Merge pull request #54 from ipb-halle/fix/project_export

Fix/project export

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -10,6 +10,7 @@ Depends:
     shiny,
     shinyBS,
     shinyjs,
+    shinybusy,
     DT,
     colourpicker,
     Matrix,
@@ -29,7 +30,7 @@ Suggests:
     testthat
 VignetteBuilder: knitr
 Maintainer: Hendrik Treutler<[email protected]>
-Description: DiffLogo is an easy-to-use tool for the discovery of regulated metabolite families.
+Description: We present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide.
 License: GPL (>= 2)
 biocViews: Software, Visualization
 Collate:

MetFamily/R/R_packages.R

@@ -13,6 +13,8 @@ library("DT")
 library("colourpicker")
 #install.packages("shinyBS")
 library("shinyBS")
+#install.packages("shinybusy")
+library("shinybusy")
 
 ##############################################################################################################
 ## mass spectrometry

MetFamily/app_files/server_functionsDownloads.R

@@ -230,10 +230,12 @@ writeTable <- function(precursorSet, file){
   #gz1 <- gzfile(description = file, open = "w")
   #write.table(x = dataFrame, file = gz1, sep = "\t", row.names = FALSE, col.names = FALSE, quote = FALSE)
   #close(gz1)
+  show_modal_spinner(spin="scaling-squares", text="\nMerging project files to csv. This can take several minutes!")
   lines <- createExportMatrix(precursorSet)
   gz1 <- gzfile(description = file, open = "w")
   writeLines(text = lines, con = gz1)
   close(gz1)
+  remove_modal_spinner()
 }
 ## individual downloads
 output$downloadGlobalMS2filteredPrecursors <- downloadHandler(
@@ -286,13 +288,22 @@ output$downloadSelectedPrecursors <- downloadHandler(
   },
   contentType = 'text/csv'
 )
-output$downloadAllPrecursors <- downloadHandler(
-  filename = function() {
-    createExportMatrixName()
-  },
-  content = function(file) {
-    precursorSet <- 1:dataList$numberOfPrecursors
-    writeTable(precursorSet = precursorSet, file = file)
+#Obvserve button for exporting the project
+observeEvent(input$prepareAllPrecursors, {
+  ExportMatrixName <<- createExportMatrixName()
+  precursorSet <- 1:dataList$numberOfPrecursors
+  writeTable(precursorSet = precursorSet, file = file.path(tempdir(),ExportMatrixName))
+  showModal(modalDialog(title = "Download", footer = NULL, size="s", fluidRow(column(12, p("Your download is ready."))), 
+                        fluidRow(column(3,downloadButton(outputId = "downloadAllpreparedPrecursors", label = "Download project"))),
+))
+})
+#Serving the modal with the download button to download the project
+output$downloadAllpreparedPrecursors <- downloadHandler(
+  filename <- ExportMatrixName, 
+  content = function(file){
+    file.copy(file.path(tempdir(),ExportMatrixName), file)
+    file.remove(file.path(tempdir(),ExportMatrixName))
+    removeModal()
   },
   contentType = 'text/csv'
 )

MetFamily/server.R

@@ -110,6 +110,7 @@ sourceTheCode()
 ## server-side logic of the Shiny app
 shinyServer(
   func = function(input, output, session) {
+    show_modal_spinner(spin = "self-building-square", text="Loading libraries")
     #########################################################################################
     #########################################################################################
     ## global variables per user
@@ -123,6 +124,9 @@ shinyServer(
     artifactColor  <- "red"
     selectionNone  <- "None"
 
+    ## Download names
+    ExportMatrixName <- NULL
+
     ## GUI constants
     runRightColumnWidthFull <- 12
     legendColumnWidthFull <- 2
@@ -214,6 +218,7 @@ shinyServer(
     #########################################################################################
     #########################################################################################
     ## observer
+    remove_modal_spinner() #Remove preparing message
 
     ## controls
     obsTabs <- observeEvent(input$runTabs, {