# Main Changes:
#    A) use library(shinyFiles) and library(fs) instead of base R's file.choose() because
#       running file.choose() fails in a non-Rstudio environment like jupyter.
#       In jupyter, can set the default port/host first with either of:
#            options(shiny.port=5001, shiny.host="0.0.0.0", shiny.launch.browser=FALSE); paneleditor_GUI()
#            paneleditor_GUI(launch.browser=FALSE, port=5001, host='0.0.0.0')
#    B) While we're at it, created a new button which allows (re)choosing folder to trigger refreshing the panel
#            which has the side effect of allowing repeated use of the gui without needing to restart

render_paneleditor_ui <- function(working.directory, ...) {renderUI({
    fluidPage(
        fluidRow(
            column(6,
                textInput("paneleditorui_output_folder", label = "Output folder name", value = "renamed")
            ),
            column(3,
                actionButton("paneleditorui_process_files", "Process files")
            )
        ),
        fluidRow(
            column(12,
                    rhandsontable::rHandsontableOutput("paneleditorui_panel_table")
            )
        )
    )
})}


get_panel_table <- function(files.list) {
    message("Reading FCS parameters...")
    panel.table <- premessa:::read_parameters(files.list)
    message("Done")
    common.names <- premessa:::get_common_names(panel.table)
    problem.idx <- premessa:::get_problem_idx(panel.table, common.names)
    panel.table <- panel.table[, order(colSums(problem.idx), decreasing = T), drop = F]

    panel.table <- data.frame(Parameter = row.names(panel.table), common.names, panel.table, check.names = F, stringsAsFactors = F)
    names(panel.table)[2] <- "Most common"
    return(panel.table)
}



shinyServer(function(input, output, session) {

    volumes <- c(Home = fs::path_home(), "R Installation" = R.home(), shinyFiles::getVolumes()())
    shinyFiles::shinyDirChoose(input, "directory", roots = volumes, session = session)

    output$directorypath <- renderPrint({
        shinyFiles::parseDirPath(volumes, input$directory)
    })

    working.directory <- NULL
    panel.table <- NULL

    observeEvent(input$directory, {
        working.directory <- shinyFiles::parseDirPath(volumes, input$directory)

        if( length(working.directory) > 0 && dir.exists(working.directory) ) {

            output$paneleditorUI <- render_paneleditor_ui(working.directory)

            files.list <- list.files(working.directory, pattern = "*.fcs$", ignore.case = T)
            files.list <- file.path(working.directory, files.list)

            panel.table <- get_panel_table(files.list)

            showModal(modalDialog(
                title = "Panel editor report",
                sprintf("FCS files ingested from: %s", file.path(working.directory))
            ))

            #moved rhandsontable invocation here to (re)trigger upon valid working.directory
            output$paneleditorui_panel_table <- rhandsontable::renderRHandsontable({
                temp <- panel.table

                for(i in 1:ncol(temp))
                    temp[, i][is.na(temp[, i])] <- "absent"

                df <- data.frame(Remove = FALSE, temp, check.names = F, stringsAsFactors = F)


                hot <- rhandsontable::rhandsontable(df, rowHeaderWidth = 100)
                hot <- rhandsontable::hot_cols(hot, fixedColumnsLeft = 3, renderer = "
                    function(instance, td, row, col, prop, value, cellProperties) {
                        if(col == 0)
                            Handsontable.renderers.CheckboxRenderer.apply(this, arguments)
                        else {
                            Handsontable.renderers.TextRenderer.apply(this, arguments)
                            if(instance.params != null) {
                                if(instance.params.data[row][0])
                                    td.style.background = 'lightgrey'
                                else {
                                    if(value == 'absent')
                                        td.style.background = 'orange'
                                    else if(value != instance.params.data[row][2] && col > 2)
                                        td.style.background = 'lightpink'
                                }
                            }
                        }
                        return(td)
                    }"
                )
                hot
            })
            #

        }
    })


    observeEvent(input$paneleditorui_process_files, {
        working.directory <- shinyFiles::parseDirPath(volumes, input$directory)
        message(paste("writing to", file.path(working.directory, input$paneleditorui_output_folder)))

        if( ! is.null(input$paneleditorui_process_files) &&
            input$paneleditorui_process_files != 0 &&
            length(working.directory) > 0 &&
            dir.exists(working.directory) ) {

                df <- rhandsontable::hot_to_r(input$paneleditorui_panel_table)
                for(i in 1:ncol(df))
                    df[, i] <- gsub("absent", NA, df[, i])
                df$Remove <- as.logical(df$Remove)

                panel.table$"Most common" <- df$"Most common" <- NULL

                showModal(modalDialog(
                    title = "Panel editor report",
                    "File processing started, please wait..."
                ))

                premessa:::rename_parameters_in_files(working.directory, input$paneleditorui_output_folder, df)

                showModal(modalDialog(
                    title = "Panel editor report",
                    sprintf("File processing completed. The output files are located in: %s", file.path(working.directory, input$paneleditorui_output_folder))
                ))

        }
    })

})