file.copy, loadworkbook not working in R shiny reactive environment but working outside reactive environment

Question

I have created the following app to read an excel file from the temp folder in R. I would like to retain the file format in R shiny

library(XLConnect)
library(shiny)
library(openxlsx)
library(readxl)

ui <- fluidPage(   
titlePanel("Writer App"),
sidebarLayout(sidebarPanel(fileInput(inputId = "file", label = "Read File Here", accept = c(".xlsx")), downloadLink("downloadData", "Download")), mainPanel(dataTableOutput(outputId = "table1"))))



server <- function(input, output) {
datasetInput <- reactive({
infile<- input$file
if (is.null(infile))
  return(NULL)    
#READ .XLSX AND .CSV FILES
if(grepl(infile, pattern = ".xlsx" )==T){data=read_excel(infile$datapath)} else 
if(grepl(infile , pattern = ".csv" )==T){data=read.csv(infile$datapath )}

#RENAME DATAFRAME WITH UNDERSCORES
names(data)<-gsub(pattern = " ", replacement = "_", x =  names(data))
return(data) })
output$table1 <- renderDataTable({     
return(datasetInput())})


 output$downloadData <- downloadHandler(
  filename = function() {
  paste("data-", Sys.Date(), ".xlsx", sep="")},
  content = function(file) {
  tf<-tempdir()
  Files=list.files(path=tf, pattern=".xlsx", recursive = TRUE)[1]       
  file.copy(from =paste0(tf, "/",Files ), to= "temp_1.xlsx")     
  wb2 <- loadWorkbook(file = "temp_1.xlsx")
  df_1<-data.frame("DF"= c(1:3))      
  addWorksheet(wb = wb2,sheetName =  "Parameters1")
  writeData(wb2, "Parameters1", df_1, startCol = 1, startRow = 2, rowNames = TRUE)
  saveWorkbook(wb2, file)})
  }

 shinyApp(ui = ui, server = server)

The Download button(output$downloadData) has a command to copy the file including the format from a temporary location to a new file temp.xlsx. this file is next loaded as workbook. a New sheet Parameters1 is added to the workbook wb2. Next, data frame(df_1) is written to sheet Parameters1 and the file is downloaded.

Now, the code within the output$downloadData works in the R console but doesnt work in the reactive environment of R shiny.

There seems to be an error in loadworkbook command. I am able to get the file by means of read_excel and then inserting the data. That however doesnt prserve the format of the loaded excel sheet. I request someone to guide me in this.

Which file is this that you are reading? `Files=list.files(path=tf, pattern=".xlsx", recursive = TRUE)[1] ` Is it the same excel file that the user uploads ? — Ronak Shah, Sep 14 '21 at 11:37
yes. it is the same file. But it is stored in a temporary folder by shiny for reasons of data security. The wb2 object gets created. apparently the issue is with save function. thats where the issue appears to be — Raghavan vmvs, Sep 14 '21 at 11:51

score 1 · Accepted Answer · answered Sep 14 '21 at 12:43

This works for me without any error.

library(shiny)
library(openxlsx)
library(readxl)

ui <- fluidPage(   
  titlePanel("Writer App"),
  sidebarLayout(sidebarPanel(fileInput(inputId = "file", label = "Read File Here", accept = c(".xlsx")), downloadLink("downloadData", "Download")), 
                mainPanel(dataTableOutput(outputId = "table1"))))



server <- function(input, output) {
  datasetInput <- reactive({
    infile<- input$file
    if (is.null(infile))
      return(NULL)   
    #READ .XLSX AND .CSV FILES
    if(grepl(infile$datapath, pattern = ".xlsx" )){data=read_excel(infile$datapath)} else 
      if(grepl(infile$datapath , pattern = ".csv" )){data=read.csv(infile$datapath )}
    
    #RENAME DATAFRAME WITH UNDERSCORES
    names(data)<-gsub(pattern = " ", replacement = "_", x =  names(data))
    return(data) 
})
  
  output$table1 <- renderDataTable({     
    return(datasetInput())})
  
  
  output$downloadData <- downloadHandler(
    filename = function() {
      paste("data-", Sys.Date(), ".xlsx", sep="")},
    content = function(file) {
      tf<-tempdir()
      Files=list.files(path=tf, pattern=".xlsx", recursive = TRUE)[1]    
      file.copy(from =paste0(tf, "/",Files ), to= "temp_1.xlsx")     
      wb2 <- loadWorkbook(file = "temp_1.xlsx")
      df_1<-data.frame("DF"= c(1:3))      
      addWorksheet(wb = wb2,sheetName =  "Parameters1")
      writeData(wb2, "Parameters1", df_1, startCol = 1, startRow = 2, rowNames = TRUE)
      saveWorkbook(wb2, file)
})
}

shinyApp(ui = ui, server = server)

I get this error" Warning: Error in [[: subscript out of bounds [No stack trace available]" — Raghavan vmvs, Sep 14 '21 at 12:47
It may be a version issue. will reinstall R and my packages and check — Raghavan vmvs, Sep 14 '21 at 13:27

score 0 · Answer 2 · answered Sep 15 '21 at 04:53

The issue is solved with the use of xlconnect package. Here is the code I employed

library(XLConnect)
library(shiny)
library(readxl)

 ui <- fluidPage(   
 titlePanel("Writer App"),
 sidebarLayout(sidebarPanel(fileInput(inputId = "file", label = "Read File 
 Here", accept =c(".xlsx")), downloadButton("downloadData", "Download")),                  
 mainPanel(dataTableOutput(outputId = "table1"))))

 server <- function(input, output) {
 datasetInput <- reactive({
 infile<- input$file
 if (is.null(infile))
  return(NULL)    
#READ .XLSX AND .CSV FILES
if(grepl(infile, pattern = ".xlsx" )==T){
  data=read_excel(infile$datapath)
} else if(grepl(infile , pattern = ".csv" )==T)
{data=read.csv(infile$datapath )}

#RENAME DATAFRAME WITH UNDERSCORES
names(data)<-gsub(pattern = " ", replacement = "_", x =  names(data))
return(data) })
output$table1 <- renderDataTable({     
return(datasetInput())})
 output$downloadData <- downloadHandler(
 filename = function() {
  "file.xlsx"},
content = function(file) {
wdf<-getwd()      
tf<-tempdir()      
Files=list.files(path=tf, pattern=".xlsx", recursive = TRUE)[1]
newWB <- loadWorkbook(filename=paste0(tf,"/",Files),create=TRUE)
createSheet(object = newWB,name='Parameters')
writeWorksheet(newWB,data=data.frame("X"=c(1:10),"Y"= 
c(1:10)),sheet='Parameters',header=TRUE,rownames=NULL)
saveWorkbook(object = newWB, file = file)})
}
shinyApp(ui = ui, server = server)

Note: I have commented openxlsx to avoid incompatibility between openxlsx and xlconnect. Another change involves the removal of xlsx package as this is also incompatible with xlconnect

file.copy, loadworkbook not working in R shiny reactive environment but working outside reactive environment

2 Answers2