R/Module_SaveNetworkModule.R

In mjhelf/Mosaic: Metaboseek platform

#' SaveNetworkModule
#' 
#' Module for saving molecular network data
#' 
#' @inherit MseekModules
#' 
#' @return Returns nothing
#' 
#' @describeIn SaveNetworkModule Server logic
#' 
#' @export 
SaveNetworkModule <- function(input,output, session,
                            values = reactiveValues(Networks = NULL,
                                                    projectData = NULL),
                            reactives = reactive({list(graphname = NULL,
                                                       filename = "table.graphml")}),
                            static = list(tooltip = "Save Network as a graphml file",
                                          label = "Save Network",
                                          allowformats = list("Metaboseek Graph (.mskg)" = ".mskg",
                                              "graphML" = ".graphML"))
){
  ns <- NS(session$ns(NULL))
  
  internalValues <- reactiveValues(selectedFormat = if(length(static$allowedformats)){static$allowedformats[[1]]}else{".graphML"})
  
  output$saveNetworkButton <- renderUI({
    div(title = static$tooltip,
    actionButton(ns("savenetwork"), static$label, icon = icon("floppy-save", lib = "glyphicon"))
    )
  })
  
  observeEvent(input$savenetwork,{
    
    if(!is.null(reactives()$graphname) &&  reactives()$graphname %in% names(values$Networks) ){
    
    showModal(
      modalDialog(
        fluidPage(
          fluidRow(
            p(strong("You can save this network in your project folder, or download it through your browser"))
          ),
          hr(),
          tagList(if(length(static$allowformats) > 0){
              tagList(
                  fluidRow(
                      div(title = "Select a file format for export",
                          selectizeInput(ns("selFormat"), "Format:",
                                         choices = static$allowformats))
                  )
              )
          }),
          fluidRow(
            column(6, div(title = "Download table through Browser",     downloadButton(ns("modalDownload"),"Download"))),
            column(6, div( title = "Save directly to current projectFolder (only works if you are working in a project folder). WIll save in both graphML and .mskg formats",
                           actionButton(ns("modalProjectFolder"), "Save locally")))
          )),
        title = "Save table",
        easyClose = T,
        fade = F,
        size = "s",
        footer = modalButton("Cancel") 
      ))
    
    
  }else{
    showNotification(paste("No network available to be saved!"), type = "error", duration = 10)
    
    
    
  }
    
  })
  observeEvent(input$selFormat,{
      if(length(input$selFormat)){
      internalValues$selectedFormat <- input$selFormat
      }
  })
  
  output$modalDownload <- downloadHandler(filename= function(){paste0(basename(reactives()$filename),internalValues$selectedFormat)}, 
                                          content = function(file){
                                            try({
                                                saveMseekGraph(values$Networks[[reactives()$graphname]],
                                                               file,
                                                               writeGraphML = internalValues$selectedFormat == ".graphML",
                                                               writeRDS = internalValues$selectedFormat == ".mskg"
                                                )
                                            
                                            showNotification(paste("Downloading file: ", basename(reactives()$filename)), duration = 10)
                                            })
                                            removeModal()
                                          }#,
                                          #contentType = "text/xml"
                                          )
  
  
  # observeEvent(output$modalDownload,{
  #   print(output$modalDownload)
  # 
  # })
  
  observeEvent(input$modalProjectFolder,{
    
    if(!is.null(values$projectData$projectFolder)){
      
      if(!dir.exists(dirname(file.path(values$projectData$projectFolder, reactives()$filename)))){
        dir.create(dirname(file.path(values$projectData$projectFolder, reactives()$filename)), recursive = T)
      }
      
        saveMseekGraph(values$Networks[[reactives()$graphname]],
                       file.path(values$projectData$projectFolder, reactives()$filename),
                       writeGraphML = TRUE, writeRDS = TRUE
                       )

      showNotification(paste("Network saved in project folder as: ", file.path(values$projectData$projectFolder, reactives()$filename)), duration = 10)
      removeModal()
      
    }
    else{
      showNotification(paste("You have to work in a Project Folder to save files this way!"), type = "error", duration = 10)
    }
  })
  
  
  
}

#' @describeIn SaveNetworkModule UI elements
#' @export
SaveNetworkModuleUI <- function(id)
{
  ns <- NS(id)
  
  htmlOutput(ns("saveNetworkButton"))
  
}