inst/shiny/Gui/server-convert.R

In YonghuiDong/RawHummus: Raw Data Quality Control Tool for LC-MS System

chartr0 <- function(x) chartr('\\','/', x)

msconvertPath <- reactive({
  chartr0(input$msconvert)
})

outPath <- reactive({
  chartr0(input$outdir)
})

volumes <- shinyFiles::getVolumes()
rawPath <- NULL

observe({
  # 1. choose MSConvert software path
  output$msconvertPath <- renderText(msconvertPath())

  # 2. choose raw files
  shinyFiles::shinyFileChoose(input, "files", roots = volumes())

  rawPath <<- shinyFiles::parseFilePaths(volumes(), input$files) # dataframe type

  output$filesPath <- shiny::renderDataTable({
    rawPath[, c(1, 2, 4)] # show only name, size and filepath
  })

})

# 4. execute conversion
output$convertMessage <- NULL

observeEvent(input$convert, {
  output$convertMessage <- renderText({

    shiny::validate(
      need(file.exists(msconvertPath()), 'MSconvert software not found! Please add correct software path'),
      need(nrow(rawPath) > 0, "Please select (correct) data for conversion"),
      need(dir.exists(outPath()), 'Directory not exist! Please choose a directory to save converted data.')
    )

    for (i in 1:nrow(rawPath)) {
      msconvert_command <- paste0('"', msconvertPath(), '"', " msconvert --zlib --filter ", '"', "peakPicking true [1,2]", '"', " ",'"', rawPath$datapath[i], '"', " -o ", '"', outPath(), '"')
      system(msconvert_command)
    }

    print("Congratulations! File Conversion Done.")

  })

})