984][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:53.986][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[2024-03-27 23:52:53.989][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:54.585][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:52:54.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:54.588][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:54.590][rule$waitAsNeeded] Wait 0.086551 second(s).
biodb.TRACE[2024-03-27 23:52:54.694][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:55.002][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:55.003][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:55.006][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:55.007][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:55.602][private$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[2024-03-27 23:52:55.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:55.607][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:55.609][rule$waitAsNeeded] Wait 0.0838511 second(s).
biodb.TRACE[2024-03-27 23:52:55.710][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:56.020][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:56.022][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:56.025][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[2024-03-27 23:52:56.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:56.617][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:52:56.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:56.621][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:56.622][rule$waitAsNeeded] Wait 0.0864189 second(s).
biodb.TRACE[2024-03-27 23:52:56.725][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:57.033][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:57.035][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:57.038][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:57.040][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:57.634][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:52:57.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:57.639][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:57.641][rule$waitAsNeeded] Wait 0.083873 second(s).
biodb.TRACE[2024-03-27 23:52:57.742][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:58.046][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:58.048][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:58.050][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[2024-03-27 23:52:58.051][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:58.634][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:52:58.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:58.639][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:58.642][rule$waitAsNeeded] Wait 0.099776 second(s).
biodb.TRACE[2024-03-27 23:52:58.758][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:52:59.058][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:52:59.060][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:52:59.062][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:52:59.064][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:52:59.651][private$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[2024-03-27 23:52:59.653][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:52:59.655][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:52:59.658][rule$waitAsNeeded] Wait 0.0995319 second(s).
biodb.TRACE[2024-03-27 23:52:59.774][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:53:00.077][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:00.079][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:00.080][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[2024-03-27 23:53:00.082][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:53:00.667][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:00.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:00.671][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:00.674][rule$waitAsNeeded] Wait 0.099704 second(s).
biodb.TRACE[2024-03-27 23:53:00.790][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 23:53:01.106][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:01.109][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:01.112][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:01.115][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 23:53:01.714][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:53:01.720][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-27 23:53:01.724][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:53:01.726][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 23:53:01.729][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:53:01.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:01.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:01.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:01.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:01.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:01.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:01.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:53:01.767][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:01.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.773][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:01.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:01.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:01.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:01.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:53:01.840][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-27 23:53:01.842][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-27 23:53:01.923][biodb::testThat]
biodb.INFO [2024-03-27 23:53:01.924][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-27 23:53:01.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:01.927][biodb::testThat]
biodb.DEBUG[2024-03-27 23:53:01.940][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-27 23:53:01.942][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-27 23:53:01.944][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:53:01.946][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-27 23:53:01.948][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 23:53:01.949][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:53:01.951][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:53:01.952][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:53:01.953][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:53:01.954][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:53:01.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:01.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:01.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:01.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:01.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:01.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:02.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:02.002][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-27 23:53:02.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:02.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:02.009][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:02.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:02.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:02.319][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[2024-03-27 23:53:02.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:02.918][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:02.920][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:02.922][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:02.924][rule$waitAsNeeded] Wait 0.084713 second(s).
biodb.TRACE[2024-03-27 23:53:03.026][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:03.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:03.341][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:03.343][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:03.344][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:03.934][private$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[2024-03-27 23:53:03.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:03.939][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:03.941][rule$waitAsNeeded] Wait 0.0845351 second(s).
biodb.TRACE[2024-03-27 23:53:04.042][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:04.345][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:04.348][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:04.350][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[2024-03-27 23:53:04.353][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:04.950][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:04.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:04.955][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:04.957][rule$waitAsNeeded] Wait 0.0843499 second(s).
biodb.TRACE[2024-03-27 23:53:05.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:05.365][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:05.367][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:05.369][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:05.370][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:05.966][private$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[2024-03-27 23:53:05.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:05.972][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:05.974][rule$waitAsNeeded] Wait 0.083734 second(s).
biodb.TRACE[2024-03-27 23:53:06.074][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:06.377][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:06.378][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:06.380][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[2024-03-27 23:53:06.381][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:06.966][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:06.968][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:06.969][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:06.970][rule$waitAsNeeded] Wait 0.1028 second(s).
biodb.TRACE[2024-03-27 23:53:07.090][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:07.406][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:07.408][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:07.410][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:07.412][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:07.999][private$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[2024-03-27 23:53:08.002][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:08.004][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:08.006][rule$waitAsNeeded] Wait 0.0837409 second(s).
biodb.TRACE[2024-03-27 23:53:08.107][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:08.409][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:08.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:08.412][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[2024-03-27 23:53:08.414][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:08.999][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:09.002][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:09.004][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:09.006][rule$waitAsNeeded] Wait 0.100023 second(s).
biodb.TRACE[2024-03-27 23:53:09.123][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:09.432][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:09.434][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:09.436][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:09.437][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:10.030][private$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[2024-03-27 23:53:10.032][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:10.033][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:10.035][rule$waitAsNeeded] Wait 0.0869691 second(s).
biodb.TRACE[2024-03-27 23:53:10.138][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:10.444][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:10.446][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:10.449][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[2024-03-27 23:53:10.451][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:11.047][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:11.050][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:11.052][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:11.054][rule$waitAsNeeded] Wait 0.0842659 second(s).
biodb.TRACE[2024-03-27 23:53:11.155][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 23:53:11.465][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:11.467][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:11.470][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:11.472][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 23:53:12.062][private$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[2024-03-27 23:53:12.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:12.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:12.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:13.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:13.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:13.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:13.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:13.071][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-27 23:53:13.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:13.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:13.078][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:13.387][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:13.388][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:13.390][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[2024-03-27 23:53:13.391][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:13.986][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:13.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:13.991][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:13.993][rule$waitAsNeeded] Wait 0.0847969 second(s).
biodb.TRACE[2024-03-27 23:53:14.094][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:14.409][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:14.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:14.413][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:14.416][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:15.002][private$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[2024-03-27 23:53:15.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:15.007][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:15.009][rule$waitAsNeeded] Wait 0.084362 second(s).
biodb.TRACE[2024-03-27 23:53:15.110][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:15.412][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:15.414][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:15.415][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[2024-03-27 23:53:15.417][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:16.003][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:16.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:16.007][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:16.009][rule$waitAsNeeded] Wait 0.100266 second(s).
biodb.TRACE[2024-03-27 23:53:16.126][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:16.554][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:16.557][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:16.559][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:16.561][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:17.144][private$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[2024-03-27 23:53:17.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:17.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:17.157][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:17.470][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:17.472][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:17.474][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:17.476][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:18.069][private$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[2024-03-27 23:53:18.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:18.073][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:18.076][rule$waitAsNeeded] Wait 0.0811849 second(s).
biodb.TRACE[2024-03-27 23:53:18.160][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:18.466][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:18.468][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:18.470][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[2024-03-27 23:53:18.473][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:19.057][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:19.059][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:19.061][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:19.064][rule$waitAsNeeded] Wait 0.096606 second(s).
biodb.TRACE[2024-03-27 23:53:19.165][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:19.465][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:19.466][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:19.468][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:19.469][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:20.058][private$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[2024-03-27 23:53:20.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:20.063][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:20.065][rule$waitAsNeeded] Wait 0.0994101 second(s).
biodb.TRACE[2024-03-27 23:53:20.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:20.484][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:20.485][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:20.487][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[2024-03-27 23:53:20.488][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:21.074][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:21.077][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:21.079][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:21.081][rule$waitAsNeeded] Wait 0.099755 second(s).
biodb.TRACE[2024-03-27 23:53:21.197][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:21.507][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:21.509][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:21.511][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:21.513][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:22.106][private$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[2024-03-27 23:53:22.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:22.110][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:22.112][rule$waitAsNeeded] Wait 0.08442 second(s).
biodb.TRACE[2024-03-27 23:53:22.213][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 23:53:22.526][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:22.528][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:22.530][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[2024-03-27 23:53:22.531][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 23:53:23.124][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:53:23.129][private$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[2024-03-27 23:53:23.134][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:53:23.137][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:53:23.139][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:53:23.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:23.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:23.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:23.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:23.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:23.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:23.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:53:23.273][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:53:23.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:23.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:23.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:23.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:23.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:23.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:23.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:53:23.341][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:53:23.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:23.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:53:23.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:53:23.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:23.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:53:23.413][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-27 23:53:23.415][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 23:53:23.416][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-27 23:53:23.837][biodb::testThat]
biodb.INFO [2024-03-27 23:53:23.839][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-27 23:53:23.840][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:23.842][biodb::testThat]
biodb.INFO [2024-03-27 23:53:23.936][biodb::testThat]
biodb.INFO [2024-03-27 23:53:23.939][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-27 23:53:23.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:23.943][biodb::testThat]
biodb.INFO [2024-03-27 23:53:23.983][biodb::testThat]
biodb.INFO [2024-03-27 23:53:23.985][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-27 23:53:23.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:23.988][biodb::testThat]
biodb.DEBUG[2024-03-27 23:53:23.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 23:53:23.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:23.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:24.001][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-27 23:53:24.303][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-03-27 23:53:24.304][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:24.306][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[2024-03-27 23:53:24.308][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-27 23:53:29.456][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:29.459][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-27 23:53:29.591][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-27 23:53:31.287][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 23:53:31.288][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 23:53:31.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:31.291][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:53:31.293][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:53:31.294][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 23:53:31.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:53:31.297][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 23:53:31.300][biodb::testThat]
biodb.INFO [2024-03-27 23:53:31.301][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-27 23:53:31.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:31.303][biodb::testThat]
biodb.ERROR[2024-03-27 23:53:31.322][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-27 23:53:31.348][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-27 23:53:31.374][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:53:31.378][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:53:31.381][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:53:31.382][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:53:31.384][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:31.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:31.387][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.389][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 23:53:31.402][biodb::testContext]
biodb.INFO [2024-03-27 23:53:31.404][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:53:31.405][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-27 23:53:31.407][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:53:31.408][biodb::testContext]
biodb.INFO [2024-03-27 23:53:31.411][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:53:31.414][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:53:31.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:31.422][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:53:31.424][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.431][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:53:31.432][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.438][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:53:31.439][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.446][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:53:31.447][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:53:31.450][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:53:31.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.456][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:53:31.458][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:53:31.459][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.464][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:53:31.465][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:53:31.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.471][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:53:31.472][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:53:31.473][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:53:31.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.479][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:53:31.481][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.488][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:53:31.490][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:53:31.492][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:53:31.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.499][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:53:31.500][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:53:31.501][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:53:31.503][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:53:31.504][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:53:31.505][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:53:31.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.510][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:53:31.512][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:53:31.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.517][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:53:31.519][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:53:31.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.526][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:53:31.528][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:53:31.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.537][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:53:31.539][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:53:31.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.544][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:53:31.545][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:53:31.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.550][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:53:31.551][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:53:31.558][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:53:31.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.566][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:53:31.568][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:53:31.569][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:53:31.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.574][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:53:31.601][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.602][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:53:31.604][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:31.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.608][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.609][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.612][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:31.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:31.614][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.616][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:53:31.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:31.618][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:31.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:31.621][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:53:31.621][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:53:31.621][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:53:31.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:31.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:31.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.630][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.631][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:31.634][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:31.636][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.637][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.639][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:53:31.665][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.666][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:53:31.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:31.670][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.671][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.675][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:53:31.676][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:31.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.679][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:53:31.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:31.682][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.684][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:31.684][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:31.684][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:53:31.684][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:53:31.684][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:53:31.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:31.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.690][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:31.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.695][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:31.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:31.699][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.701][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.702][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:53:31.704][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.706][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:53:31.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:31.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.713][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.717][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:31.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:31.720][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.721][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:53:31.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:31.724][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.725][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.727][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.728][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:31.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:31.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.735][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.736][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:31.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:31.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.741][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.743][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:53:31.745][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.746][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:53:31.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:31.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:53:31.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:31.759][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.761][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:53:31.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:31.764][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:31.767][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.768][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:31.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.772][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:31.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:31.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:31.776][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:31.777][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.779][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:31.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:31.781][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:31.782][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:31.784][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:31.785][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.832][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[2024-03-27 23:53:31.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.851][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[2024-03-27 23:53:31.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:31.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:31.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:31.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:31.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:31.946][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:53:31.949][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:53:31.952][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:53:31.954][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:53:31.957][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:53:31.960][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:53:31.962][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:53:31.965][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:53:31.968][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:53:31.970][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:53:31.973][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:53:31.976][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:53:31.979][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:53:31.982][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:53:31.984][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:53:31.987][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:53:31.990][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:53:31.992][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:53:31.995][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:53:31.998][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:53:32.001][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:53:32.003][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:53:32.006][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:53:32.009][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:53:32.012][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:53:32.015][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:53:32.017][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:53:32.020][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:53:32.023][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:53:32.026][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:53:32.028][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:53:32.031][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:53:32.034][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:53:32.036][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:53:32.039][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:53:32.042][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:53:32.044][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:53:32.047][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:53:32.050][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:53:32.052][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:53:32.055][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:53:32.058][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:53:32.061][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:53:32.064][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:53:32.066][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:53:32.069][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:53:32.072][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:53:32.075][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:53:32.077][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:53:32.080][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:53:32.082][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:53:32.085][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:53:32.114][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:53:32.117][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:53:32.120][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:53:32.123][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:53:32.125][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:53:32.128][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:53:32.131][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:53:32.133][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:53:32.136][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:53:32.139][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:53:32.142][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:53:32.144][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:53:32.147][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:53:32.150][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:53:32.152][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:53:32.155][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:53:32.157][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:53:32.160][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:53:32.163][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:53:32.165][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:53:32.168][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:53:32.171][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:53:32.173][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:53:32.176][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:53:32.178][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:53:32.181][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:53:32.184][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:53:32.187][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:53:32.189][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:53:32.192][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:53:32.194][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:53:32.197][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:53:32.201][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:53:32.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:32.205][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.213][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:32.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:32.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:32.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:32.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:32.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:32.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:32.428][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:53:32.430][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:32.432][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:32.434][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:53:32.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:32.436][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:32.437][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:32.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:32.440][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:32.441][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:32.443][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:32.444][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:32.445][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:32.446][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:53:32.448][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:53:32.449][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:53:32.450][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:32.452][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:32.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:32.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:32.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:32.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:32.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:32.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:32.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:32.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:32.463][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:53:32.463][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:53:32.465][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:32.467][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:32.469][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:32.471][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:32.474][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:53:32.476][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:53:32.483][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:32.484][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:53:32.486][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:32.488][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:53:32.491][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:53:32.493][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:53:32.496][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:53:32.498][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:53:32.502][biodb::testThat]
biodb.INFO [2024-03-27 23:53:32.504][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-27 23:53:32.506][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:32.507][biodb::testThat]
biodb.DEBUG[2024-03-27 23:53:32.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-27 23:53:32.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:32.522][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:32.524][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-27 23:53:32.845][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-03-27 23:53:32.848][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:32.851][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:32.854][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-03-27 23:53:33.447][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:33.452][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-27 23:53:33.459][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-27 23:53:33.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-03-27 23:53:33.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:33.509][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:33.512][rule$waitAsNeeded] Wait 0.0122929 second(s).
biodb.TRACE[2024-03-27 23:53:33.566][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-27 23:53:33.883][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2024-03-27 23:53:33.885][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:33.887][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:33.889][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-03-27 23:53:34.478][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:34.482][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-27 23:53:34.491][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-27 23:53:34.527][biodb::testThat]
biodb.INFO [2024-03-27 23:53:34.529][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-27 23:53:34.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:34.533][biodb::testThat]
biodb.INFO [2024-03-27 23:53:34.619][biodb::testThat]
biodb.INFO [2024-03-27 23:53:34.621][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-27 23:53:34.622][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:34.623][biodb::testThat]
biodb.DEBUG[2024-03-27 23:53:34.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:53:34.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:34.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:34.634][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 23:53:34.947][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-03-27 23:53:34.949][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:34.952][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[2024-03-27 23:53:34.955][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 23:53:35.366][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:35.371][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-27 23:53:35.377][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-27 23:53:35.384][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:53:35.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:53:35.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-27 23:53:35.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:53:35.404][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-27 23:53:35.411][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 23:53:35.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:35.418][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:35.419][rule$waitAsNeeded] Wait 0.214582 second(s).
biodb.TRACE[2024-03-27 23:53:35.650][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 23:53:35.958][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[2024-03-27 23:53:35.960][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:35.963][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[2024-03-27 23:53:35.967][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[2024-03-27 23:53:36.381][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:36.386][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-27 23:53:36.394][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-27 23:53:36.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-27 23:53:36.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:36.416][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:36.419][rule$waitAsNeeded] Wait 0.230077 second(s).
biodb.TRACE[2024-03-27 23:53:36.666][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-27 23:53:36.970][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-03-27 23:53:36.972][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:36.974][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[2024-03-27 23:53:36.976][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-27 23:53:38.517][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:38.520][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-27 23:53:38.541][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-27 23:53:38.776][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-03-27 23:53:38.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:38.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:38.784][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-03-27 23:53:39.088][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-03-27 23:53:39.090][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:39.094][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:39.098][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-03-27 23:53:40.616][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 23:53:40.619][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-27 23:53:40.638][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-27 23:53:40.868][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:53:40.869][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:53:40.871][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:53:40.872][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:53:40.873][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:40.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:40.876][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:40.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:40.878][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 23:53:40.885][biodb::testContext]
biodb.INFO [2024-03-27 23:53:40.887][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:53:40.888][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-27 23:53:40.890][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 23:53:40.891][biodb::testContext]
biodb.INFO [2024-03-27 23:53:40.894][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:53:40.896][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 23:53:40.902][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:40.904][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 23:53:40.905][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.909][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[2024-03-27 23:53:40.910][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 23:53:40.911][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.916][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 23:53:40.918][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.922][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 23:53:40.924][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 23:53:40.945][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 23:53:40.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.951][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 23:53:40.952][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 23:53:40.954][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.958][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 23:53:40.960][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 23:53:40.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.965][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 23:53:40.966][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 23:53:40.968][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 23:53:40.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.972][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 23:53:40.974][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.979][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 23:53:40.980][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 23:53:40.982][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 23:53:40.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.987][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:53:40.988][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 23:53:40.990][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 23:53:40.991][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 23:53:40.992][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 23:53:40.993][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 23:53:40.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:40.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:40.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:40.998][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 23:53:41.000][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 23:53:41.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.005][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 23:53:41.006][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 23:53:41.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.011][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 23:53:41.012][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 23:53:41.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.019][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 23:53:41.022][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 23:53:41.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.027][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 23:53:41.028][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 23:53:41.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.032][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.DEBUG[2024-03-27 23:53:41.033][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 23:53:41.034][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 23:53:41.038][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 23:53:41.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.042][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 23:53:41.044][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 23:53:41.045][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 23:53:41.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.050][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 23:53:41.052][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.053][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 23:53:41.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.056][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:41.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.062][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:41.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:41.065][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.066][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 23:53:41.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:41.069][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.072][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:41.072][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:41.072][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:53:41.072][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:53:41.072][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:53:41.073][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:41.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:41.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.082][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:41.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:41.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.087][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.088][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 23:53:41.090][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.092][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:53:41.093][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:41.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.097][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.099][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.101][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:53:41.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:41.103][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.105][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 23:53:41.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:41.107][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.110][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:41.110][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:41.110][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 23:53:41.110][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 23:53:41.110][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 23:53:41.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:41.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:41.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.120][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:41.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:41.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.125][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.127][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 23:53:41.129][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.130][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 23:53:41.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:41.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.136][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.139][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:41.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:41.142][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.143][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 23:53:41.145][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:41.146][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.149][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.151][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:41.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.154][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:41.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.159][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:41.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:41.163][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.164][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.166][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 23:53:41.168][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.169][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 23:53:41.171][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.172][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:41.173][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.175][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.176][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.177][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.179][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 23:53:41.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:41.181][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.183][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 23:53:41.184][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:41.185][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.186][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.188][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.189][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:41.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.193][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:41.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.198][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.199][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:41.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:41.202][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.203][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.204][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:41.206][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.213][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[2024-03-27 23:53:41.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.225][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[2024-03-27 23:53:41.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.326][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 23:53:41.328][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 23:53:41.329][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 23:53:41.331][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 23:53:41.333][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 23:53:41.334][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 23:53:41.336][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 23:53:41.338][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 23:53:41.339][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 23:53:41.341][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 23:53:41.343][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 23:53:41.344][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 23:53:41.346][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 23:53:41.347][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 23:53:41.349][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 23:53:41.351][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:53:41.352][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 23:53:41.354][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 23:53:41.356][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 23:53:41.357][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 23:53:41.359][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 23:53:41.361][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 23:53:41.362][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 23:53:41.364][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 23:53:41.366][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 23:53:41.367][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 23:53:41.369][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 23:53:41.371][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 23:53:41.372][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 23:53:41.374][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 23:53:41.376][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 23:53:41.378][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 23:53:41.379][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 23:53:41.381][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 23:53:41.383][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 23:53:41.384][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 23:53:41.386][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 23:53:41.388][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 23:53:41.389][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 23:53:41.391][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 23:53:41.393][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 23:53:41.394][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 23:53:41.396][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 23:53:41.398][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 23:53:41.400][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 23:53:41.403][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 23:53:41.405][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 23:53:41.407][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 23:53:41.408][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 23:53:41.410][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 23:53:41.412][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 23:53:41.414][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 23:53:41.415][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 23:53:41.417][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 23:53:41.419][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 23:53:41.420][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 23:53:41.422][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 23:53:41.424][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 23:53:41.426][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 23:53:41.427][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 23:53:41.429][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 23:53:41.431][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 23:53:41.432][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 23:53:41.434][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 23:53:41.436][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 23:53:41.437][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 23:53:41.439][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 23:53:41.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 23:53:41.442][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 23:53:41.444][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 23:53:41.446][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 23:53:41.447][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 23:53:41.449][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 23:53:41.451][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 23:53:41.452][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 23:53:41.454][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 23:53:41.456][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 23:53:41.457][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 23:53:41.459][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 23:53:41.461][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 23:53:41.462][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 23:53:41.464][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 23:53:41.466][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 23:53:41.467][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 23:53:41.470][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 23:53:41.471][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 23:53:41.472][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.475][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.484][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[2024-03-27 23:53:41.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.518][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[2024-03-27 23:53:41.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.526][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[2024-03-27 23:53:41.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.569][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.DEBUG[2024-03-27 23:53:41.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.627][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[2024-03-27 23:53:41.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 23:53:41.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:41.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:41.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:41.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:41.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:41.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:41.647][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 23:53:41.649][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:41.652][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.653][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 23:53:41.658][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.661][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.664][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 23:53:41.665][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 23:53:41.667][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.668][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 23:53:41.669][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 23:53:41.671][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 23:53:41.672][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 23:53:41.674][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 23:53:41.674][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 23:53:41.676][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 23:53:41.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 23:53:41.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 23:53:41.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 23:53:41.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 23:53:41.686][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:53:41.686][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 23:53:41.688][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 23:53:41.689][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 23:53:41.690][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 23:53:41.691][self$setPropertyValue]
biodb.DEBUG[2024-03-27 23:53:41.693][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 23:53:41.695][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 23:53:41.699][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:41.700][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 23:53:41.701][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 23:53:41.703][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 23:53:41.705][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:53:41.706][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 23:53:41.708][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 23:53:41.709][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 23:53:41.712][biodb::testThat]
biodb.INFO [2024-03-27 23:53:41.713][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-03-27 23:53:41.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 23:53:41.715][biodb::testThat]
biodb.DEBUG[2024-03-27 23:53:41.720][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 23:53:41.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 23:53:41.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-27 23:53:41.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 23:53:41.892][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-27 23:53:43.806][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-27 23:53:43.808][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 23:53:43.810][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-27 23:53:43.811][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 23:53:43.813][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 23:53:43.815][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 23:53:43.816][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 23:53:43.818][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 23:53:43.819][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 23:53:43.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:43.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:43.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:43.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:43.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:43.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:43.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:43.839][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-03-27 23:53:43.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:43.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:53:43.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:44.157][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:44.159][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:44.161][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:44.162][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:44.754][private$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[2024-03-27 23:53:44.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:44.759][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:44.761][rule$waitAsNeeded] Wait 0.0837822 second(s).
biodb.TRACE[2024-03-27 23:53:44.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:45.180][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:45.183][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:45.185][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[2024-03-27 23:53:45.187][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:45.771][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:45.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:45.775][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:45.778][rule$waitAsNeeded] Wait 0.084048 second(s).
biodb.TRACE[2024-03-27 23:53:45.878][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:46.184][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:46.185][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:46.186][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:46.188][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:46.770][private$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[2024-03-27 23:53:46.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:46.773][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:46.775][rule$waitAsNeeded] Wait 0.1027 second(s).
biodb.TRACE[2024-03-27 23:53:46.894][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:47.194][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:47.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:47.197][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[2024-03-27 23:53:47.198][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:47.787][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:47.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:47.791][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:47.793][rule$waitAsNeeded] Wait 0.100491 second(s).
biodb.TRACE[2024-03-27 23:53:47.910][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:48.218][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:48.220][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:48.222][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:48.224][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:48.822][private$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[2024-03-27 23:53:48.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:48.827][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:48.829][rule$waitAsNeeded] Wait 0.080893 second(s).
biodb.TRACE[2024-03-27 23:53:48.927][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:49.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:49.233][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:49.236][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[2024-03-27 23:53:49.238][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:49.835][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:49.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:49.838][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:49.839][rule$waitAsNeeded] Wait 0.086278 second(s).
biodb.TRACE[2024-03-27 23:53:49.942][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:50.254][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:50.256][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:50.257][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:50.259][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:50.850][private$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[2024-03-27 23:53:50.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:50.853][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:50.854][rule$waitAsNeeded] Wait 0.08729 second(s).
biodb.TRACE[2024-03-27 23:53:50.959][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:51.283][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:51.285][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:51.286][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[2024-03-27 23:53:51.287][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:51.882][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:51.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:51.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:51.887][rule$waitAsNeeded] Wait 0.0713172 second(s).
biodb.TRACE[2024-03-27 23:53:51.975][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:52.282][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:52.283][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:52.285][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:52.286][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:52.883][private$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[2024-03-27 23:53:52.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:52.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:52.887][rule$waitAsNeeded] Wait 0.087188 second(s).
biodb.TRACE[2024-03-27 23:53:52.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-27 23:53:53.305][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:53.307][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:53.309][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[2024-03-27 23:53:53.310][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-27 23:53:53.899][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:53.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:53:53.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:53:53.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:53:53.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:53:53.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:53:53.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:53:53.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 23:53:53.925][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-27 23:53:53.930][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:53.932][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:53.935][rule$waitAsNeeded] Wait 0.0559819 second(s).
biodb.TRACE[2024-03-27 23:53:54.007][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:53:54.317][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:54.319][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:54.322][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[2024-03-27 23:53:54.324][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:53:54.915][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:54.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:54.919][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:54.922][rule$waitAsNeeded] Wait 0.0852611 second(s).
biodb.TRACE[2024-03-27 23:53:55.023][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:53:55.325][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:55.327][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:55.328][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:55.330][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:53:55.920][private$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[2024-03-27 23:53:55.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:55.923][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:55.924][rule$waitAsNeeded] Wait 0.098417 second(s).
biodb.TRACE[2024-03-27 23:53:56.029][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:53:56.338][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:56.341][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:56.343][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[2024-03-27 23:53:56.345][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:53:56.934][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:56.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:56.939][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:56.941][rule$waitAsNeeded] Wait 0.087369 second(s).
biodb.TRACE[2024-03-27 23:53:57.031][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:53:57.345][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:57.347][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:57.349][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:53:57.352][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:53:57.943][private$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[2024-03-27 23:53:57.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:57.946][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:57.947][rule$waitAsNeeded] Wait 0.0832479 second(s).
biodb.TRACE[2024-03-27 23:53:58.036][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:53:58.357][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:53:58.359][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:53:58.361][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[2024-03-27 23:53:58.363][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:53:58.953][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:53:58.955][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:53:58.956][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:53:58.958][rule$waitAsNeeded] Wait 0.0776141 second(s).
biodb.TRACE[2024-03-27 23:53:59.039][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:54:00.006][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:54:00.008][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:54:00.010][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:54:00.012][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:54:00.611][private$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[2024-03-27 23:54:00.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:54:00.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 23:54:00.617][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:54:00.922][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:54:00.924][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:54:00.925][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:54:00.927][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:54:01.522][private$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[2024-03-27 23:54:01.524][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:54:01.526][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:54:01.527][rule$waitAsNeeded] Wait 0.0897691 second(s).
biodb.TRACE[2024-03-27 23:54:01.631][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:54:01.930][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:54:01.932][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:54:01.934][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[2024-03-27 23:54:01.935][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:54:02.525][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 23:54:02.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:54:02.530][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:54:02.531][rule$waitAsNeeded] Wait 0.098947 second(s).
biodb.TRACE[2024-03-27 23:54:02.633][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:54:02.943][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:54:02.945][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:54:02.947][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 23:54:02.949][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:54:03.542][private$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[2024-03-27 23:54:03.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 23:54:03.545][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-03-27 23:54:03.547][rule$waitAsNeeded] Wait 0.085608 second(s).
biodb.TRACE[2024-03-27 23:54:03.635][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 23:54:03.940][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-03-27 23:54:03.942][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 23:54:03.943][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[2024-03-27 23:54:03.945][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-03-27 23:54:04.731][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-27 23:54:04.734][private$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[2024-03-27 23:54:04.737][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 23:54:04.739][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 23:54:04.741][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 23:54:04.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:54:04.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:54:04.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:54:04.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:54:04.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:54:04.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:54:04.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:54:04.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:54:04.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:54:04.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:54:04.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:54:04.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:54:04.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:54:04.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:54:04.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:54:04.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 23:54:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 23:54:04.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 23:54:04.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 23:54:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 23:54:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 23:54:04.880][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-27 23:54:04.881][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 23:54:04.884][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 23:54:04.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:54:04.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:54:04.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:54:05.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:54:05.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:54:05.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:54:05.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:54:05.022][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-03-27 23:54:05.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 23:54:05.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:54:05.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:54:05.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:54:05.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:54:05.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:54:05.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 23:54:05.038][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-03-27 23:54:05.039][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 23:54:05.040][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-27 23:54:05.048][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 23:54:05.050][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 23:54:05.052][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 23:54:05.053][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 23:54:05.054][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 23:54:05.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 23:54:05.056][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 23:54:05.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 23:54:05.059][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 23:54:05.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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 | 4.08 | 2.19 | 156.78 | |
| LipidmapsStructureEntry | 0.62 | 0.03 | 0.65 | |