Problem with opening .sdf file on Shiny

[saura...@shiats.edu.in]

Dear All,

I am trying to upload structure-data file on shiny server using fileInput function in ui.R.

I wish to analyse the uploaded file using another package viz. ChemmineR and the resultant I want again to print on browser.

###############################################################

#My ui.R

library("shiny")

library("ChemmineR")

shinyUI(fluidPage(

  titlePanel("SDF input"),

  sidebarLayout(

    sidebarPanel(

      fileInput("file1", "Browse")

    ),

    mainPanel(dataTableOutput('ofile'))

    

)))

#My server.R

library("shiny")

library("ChemmineR")

shinyServer(function(input,output){

  

  data <- reactive({

   

   read.SDFset(sdfstr=input$file1)

      })

  output$ofile<- renderDataTable(data())

})

#My console

> runApp('C:/Users/saurav/Dropbox/office/Saurav_Saha_SHIATS/Chemoinformatics_uCARE/analysis/drug_class_based_Classification/r_scripts/web_gui/test')

Listening on http://127.0.0.1:5837

Warning: Error in seq: trying to get slot "a" from an object of a basic class ("NULL") with no slots

Stack trace (innermost first):

    94: seq

    93: lapply

    92: read.SDFset

    91: <reactive:data> [C:\Users\saurav\Dropbox\office\Saurav_Saha_SHIATS\Chemoinformatics_uCARE\analysis\drug_class_based_Classification\r_scripts\web_gui\test/server.R#8]

    80: data

    79: renderDataTable

    78: func

    77: origRenderFunc

    76: output$ofile

     1: runApp

#################################################

Please help. Thanks in advance,

Saurav

[Bárbara Borges]

Can you open the same file (using the same function) from the console? If you can't, then Shiny is not the problem. If you can, then please send along the file, and I can try to see if it's a problem in Shiny.

[Bárbara Borges]

Although just looking at your code, I also noticed you're not using fileInput() correctly. To get the datapath on the server, you should call input$file1$datapath, as demoed in the documentation (?fileInput):

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)

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

  })

[saura...@shiats.edu.in]

Thanks Barbara for your help,

With some help, I was able to do the sdf reaching.

The code is attached herewith this post.

Regards,

Saurav