Read pipelines configuration files

Read the configuration file of a pipeline and extract formatted (as a list) information

Usage

readConfigFile(path, usermod = "user")

Arguments

path

A `character()` which is the path to the directory which contains the files and directories of the pipeline.

usermod

A `character()` to specifies the running mode of MagellanNTK: 'user' (default) or 'dev'.

Value

A list containing the following items: value <- list( * funcs = tmp, * verbose = get_data(lines, "verbose") == "enabled", * UI_view_debugger: a `boolean` to show (TRUE) of hide (FALSE) the debugger interface * UI_view_open_pipeline: a `boolean` to show (TRUE) of hide (FALSE) the UI to open a pipeline * UI_view_convert_dataset a `boolean` to show (TRUE) of hide (FALSE) the UI for convert/import a dataset * UI_view_change_Look_Feel a `boolean` to show (TRUE) of hide (FALSE) the UI to change the L&F * UI_view_change_core_funcs a `boolean` to show (TRUE) of hide (FALSE) the UI to change the generic functions * extension A `character()` which specifies the extension file allowed to be processed in the pipeline, * class A `character()` which specifies the class of the dataset to be processed in the pipeline, * package A `character()` which specifies the package which owns the pipeline * demo_package A `character()` which specifies a particular package to search * URL_manual The path to the Rmd file containing the user manual of the pipeline. It can be a path to a file on the computer or a link to a file over internet. * URL_ReleaseNotes The path to the Rmd file containing release notes about the pipeline. It can be a path to a file on the computer or a link to a file over internet.

Examples

path <- system.file("workflow/PipelineDemo", package = "MagellanNTK")
readConfigFile(path)
#> $funcs
#> $funcs$open_dataset
#> [1] "MagellanNTK::open_dataset"
#> 
#> $funcs$view_dataset
#> [1] "MagellanNTK::view_dataset"
#> 
#> $funcs$download_dataset
#> [1] "MagellanNTK::download_dataset"
#> 
#> $funcs$build_report
#> NULL
#> 
#> $funcs$infos_dataset
#> [1] "MagellanNTK::infos_dataset"
#> 
#> $funcs$history_dataset
#> [1] "MagellanNTK::history_dataset"
#> 
#> $funcs$addDatasets
#> [1] "MagellanNTK::addDatasets"
#> 
#> $funcs$keepDatasets
#> [1] "MagellanNTK::keepDatasets"
#> 
#> $funcs$InitializeHistory
#> [1] "MagellanNTK::InitializeHistory"
#> 
#> $funcs$Add2History
#> [1] "MagellanNTK::Add2History"
#> 
#> $funcs$GetHistory
#> [1] "MagellanNTK::GetHistory"
#> 
#> $funcs$SetHistory
#> [1] "MagellanNTK::SetHistory"
#> 
#> 
#> $verbose
#> logical(0)
#> 
#> $UI_view_debugger
#> logical(0)
#> 
#> $UI_view_open_pipeline
#> logical(0)
#> 
#> $UI_view_convert_dataset
#> logical(0)
#> 
#> $UI_view_change_Look_Feel
#> logical(0)
#> 
#> $UI_view_change_core_funcs
#> logical(0)
#> 
#> $extension
#> [1] ".RData"
#> 
#> $class
#> [1] "RData"
#> 
#> $package
#> [1] "MagellanNTK"
#> 
#> $URL_manual
#> [1] "http://www.prostar-proteomics.org/md/versionNotes.md"
#> 
#> $URL_ReleaseNotes
#> [1] "http://www.prostar-proteomics.org/md/versionNotes.md"
#>