"read_excel" in a Shiny app

Question

I have a Shiny app that uses the read.xlsx function from package xlsx. All works fine, but I want to change to read_excel from readxl, hoping it would be faster and able to cope with large files.

ui part:

fileInput("inputFile","Upload file...")

server part:

  data <- reactive({
    inFile <- input$inputFile
    if (is.null(inFile)) { return(NULL) }    
    dataFile <- read_excel(inFile$datapath,sheet=1)
    return(dataFile)
  })

I get the "Unknown format" error.

inFile$datapath is "/tmp/.../60974676c7287e913d1c0dc5/0"
inFile$type is "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"

Question 1: is there a way to tell read_excel that it's a xlsx type file?
Question 2: is it possible to control the location where the uploaded file will be stored?

Have you tried it in the *R* console with the same input file? — r2evans, Jun 03 '15 at 15:39

cdeterman · Accepted Answer · 2018-09-12T15:32:50.273

This was an open issue with the readxl package. The current workaround provided there is to copy the file data path and append .xlsx. Here is a working example on my machine limited to .xlsx files edited to use file.rename instead of file.copy.

library(shiny)
library(readxl)

runApp(
    list(
        ui = fluidPage(
            titlePanel("Use readxl"),
            sidebarLayout(
                sidebarPanel(
                    fileInput('file1', 'Choose xlsx file',
                              accept = c(".xlsx")
                              )
                    ),
                mainPanel(
                    tableOutput('contents'))
                )
            ),
        server = function(input, output){
            output$contents <- renderTable({
                inFile <- input$file1

                if(is.null(inFile))
                    return(NULL)
                file.rename(inFile$datapath,
                          paste(inFile$datapath, ".xlsx", sep=""))
                read_excel(paste(inFile$datapath, ".xlsx", sep=""), 1)
            })
        }
        )
    )

EDIT Note that with the 1.1.0 version of readxl it no longer needs to have the file renamed. The following works without a problem for me now.

library(shiny)
library(readxl)

runApp(
  list(
    ui = fluidPage(
      titlePanel("Use readxl"),
      sidebarLayout(
        sidebarPanel(
          fileInput('file1', 'Choose xlsx file',
                    accept = c(".xlsx")
          )
        ),
        mainPanel(
          tableOutput('contents'))
      )
    ),
    server = function(input, output){
      output$contents <- renderTable({

        req(input$file1)

        inFile <- input$file1

        read_excel(inFile$datapath, 1)
      })
    }
  )
)

Can you just rename it with `file.rename`? You'll likely need to clean up manually, but that is necessary anyway. — r2evans, Jun 03 '15 at 15:56

score 1 · Answer 2 · answered Jul 13 '15 at 14:17

to ensure that the user does upload an .xlsx file, or you need to check the extension you're self to switch between read functions. You can extract the extension as following:

library(shiny)
library(readxl)

runApp(
list(
    ui = fluidPage(
        titlePanel("Use readxl"),
        sidebarLayout(
            sidebarPanel(
                fileInput('file1', 'Choose xlsx file',
                          accept = c(".xlsx")
                          )
                ),
            mainPanel(
                tableOutput('contents'))
            )
        ),
    server = function(input, output){
        output$contents <- renderTable({
            inFile <- input$file1

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

            ext <- tools::file_ext(inFile$name)
            file.rename(inFile$datapath,
               paste(inFile$datapath, ext, sep="."))
            read_excel(paste(inFile$datapath, ext, sep="."), 1)
         })
        }
    )
)

"read_excel" in a Shiny app

2 Answers2

Linked