Replace download handler to be excel only

app.R

@@ -81,7 +81,7 @@ ui <- dashboardPage(
             #menuItem("Habitats", tabName = "3", icon = icon("atlas")),
             #menuItem("Ingestion", tabName = "3", icon = icon("utensils")),
             selectInput("modelSelect", "Select MESO model", choices = c(""), selected = NULL, multiple = FALSE),
-            downloadButton("download", "", icon = icon("download")),
+            #downloadButton("download", "", icon = icon("download")),
             uiOutput("pressureList")
         )
       ),
@@ -149,8 +149,16 @@ ui <- dashboardPage(
                 actionButton("layer1Slider", "1", icon = icon("sliders-h"))
               ),
               column(
-                width = 5,
+                width = 2,
-                strong("Customise sensitivity weightings")
+                p("Custom sense weighting")
+              ),
+              column(
+                width = 1,
+                downloadButton("download", "", icon = icon("download"))
+              ),
+              column(
+                width = 2,
+                p("Download results as Excel workbook")
               )
             ),
             plotlyOutput("layer1", height = "270px") %>% withSpinner(),
@@ -281,7 +289,7 @@ server <- function(input, output, session) {
   modelList <- getAvailableModels()
 
 
-  calcLikelihood <- function(layer, pressStatus) {
+  calcLikelihood <- function(layer, pressStatus, forPlotly) {
 
     isolate({
 
@@ -329,21 +337,36 @@ server <- function(input, output, session) {
 
     print(paste("Building likelihoods from model, sample dists", length(thisModel$p_es$nodes$name), length(sampleDists)))
 
-    return(data.frame(
+    if (forPlotly) {
-      name = thisModel$p_es$nodes$name,
+      return(data.frame(
-      code = thisModel$p_es$nodes$code,
+        name = thisModel$p_es$nodes$name,
-      layer = thisModel$p_es$nodes$layer,
+        code = thisModel$p_es$nodes$code,
-      range = c(
+        layer = thisModel$p_es$nodes$layer,
-        apply(sampleDists, 2, min),
+        range = c(
-        means - 2*stdDev,
+          apply(sampleDists, 2, min),
-        means - stdDev,
+          means - 2*stdDev,
-        means,
+          means - stdDev,
-        means + stdDev,
+          means,
-        means + 2*stdDev,
+          means + stdDev,
-        apply(sampleDists, 2, max)
+          means + 2*stdDev,
-      ),
+          apply(sampleDists, 2, max)
-      stringsAsFactors = FALSE
+        ),
-    ))
+        stringsAsFactors = FALSE
+      ))
+    } else {
+
+      return(data.frame(
+        name = thisModel$p_es$nodes$name,
+        code = thisModel$p_es$nodes$code,
+        layer = thisModel$p_es$nodes$layer,
+        means = means,
+        stdDev = stdDev,
+        mins = apply(sampleDists, 2, min),
+        maxes = apply(sampleDists, 2, max),
+        stringsAsFactors = FALSE
+      ))
+      
+    }
   }
 
 
@@ -367,7 +390,7 @@ server <- function(input, output, session) {
       if (!identical(newStatus, .selections$pressStatus)) { #} || .selections$runOnce) {
         #.selections$runOnce = FALSE
         print("Running calc")
-        .likelihoods$p_es <<- calcLikelihood(0, newStatus)
+        .likelihoods$p_es <<- calcLikelihood(0, newStatus, TRUE)
         .selections$pressStatus <<- newStatus
       }
 
@@ -447,7 +470,7 @@ server <- function(input, output, session) {
     .resistanceScores["pressSD"] <<- input$l1PressSD
 
     print("Running calc")
-    .likelihoods$p_es <<- calcLikelihood(0, .selections$pressStatus)
+    .likelihoods$p_es <<- calcLikelihood(0, .selections$pressStatus, TRUE)
     removeModal()
 
   })
@@ -633,64 +656,6 @@ server <- function(input, output, session) {
       return(FALSE);
   }
 
-  exportOrca <- function (p, file = "plot.png", format = tools::file_ext(file),
-    scale = NULL, width = NULL, height = NULL,
-    verbose = FALSE, debug = FALSE, safe = FALSE)
-  {
-      if (Sys.which("orca") == "") {
-          stop("The orca command-line utility is required to use the `orca()` function.\n\n",
-              "Follow the installation instructions here -- https://github.com/plotly/orca#installation",
-              call. = FALSE)
-      }
-
-      b <- plotly_build(p)
-
-      plotlyjs <- b$dependencies[sapply(b$dependencies, function(d) { d$name == "plotly-main" })][[1]]
-
-      if (!isAbsolutePath(plotlyjs$src$file)) {
-        plotlyjs_file <- NULL
-        for(n in 1:length(.Library.site)) {
-          if (!is.null(plotlyjs_file)) {
-            next
-          }
-          f <- paste0(.Library.site[[n]], "/plotly/", plotlyjs$src$file, "/", plotlyjs$script)
-          if (file.exists(f)) {
-            plotlyjs_file <- f
-          }
-        }
-      } else {
-        plotlyjs_file <- file.path(plotlyjs$src$file, plotlyjs$script)
-      }
-
-      args <- c(
-        "graph", paste0("'", jsonlite::toJSON(
-          b$x[c("data", "layout")],
-          digits = 50,
-          auto_unbox = TRUE,
-          force = TRUE,
-          null = "null",
-          na = "null"
-        ), "'"),
-        "-o", file,
-        "--format", format,
-        "--plotlyjs", plotlyjs_file
-      )
-      if (debug)
-          args <- c(args, "--debug")
-      if (verbose)
-          args <- c(args, "--verbose")
-      if (safe)
-          args <- c(args, "--safe-mode")
-      if (!is.null(scale))
-          args <- c(args, "--scale", scale)
-      if (!is.null(width))
-          args <- c(args, "--width", width)
-      if (!is.null(height))
-          args <- c(args, "--height", height)
-
-      invisible(system2("orca", args))
-  }
-
   output$linkBackgroundData <- downloadHandler(
     filename = getModelName(),
     content = function(file) {
@@ -700,8 +665,12 @@ server <- function(input, output, session) {
   )
 
   output$download <- downloadHandler(
-    filename = function() { paste0("MESO-", format(Sys.time(), "%m%d_%H%M"), ".zip") },
+    
+    
+    filename = function() { paste0("MESO-", format(Sys.time(), "%m%d_%H%M"), ".xlsx") },
     content = function(file) {
+      print("STARTING download")
+      
       showModal(
         modalDialog(
           fluidRow(
@@ -718,29 +687,33 @@ server <- function(input, output, session) {
       setwd(tmp)
 
       #Get the network graph
-      l1 <- exportOrca(prepPlot("ba", "Bio-Assemblage"), "layer1.png")
+      #l1 <- exportOrca(prepPlot("ba", "Bio-Assemblage"), "layer1.png")
-      l2 <- exportOrca(prepPlot("op", "Output Processes"),"layer2.png")
+      #l2 <- exportOrca(prepPlot("op", "Output Processes"),"layer2.png")
-      l3 <- exportOrca(prepPlot("es", "Ecosystem Services"),"layer3.png")
+      #l3 <- exportOrca(prepPlot("es", "Ecosystem Services"),"layer3.png")
 
       #Save pressure list, confidence levels, node and edge tables in xlsx
+      
       l <- list(
         pressures = .selections$pressStatus,
         nodes = modelList[[.selections$model]]$p_es$nodes,
         edges = modelList[[.selections$model]]$p_es$edges,
-        settings = as.data.frame(cbind(names(.resistanceScores), .resistanceScores), stringsAsFactors = FALSE)
+        settings = as.data.frame(cbind(names(.resistanceScores), .resistanceScores), stringsAsFactors = FALSE),
+        likelihoods = calcLikelihood(0, .selections$pressStatus, FALSE)
       )
       xl <- write.xlsx(l,  "dataset.xlsx")
 
-      zipFile <- zipr(file, c("layer1.png", "layer2.png", "layer3.png", "dataset.xlsx"))
+      #zipFile <- zipr(file, c("dataset.xlsx"))
       
-      print(paste("zip file complete", zipFile))
+      file.copy("dataset.xlsx", file)
+
+      #print(paste("zip file complete", zipFile))
 
       setwd(oldDir)
       unlink(tmp)
 
       removeModal()
     },
-    contentType = "application/zip"
+    contentType = "application/xlsx"
   )