#' ### Author: Franck Soubès
#' ### Bioinformatics Master Degree - University of Bordeaux, France
#' ### Link: https://github.com/fsoubes/MA_Trix_App
#' ### Where: GET-TRiX's facility
#' ### Application: MATRiX is a shiny application for Microarray Analysis on Transcriptomic impact of Xenobiotics
#' ### Licence: GPL-3.0


#' csvFileInput is a shiny widget for uploading data locally
#'
#' @param id Shiny id
#' @param label Shiny label
#' @param multiple Shiny boolean for selecting or not multiple files in the browser
#'
#' @return Widget in the gui
#'
#' @export
#'


csvFileInput <- function(id, label = "CSV file", multiple = T) {
  ns <- NS(id)
  fileInput(ns("file"),multiple = T, accept = c("text/csv","text/comma-separated-values,text/plain",".csv"), label)

}

#' csvIdentifier is a shiny widget for loading data from the server
#'
#' @param id Shiny id
#' @param label Shiny label
#'
#' @return Widget in the gui
#'
#' @export
#'


csvIdentifier <- function(id, label = "Unique Identifier") {
  ns <- NS(id)
  selectInput(ns("identifier"), label, choices = c("ProbeName", "Transcript"))

}


#' csvDecimal is a shiny widget to select the decimal separator
#'
#' @param id Shiny id
#' @param label Shiny label
#'
#' @return Widget in the gui
#'
#' @export
#'

csvDecimal <- function(id, label="Decimal"){
  ns <- NS(id)
  radioButtons(ns("csvdec"), label ,
               choices = c(Comma=',', Point='.' ), selected = ',')
}


#' ordinput is a function which aims to reorder an input list of dataframes
#'
#' @param csvnord A list of the 3 data filenames to be imported
#' @param identifier Character identifier (probes/transcripts)
#' @param dec Character to select the decimal separator
#'
#' @return An ordered list (WorkingSet, pData, restable)
#' @export
#'


ordinput <- function(csvnord, identifier, dec){

  csv <- lapply(csvnord, FUN = function (x) fread(x, data.table = F, check.names = F, header = T, dec = dec))
## the result list contain dataframes in no predifined order
## so it is important to identify the position of each dataset and attribute a defined position  in a new list 'csvord'

  csvord = list()
  for (i in 1:length(csv)) {# pData (#2)
    if (length(csv[[i]]) == 2) {
      csvord[[2]] <- csv[[i]]
      colnames(csvord[[2]]) <- c("X", "Grp")
    }
    else if (any(grepl("^adj.P.Val|^FDR|^padj_" , colnames(csv[[i]])))){# ResTable (#3)
      csvord[[3]] <- csv[[i]]
      if(!any(grepl("GeneName", colnames(csvord[[3]]))))
        colnames(csvord[[3]])[[2]] <- "GeneName"
    }
    else #NormData (#1)
      csvord[[1]] <- csv[[i]]
  }

  csvord[[2]] <- chartofa(csvord[[2]]) # transform dataframe containing characters to factors


  if(class(csvord[[3]][[1]]) == "integer"){
    csvord[[3]] <- csvord[[3]][-1] #remove useless column
    csvord[[3]] <- csvord[[3]] %>%
      select(ProbeName,  everything())
  }


  colnames(csvord[[3]])[[1]] <- identifier
  colnames(csvord[[1]])[[1]] <- identifier
  csvord[[1]][1] <- csvord[[3]][1]
  
#~   # delete lines containing NA in ResTable
#~   idDel <- which(apply(is.na(csvord[[3]]),1,sum)>0)
#~   if(length(idDel)){
#~ 	csvord[[3]] <- csvord[[3]][-idDel,]
#~ 	csvord[[1]] <- csvord[[1]][-idDel,]
#~ 	message("NA values in ResTable. Lines deleted:\n",idDel)
#~   }
  return(csvord)
}

#' dirModuleUI is a shiny widget for loading data from the server
#'
#' @param id Shiny id
#' @param multiple Shiny boolean for selecting or not multiple files in the browser
#'
#' @return Widget in the gui
#'
#' @export
#'

dirModuleUI = function(id, multiple =T) {
  ns = NS(id)

  fluidPage(
    fluidRow(
      shinyFilesButton(ns('files'), label='File select', title='Please select all the files', multiple=T)
    )
  )
}



#' csvFile is shiny module which aims is to alert users on the status of his upload and return an ordered list of dataframe
#'
#' @param input Internal
#' @param output Internal
#' @param session Internal
#' @param stringsAsFactors
#'
#' @return The reactive that yields a list of dataframes
#'
#' @export
#'
#'

csvFile <- function(input, output, session, stringsAsFactors) {

  shinyFileChoose(input, 'files', roots = root, session = session,filetype=c("csv"))
  shinyDirChoose(input, "directory", roots = root, session = session)
  shinyFileSave(input, "fileSave", roots = root, session = session)


  showmark <- T # Boolean uses to hide or show the mardkwon serving to load data

  isuploading <- F

  #' Reactive function returned to the tab1.R
  #'
  #' @return  a reactive value of type boolean corresponding to the loading status by default it is set to True
  #'

  output$boolmark <- reactive({
    showmark
  })

  observe({
    print(showmark)
  })


  outputOptions(output,"boolmark",suspendWhenHidden=F)

  csvlocpath <- eventReactive(input$files, { print(parseFilePaths(root, input$files)$datapath)})


  csvf <- reactive({

    isuploading = ifelse( (length(parseFilePaths(root, input$files)$datapath) !=0) || !is.null(input$file)  , T, F)
    validate(need(isuploading == T, "You need to import the data"))
    inFile <- input$file

    if(!is.null(inFile)){ ## files uploaded from 'Browse' widget (local)

    data <- as.list(inFile$datapath)
    csvnord = list()
    name = inFile$datapath
    iscsv = grep(pattern = '.csv$', name, value = T)

      if (length(data) != 3)
      {
        createAlert(
          session,
          "alert",
          "exampleAlert",
          style = "danger",
          title = "Oops Error",
          content = paste0("You selected ",length(data)," csv files but 3 must be selected.  Tips: Use `Ctrl+left` click to selecte pultiple files."),
          append = FALSE
        )
        return (NULL)
      }else{
        for (i in 1:length(data)) {
          for (elem in input$file[[i, 'datapath']]) {
            cat("loading file number" , i, "\n")
          }
          csvnord[i] <- elem
        }
      }

      csvord <- ordinput(csvnord, input$identifier, input$csvdec)


      observe({showmark <<-F
      print(showmark)
      }) # modify and lock the bool value to false

      output$boolmark <- reactive({
        showmark
      })

    simil <- isimilar(csvord[[3]], csvord[[2]], csvord[[1]])

    if(!simil[[1]] ||!simil[[2]]){
      createAlert(
        session,
        "alert",
        "exampleAlert",
        style = "danger",
        title = "Oops Error",
        content = "Datatabels Identifier error: The first column identifiers are not the same or are not in same order between ResTable and NormData. Or the SampleNames are dot identical between pdata file and NormData file.",
        append = FALSE
      )
      return(NULL)
    }


    createAlert(
      session,
      "alert",
      "succeeded",
      style = "success",
      title = "Sucess",
      content = " Your files have been successfully loaded.",
      append = FALSE

    )

    Sys.sleep(1)
    closeAlert(session, "succeeded")
    csvord[[4]] <- inFile
    print(inFile$name)

    return (csvord)
  }else{ ## files loaded using 'File select' widget (server)

    req(length(csvlocpath())==3)

    csvnord <- list()
    csvnord[1] <-csvlocpath()[[1]]
    csvnord[2] <-csvlocpath()[[2]]
    csvnord[3] <-csvlocpath()[[3]]

    csvord <- ordinput(csvnord, input$identifier, input$csvdec)


    observe({showmark <<-F
    print(showmark)
    }) # modify and lock the bool value to false

    output$boolmark <- reactive({
      showmark
    })



    #' Reactive function returned to the tab1.R
    #'
    #' @return \showmark a reactive value of type boolean set to False
    #'

    createAlert(
      session,
      "alert",
      "succeeded",
      style = "success",
      title = "Sucess",
      content = " Your files have been successfully loaded.",
      append = FALSE
    )

    Sys.sleep(1)
    closeAlert(session, "succeeded")
    csvord[[4]] <- csvlocpath()
    return (csvord)

   }
  })

}