How to fix 'File not found' when using the downloadHandler?

Question

I just started to play around in shiny and made a simple app that reads a CSV file and replaces rows of one column with tokens. I would like the user to be able to download the tokenized data as a CSV file.

To do this I am using the downloadHandler() function. I have been looking in the documentation for this function, as well as similar questions in here but haven't been able to find a solution. I tried running the app externally as suggested in other similar questions.

app.R

# Only run examples in interactive R sessions
if (interactive()) {

  ui <- fluidPage(
    sidebarLayout(
      sidebarPanel(
        fileInput("file1", "Choose CSV File",
                  accept = c(
                    "text/csv",
                    "text/comma-separated-values,text/plain",
                    ".csv")
        ),
        tags$hr(),
        checkboxInput("header", "Header", TRUE),
        textInput(inputId = 'variable', label = 'Name of variable to pseudonymize', placeholder = 'e.g., ID_PA'),
        helpText("Case sensitive!"),
        downloadButton('downloadData', 'Download')
      ),
      mainPanel(
        tableOutput("contents"),
        br(), br(),
        tableOutput('results')
      )
    )
  )

  server <- function(input, output) {
    output$contents <- renderTable({
      # input$file1 will be NULL initially. After the user selects
      # and uploads a file, it will be a data frame with 'name',
      # 'size', 'type', and 'datapath' columns. The 'datapath'
      # column will contain the local filenames where the data can
      # be found.
      inFile <- input$file1

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

      head(read.csv(inFile$datapath, header = input$header))

    })

    output$results <- renderTable({
      # input$file1 will be NULL initially. After the user selects
      # and uploads a file, it will be a data frame with 'name',
      # 'size', 'type', and 'datapath' columns. The 'datapath'
      # column will contain the local filenames where the data can
      # be found.
      inFile <- input$file1

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

      df <- read.csv(inFile$datapath)

      # make sure to use utils::read_csv to read in data

      #  Function generates a lookup table that associates each unique identifier to an PSN. See lillemets
      get_lookup_table <- function(data, id.var, key.length) {
        if (any(duplicated(data[, id.var]))) warning('Duplicate id values in data. For longitudinal dataset, this is expected')
        PSN <- c(1,1) # Allow the while loop to begin
        while (any(duplicated(PSN))) { # Loop until all keys are unique
          PSN <- replicate(length(unique(data[, id.var])),
                           paste(sample(c(LETTERS, 0:9), key.length, replace = T), collapse = ''))
        }
        lookup.table <- data.frame(id = unique(data[, id.var]), key = PSN)
        return(lookup.table)
      }

      # Replace names with PSN
      add_PSN <- function(data, id.var, lookup.table) {
        data[, id.var] <- lookup.table[, 'key'][match(data[, id.var], lookup.table[, 'id'])]
        return(data)
      }

      lookup_table <- get_lookup_table(df, input$variable, 10)

      # Replace names with PSN
      pseudo_df <- add_PSN(df, input$variable, lookup_table)
      head(pseudo_df)


    })


    # Download file
    output$downloadData <- downloadHandler(
      filename = function() {
        paste("data-", Sys.Date(), ".csv", sep="")
      },
      content = function(file) {
        write.csv(pseudo_df, file)
      }
    )
  }

  shinyApp(ui, server)
}

When running the app and clicking download, I get the browser error 'File not found'. In the R console I get the warning: Error in is.data.frame: object 'pseudo_df' not found

Comments on this issue would be much appreciated.

Answer 1

The download handler does not know that the pseudo_df data frame was created. You probably want to have one reactive that makes the data frame and then separate render and download handlers that call the reactive that creates the data frame. So for example

make_df <- reactive({})  # code that makes the data frame goes here
output$results <- renderTable({make_df()})
output$downloadData <- downloadHandler(
  filename = function() {
    paste("data-", Sys.Date(), ".csv", sep="")
  },
  content = function(file) {
    write.csv(make_df(), file) # notice the call to the reactive again
  }
)