Shiny app doesn't wait for file upload

[Bobbie Shaban]

Hi,

I'm new to Shiny (last 4-5 days), I've written basic R scripts before but I'm basically a PERL programmer. I am having an issue with a shiny app that I am making. I have a file input where I upload a csv file and from there, there are a couple of selectInputs which are updated according to the users choice.

The problem is that when I run the script it does't seem to wait for the file to upload before it continues on to populating the select inputs with data from the csv. I've tried incorporating pauseable.R into my app but it's giving me similar errors.

My ui.R is

Enter code here...shinyUI(fluidPage(

  

  # Application title

  withMathJax(),

  uiOutput('mj1'),

  

  # Sidebar panel

  sidebarPanel(

    #Selector for file upload

    fileInput('file1', 'Choose file to upload',

              accept = c(

                'text/csv',

                'text/comma-separated-values',

                'text/tab-separated-values',

                'text/plain',

                '.csv',

                '.tsv'

              )),

    

    #drop down for each users choice

    selectInput("gene", "Genes", choices = NULL, selected = NULL),

    selectInput("allele", "Allele", choices = NULL, selected = NULL),

    selectInput("population", "Population", choices = NULL, selected = NULL),

      

    #complete formula calculation

    actionButton("goButton", "Calculate!")

  ),

  

    mainPanel(

      textOutput("c"),

      textOutput("s" ),

      textOutput("t"),

      textOutput("f_A"),

      textOutput("Result"),

      

      plotOutput("plot1")

    )

  

))

and my server.R is

library(shiny)

source("pausable.R")

# Define server logic required to give an output

shinyServer(function(input, output, session) {

  

  #set reactive values

  values <- reactiveValues(df_data = NULL)

  

  #pause file upload

  fileupload <- pauseableReactive(input$file1)

  

  pauseFileUpload <- function(paused=TRUE){

    pause(fileupload, paused)

  }

  

  #load and read csv

  filedata <- reactive({

    if(is.null(filedata)) return (NULL)

    isolate({

      pauseFileUpload(TRUE)

      infile <- input$file1

      read.csv(infile$datapath)

      invokeLater(function(){

        pauseFileUpload(FALSE)

        }, 500)

      })

    #infile <- read.csv("KIRIMP.csv")

     # outputOptions(output, 'fileUploaded', suspendWhenHidden=FALSE)

  })

   

    #render forumula withMathJax

  output$mj1 <- renderUI({

    withMathJax('$$\\frac{N_A}{N_B}=cr^2=\\frac{c(s + t - 1) ^2}{[(s + t -1) + \\frac{ 1 - t }{f_A}]  [(s + t = 1) + \\frac{1 -s}{1-f_A}]}$$')

  })

  #observe the genes list and update genes drop down 

  observe({

    values$df_data = filedata()

    genesList = values$df_data[1]

    updateSelectInput(session, "gene", "Genes ", unique(genesList))

  })

  #observe changes in the genes dropdown and update allele drop down

  observeEvent(input$gene, {

      cvsInput = filedata()

      cvsInput.gene.sub <- as.data.frame(subset(cvsInput, Gene == input$gene, drop=FALSE, byrow=TRUE))

      updateSelectInput(session, "allele", "Allele ", cvsInput.gene.sub[, 6])

  })

  

  #observe allele drop down and populate population drop down

  observeEvent(input$allele, {

      cvsInput = filedata()

      cvsInput.allele.sub <- as.data.frame(subset(cvsInput, Allele == input$allele & Gene == input$gene, drop=FALSE, byrow=TRUE))

      updateSelectInput(session, "population", "Population ", cvsInput.allele.sub[, 12])

  })

  

  #observe population drop down and show selected rows in text output

  observeEvent(input$goButton, {

    input$goButton

    isolate({

     cvsInput = filedata()

       #perform formula calc

        output$plot1 <- renderPlot({

          plot(plotValue)

        })# end render plot

        

    }) # end isolate

  })# end observeEvent(input$goButton)

  

})# end shiny server

The error I am getting is below, which makes me think that it's continuing to the observe function without waiting for the csv upload.

Any help would be greatly appreciated, thanks!

Warning: Error in read.table: 'file' must be a character string or connection

Stack trace (innermost first):

    77: read.table

    76: read.csv

    69: isolate

    68: <reactive:filedata> [/Users/bshaban/Documents/shiny/power/power/server.R#29]

    57: filedata

    56: observerFunc [/Users/bshaban/Documents/shiny/power/power/server.R#48]

     1: runApp

Warning: Error in read.table: 'file' must be a character string or connection

Bobbie.

[Bobbie Shaban]

All good,

I've just discovered the wonderful world of eventReactive.

changing to this seems to work

filedata <- eventReactive(input$file1, {

    if(is.null(filedata)) return (NULL)

      infile <- input$file1

      read.csv(infile$datapath)

  })

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[omayma Said]

You could try req(). Here req() will check for the required value` input$file1` before proceeding to read.csv.

#load and read csv
  filedata <- reactive({

    req(input$file1)
    read.csv(input$file1$datapath)
  })

[Bobbie Shaban]

I didn't think about req, thanks!

eventReactive also worked for me. 

Thanks heaps!

Bobbie.