inst/extdata/workflow/PipelineB/PipelineB.R

In samWieczorek/DAPAR2: Tools for the Differential Analysis of Proteins Abundance with R

#' @title Shiny example module `Pipeline B`
#'
#' @description
#' This module contains the configuration information for the corresponding pipeline.
#' It is called by the nav_pipeline module of the package MagellanNTK
#' This documentation is for developpers who want to create their own pipelines nor processes
#' to be managed with `MagellanNTK`.



#' @rdname example_PiplelineB
#' @export
#' 
PipelineB_conf <- function(){
  Config(
    mode = 'pipeline',
    fullname = 'PipelineB',
    steps = c('Process1', 'Process2', 'Process3'),
    mandatory = c(FALSE, FALSE, TRUE)
  )
}



#' @param id xxx
#'
#' @rdname example_pipelineB
#'
#' @author Samuel Wieczorek
#' 
#' @export
#' 
PipelineB_ui <- function(id){
  ns <- NS(id)
}



#' @param id xxx
#'
#' @param dataIn The dataset
#'
#' @param steps.enabled A vector of boolean which has the same length of the steps
#' of the pipeline. This information is used to enable/disable the widgets. It is not
#' a communication variable between the caller and this module, thus there is no
#' corresponding output variable
#'
#'
#' @param remoteReset It is a remote command to reset the module. A boolean that
#' indicates is the pipeline has been reseted by a program of higher level
#' Basically, it is the program which has called this module
#'
#' @param steps.status xxx
#' 
#' @param current.pos xxx
#' 
#' @rdname example_pipelineA
#'
#' @import shiny
#' @importFrom stats setNames
#' 
#' @export
#'
PipelineB_server <- function(id,
                             dataIn = reactive({NULL}),
                             steps.enabled = reactive({NULL}),
                             remoteReset = reactive({FALSE}),
                             steps.status = reactive({NULL}),
                             current.pos = reactive({1}),
                             path = NULL
                             ){

  # Contrary to the simple workflow, there is no widget in this module
  # because all the widgets are provided by the simple workflows.
  widgets.default.values <- NULL
  rv.custom.default.values <- NULL
  
  ###-------------------------------------------------------------###
  ###                                                             ###
  ### ------------------- MODULE SERVER --------------------------###
  ###                                                             ###
  ###-------------------------------------------------------------###
  moduleServer(id, function(input, output, session) {
    ns <- session$ns
    
    core.code <- Get_Workflow_Core_Code(
      mode = 'pipeline',
      name = id,
      w.names = names(widgets.default.values),
      rv.custom.names = names(rv.custom.default.values)
    )
    
    eval(str2expression(core.code))
    
    rv.custom <- reactiveValues()
    
    
    # Insert necessary code which is hosted by MagellanNTK
    # DO NOT MODIFY THIS LINE
    eval(parse(text = Module_Return_Func()))
  }
  )
}