Passing the value of input$variable as an argument in Rshiny to external script call

Question

R shiny code being used is:

library(shiny)
library(shinyBS)
ui <-  fluidPage(
  headerPanel( list(tags$head(tags$style("body {background-color: #F4F6F6 ; }")))),
  titlePanel("RADP CR Prediction Tool"),
  br(),
  tags$head(tags$script(src = "message-handler.js")),
  textInput('Region', label = 'Enter the region'),
  textInput('Regulatory', label = 'Enter the regulatory status'),
  textInput('Description', label = 'Enter the description for the CR'),
  br(),
  br(),
  actionButton("goButton", "Go!"),
  mainPanel(textOutput('region'),textOutput('description')),
  bsModal("modalExample", "Your summary", "goButton", size = "large",dataTableOutput("data_summary"))
     )

server <- function(input,output,session) {
  #observe the add click and perform a reactive expression
  observeEvent( input$goButton,{
    x <- input$Region
    y <- input$Regulatory
    z<- input$Description
    print (x)
    system("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py input[[x]] ,'y', 'z'")
    MyData <- read.csv(file="/Users/ravinderbhatia/Downloads/data.csv", header=TRUE)
    #reactive expression
    output$region <- renderPrint(x)
    output$description <-renderPrint(y)
    output$data_summary <- renderDataTable({
      MyData
    })
  }
  )
}

shinyApp(ui, server)

Issue is in the follwing line:

 system("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py x,y,z")

How to pass the actual value of region in the system call. Here print(x) works fine, but when I pass x as a argument, I want to pass the value stored inside it.(input$region)

SeGa · Accepted Answer · 2018-05-14 12:15:11Z

1

Well, like that you are just passing a character x to the system, and it probably has no idea what to do with that.

What if you changed this line:

system("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py input[[x]] ,'y', 'z'")

to:

system(paste("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py", x, y, z))

just try out those few lines, where i replaced "system" with "print"

x= "desc"
y= "region"
z= "etc"
print("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py input[[x]] ,'y', 'z'")
print(paste("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py", x, y, z))

answered May 14, 2018 at 12:15

SeGa

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6 Comments

user2906657 Over a year ago

I have already tried passing x, y, z. That does not work. Python takes its x as an argument, not the value in it.

SeGa Over a year ago

What if you save the command in a variable and pass it then to system(). Like: a <- paste("/Users/ravinderbhatia/anaconda/bin/python /Users/ravinderbhatia/Downloads/Untitled3.py", x, y, z) system(a)

user2906657 Over a year ago

No success. Still it reads x,y,z only. Also not sure about the comas in between x,y and z.

SeGa Over a year ago

I tried to create a reproducible example and it works for me. It takes the values, that are assigned to x,y,z. I just changed the first part of the system-command to the full path of the python.exe. (system(paste("C:/Anaconda/python.exe C:/py_function.py", x, y, z))), as you are only pointing to python and not an executable ?

user2906657 Over a year ago

I am on Mac. Do not have executable.

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