R Shiny error - how to download uploaded file after transformation - r

Question

I would like to be able to upload a dataset, select a set of columns, transform the selected columns (i.e. apply a function), then download the modified file. I have been trying to do so with the following code:
library(shiny)
library(DT)
library(shinyWidgets)
library(plyr)
library(dplyr)
library(RecordLinkage)
library(readxl)
cleanup <- function(x){
x <- as.character(x) # convert to character
x <- tolower(x) # make all lowercase
x <- trimws(x, "both") # trim white space
return(x)
}
ui <- fluidPage(
h2("Record Linkage Data"),
fileInput("file1", "Upload file for cleaning", accept = c("xls", "csv"), multiple = F),
actionButton(inputId = "clean", label = "Clean Data"),
downloadButton("download1", "Download file1"),
pickerInput(width = "75%",
inputId = "pick_col1",
label = "Select columns to display",
choices = colnames(file1),
selected = colnames(file1),
options = list(
`actions-box` = T,
`selected-text-format` = paste("count > ", length(colnames(file1)) - 1),
`count-selected-text` = "Alle",
liveSearch = T,
liveSearchPlaceholder = T
),
multiple = T),
DT::dataTableOutput("mytable")
)
load_path <- function(path) {
req(input$file)
ext <- tools::file_ext(path)
if (ext == "csv"){
read.csv(path, header = T)
} else if (ext == "xls" || ext == "xlsx"){
read_excel(path)
} else{
stop("Unknown extension: '.", ext, "'")
}
}
server <- function(input, output, session){
file1 <- reactive(load_path(input$selection$datapath[[1]]))
#file2 <- reactive(load_path(input$selection$datapath[[2]]))
eventReactive(input$clean, {
output$mytable <- DT::renderDataTable({
data.frame(lapply(select(file1, input$pick_col1), cleanup))
})
})
output$download <- downloadhandler(
filename = function(){
paste0(tools::file_path_sans_ext(input$filename), ".csv")
},
content = function(file){
write.csv(data(), file)
}
)
}
shinyApp(ui, server)
When I run the above code, I get the error : Error in is.data.frame(x) : object 'file1' not found. I am unsure why this is but I have been struggling to understand naming things in shiny. For example: I want to upload file1, then transform it. Do I continue to refer to file1 when I want to download it? These may seem like silly questions but I am asking because I don't know and I'm trying to learn. There seem to be lots of different approaches.
I would like to:
1. Load a file
2. Select columns (pickerInput is what I have been trying, but selectInput would suffice I suppose)
3. via action button, apply a pre-specified function to the selected columns
4. download the transformed dataset as a .csv

Answer 1

I've encountered some problems
It is a very silly one (it happens to all of us). You should write downloadHandler instead of downloadhandler.
The main problem: Your pickerInput is trying to select the column names of the data frame file1 when it does not exists. When you run the application the code is trying to find a file1 data frame and look its column names, but since at that time you haven't uploaded anything yet, it throws an error.
On how you read files: I am not familiar with how you read files, I suggest you do something similar than what is done in this example. https://shiny.rstudio.com/gallery/file-upload.html. Note you need to use a read.* function and point the result to another name, df in the example.
How would I solve it:
1. Set choices and selected options to NULL by default. Something like the following should work:
pickerInput(width = "75%",
inputId = "pick_col1",
label = "Select columns to display",
choices = NULL,
selected = NULL,
options = list(
`actions-box` = T,
# `selected-text-format` = paste("count > ", length(colnames(file1)) - 1),
`count-selected-text` = "Alle",
liveSearch = T,
liveSearchPlaceholder = T
),
multiple = T)
Add an updatePickerInput in the server side within an observeEvent. Something like this should work.
observeEvent(input$file1, {
req(input$file1) # ensure the value is available before proceeding
df <- read.csv(input$file1$datapath)
updatePickerInput(session = session,
inputId = "pick_col1",
choices = colnames(df),
# ... other options)
})
I haven't looked much if there are other problems with the code.
I suggest you start from the example in the link shared and start modifying it until you get what you want.
If that does not work, let me know and I can try to figure it out
Good luck!