docs/reference/mod_pipeline_process.R

In samWieczorek/Magellan: A Pipeline Manager

mod_pipeline_process_ui <- function(id){
	ns <- NS(id)
}


mod_pipeline_process_server <- function(id,
		dataIn = reactive({NULL}),
		steps.enabled = reactive({NULL}),
		remoteReset = reactive({FALSE})
		){

	# This list contains the basic configuration of the process
	config <- list(
		# Name of the process
		name = 'process',
		# Name of the pipeline it belongs to
		parent = 'pipeline',
		# List of all steps of the process
		steps = c('Description', 'Step 1', 'Step 2', 'Save'),
		# A vector of boolean indicating if the steps are mandatory or not.
		mandatory = c(TRUE, TRUE, FALSE, TRUE)
		)

	# # Define default selected values for widgets
	widgets.default.values <- list(
		# The following lines are given as example. Our advice is to use the 
		same nomenclature for the variables of widgets:
		two strings separated by '_', the first one is the name of the step
		 while the secondone is the nameof the widget
		# Step1_select1 = 1,
		# Step1_select2 = NULL,
		# Step1_select3 = 1,
		# Step2_select2_1 = 1,
	# Step2_select2_2 = 1
	)

	###-------------------------------------------------------------###
	###                                                             ###
	### ------------------- MODULE SERVER --------------------------###
	###                                                             ###
	###-------------------------------------------------------------###
	moduleServer(id, function(input, output, session) {
		  ns <- session$ns

		# Declaration of the variables that will contain the values of the widgets
		# To avoid confusion, the first string is the name of the step while the second is the name
		# of the widget
		rv.widgets <- reactiveValues(
			#Step1_select1 = widgets.default.values$Step1_select1,
			#Step1_select2 = widgets.default.values$Step1_select2,
			#Step1_select3 = widgets.default.values$Step1_select3,
			#Step2_select2_1 = widgets.default.values$Step2_select2_1,
			#Step2_select2_2 = widgets.default.values$Step2_select2_2
		)

		# Reactive values during the run of the process
		rv <- reactiveValues(
			# Stores the object given in input of the process
			  dataIn = NULL,
			  # A vector of boolean indicating the status (UNDONE, SKIPPED or VALIDATED) of the steps
			  steps.status = NULL,
			  # xxx
			  reset = NULL,
			 # A vector of boolean indicating if the steps are enabled or disabled
			  steps.enabled = NULL
		)

		# Returned value of the process
		# * The trigger variable is used to trigger an event that can be catched by the 
		#   Shiny functions observe() and observeEvent()
		# * The value variable contains the object to return to the instance that has called the process.
		dataOut <- reactiveValues(
			  trigger = NULL,
			  value = NULL
			)

	# Initialization of the module
		observeEvent(steps.enabled(), ignoreNULL = TRUE, {
		if (is.null(steps.enabled()))
			rv$steps.enabled <- setNames(rep(FALSE, rv$length), 
	                                  rv$config$steps)
		  else
	    rv$steps.enabled <- steps.enabled()
		})

	# Set all the widgets to their default value after the remote Reset()
	observeEvent(remoteReset(), {
	  lapply(names(rv.widgets), function(x){
	    rv.widgets[[x]] <- widgets.default.values[[x]]
	  })
	})

	  ###### ------------------- Code for Description (step 0) -------------------------    #####
	  output$Description <- renderUI({
	  tagList(
	    includeMarkdown(paste0('md/', paste0(config$parent, '_', config$name, '.md'))),
	    uiOutput(ns('datasetDescription')),
	    uiOutput(ns('validationBtn_ui'))
	  )
	})


	observeEvent(input$btn_validate_Description, ignoreInit = TRUE, ignoreNULL = TRUE, {
	  rv$dataIn <- dataIn()
	  rv$steps.status['Description'] <- global$VALIDATED
	  dataOut$trigger <- Magellan::Timestamp()
	  dataOut$value <- rv$dataIn
	})

	output$validationBtn_ui <- renderUI({
	  if (isTRUE(rv$steps.enabled['Description'])  )
	    actionButton(ns('btn_validate_Description'),
	                 paste0('Start ', config$name),
	                 class = btn_success_color)
	  else
	    shinyjs::disabled(
	      actionButton(ns('btn_validate_Description'),
	                   paste0('Start ', config$name),
	                   class = btn_success_color)
	    )
	})

	# Return value of module
	# DO NOT MODIFY THIS PART
	list(config = reactive({
	  config$ll.UI <- setNames(lapply(config$steps,
	                                  function(x){
	                                    do.call('uiOutput', list(ns(x)))
	                                  }),
	                           paste0('screen_', config$steps)
				  )
			  config
			}),
		dataOut = reactive({dataOut})
	#steps.status = reactive({rv$steps.status})
	)
	}
	)