### Author: Franck Soubès
### Bioinformatics Master Degree - University of Bordeaux, France
### Link: https://github.com/GeT-TRiX/MA_Trix_App/
### Where: GET-TRiX's facility
### Application: MATRiX is a shiny application for Mining and functional Analysis of TRanscriptomics data
### Licence: GPL-3.0


plotHeight <- reactive({
  ifelse(is.null(input$plotHeight), 0, (input$plotHeight/1.25)) ## responsive plot
})


#########################################
######## Loading screen                 #
#########################################

hide(id = "loading-content", anim = TRUE, animType = "fade",time=2)
hide(id = "loading-content-bar", anim = TRUE, animType = "fade",time=2)

observe({
  collapsestate <- input$sidebarCollapsed
  session$sendCustomMessage(type="iscollapse", collapsestate)
})


#########################################
######## Redirection Panel              #
#########################################

observeEvent(input$heatmapanel, {

isolate(
  if (grepl("widgetheat", input$heatmapanel)) {

    updateTabsetPanel(session, "heatmapmainp",
                      selected = "hmmainpan")
  }
  else if (grepl("cutheatmainp", isolate(input$heatmapanel))) {

    updateTabsetPanel(session, "heatmapmainp",
                      selected = "cuthmmainpan")

  }
)
})


#################################################
######## Download data and reset button heatmap #
#################################################

### do not work with shinyproxy
#~ output$downloadData <- downloadHandler(filename <- function() {
#~   paste("sampleData", ".zip", sep = '')
#~ },
#~ 	content <- function(file) {
#~ 	  file.copy("data/sampleData.zip", file)
#~ 	},
#~ 	contentType = "zip")

observeEvent(input$resetAll, {
  reset("form")
})


#########################################
######## Citation packages              #
#########################################

#' mypacklist is a reactive function which aim is to display the different packages used in the current session
#'
#' @param sessionInfo version information about R, the OS and attached or loaded packages.
#'
#' @return a data frame
#'
#' @export
#'


mypacklist <- reactive({
  mysess <- sessionInfo()
  dfpack <- names(sessionInfo()$otherPkgs) %>%
    lapply(function(x)
      return(
        paste(mysess$otherPkgs[[x]]$Package, mysess$otherPkgs[[x]]$Version)
      )) %>%
    unlist() %>%
    cbind(., unlist(lapply(names(mysess$otherPkgs), function(x)
      return(paste(mysess$otherPkgs[[x]]$Title))))) %>%
    as.data.frame() %>%
    setNames(c('Version', "Title"))

  return(dfpack)
})


observeEvent(input$session, {
  req(mypacklist())
  #output$sessinfo <- renderDataTable(mypacklist())
  callModule(stylishTables, "sessinfo", data = mypacklist , lengthpage=  c('5', '10', '15','20'), pageLength=15 )
})



#########################################
######## Grep project name              #
#########################################

file_name <- reactive({
  req(csvf())
  inFile <- csvf()[[4]]
  if (class(inFile)== "character")
    return(tools::file_path_sans_ext(inFile))
  else
    return (tools::file_path_sans_ext(inFile$name))
})

projectname <- reactive({
  req(file_name())
  splitbyunder <- strsplit(file_name(), "_")
  MAindex = grepl("^MA", splitbyunder[[2]])
  isindex = which(MAindex == T)
  outputname = list(splitbyunder[[2]][isindex], MAindex)
  if(length(outputname[[1]]) == 0){
    return(Sys.Date())
  }
  else
    return(outputname)

})

#########################################
######## Hide Menu                      #
#########################################


observe({
  req(csvf())
  runjs("let menuitems = ['.menuitemsum','.menuitempca', '.menuitemvenn', '.menuitemhm'];
  for(let elem of menuitems){
    let div = $(elem);
    let childclone = div.children().clone();
    let parent = div.parent();
    div.remove();
    childclone.appendTo(parent);}")
  updateTabItems(session, "side", "Datasummary")
})


#########################################
######## Load gif                       #
#########################################


js$gifrandom()

observe({
  req(input$side == "PCA", subsetgroup_pca() )
  js$gifrender("statuspca")
})

observe({
  req(input$side == "Datasummary", data_summary())
  js$gifrender("statussum")
})

observe({
  req(input$side == "Venn", subsetstatRm())
  js$gifrender("statusvenn")
})


observe({
  req(input$side == "Heatmap", colors())
  js$gifrender("statushm")
})

#########################################
######## Return (transcript or probes)  #
#########################################

dataid <- reactive({
  return(colnames(csvf()[[3]][1]))
})