R/mod_upload.R

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

#' upload UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd
#'
#' @importFrom shinyjs inlineCSS useShinyjs
#' @importFrom hidecan get_example_data GWAS_data_from_gwaspoly GWAS_data DE_data CAN_data
#' @importFrom shiny NS tagList
mod_upload_ui <- function(id) {
  ns <- NS(id)
  tagList(
    fluidRow(
      column(
        width = 12,
        div(
          style = "background-color: white; padding: 15px; border: 1px solid black; position: relative; min-height: 120px;", # Wrap everything in this div
          div(
            style = "position:absolute;right:1em;top:10px;",
            actionButton(ns("goAbout"), "Go to Home", icon("arrow-circle-left", verify_fa = FALSE), style = "background-color: #A896C2 ; border-color: #A896C2 ;"),
            actionButton(ns("goQTL"), label = div("Go to QTL", icon("arrow-circle-right", verify_fa = FALSE)), style = "background-color: #A896C2 ; border-color: #A896C2 ;")
          ),
          div(
            style = "position:absolute;right:1em;bottom:10px;display:flex;gap:3px;",
            actionButton(ns("reset_all"), "Reset all", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE  ; border-color: #F2A7AE  ;"),
            dropdownButton(
              p(HTML("<b>Inputs and parameters description:</b>"), actionButton(ns("goPar"), icon("arrow-up-right-from-square", verify_fa = FALSE))), hr(),
              p(HTML("<b>Results description:</b>"), actionButton(ns("goRes"), icon("arrow-up-right-from-square", verify_fa = FALSE))), hr(),
              p(HTML("<b>How to cite:</b>"), actionButton(ns("goCite"), icon("arrow-up-right-from-square", verify_fa = FALSE))), hr(),
              circle = FALSE,
              status = "warning",
              icon = icon("info"), width = "300px",
              right = TRUE,
              tooltip = tooltipOptions(title = "Click to see info!")
            )
          ),
          tags$h2(tags$b("Input data")), br(),
          "Use this module to select an example dataset or to upload yours.", br(), br()
        ), br()
      ), br(),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_example"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = FALSE, status = "info", title = tags$b("Available example datasets"),
            radioButtons(ns("example_map"),
              label = p("They contain the entire linkage map and QTL analysis but just a subset of individuals."),
              choices = c("Potato - Atlantic x B1829-5" = "tetra_map"),
              selected = "tetra_map"
            ), br(), br(), hr(),
            tags$p(
              "Access complete example datasets ",
              tags$a(href = "https://www.polyploids.org/input-tests", "here")
            )
          )
        )
      ), br(),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_map"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = TRUE, status = "info", title = tags$b("Upload linkage map files"),
            div(
              style = "position:absolute;right:1em;",
              actionButton(ns("reset_map"), "Reset", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE  ; border-color: #F2A7AE  ;")
            ), br(), br(),
            box(
              id = ns("box_mappoly"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload MAPpoly output"),
              tags$p(
                "Access further information about how to build a linkage maps with MAPpoly ",
                tags$a(href = "https://rpubs.com/mmollin/tetra_mappoly_vignette", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using MAPpoly functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_linkage_map_files", "here")
              ),
              hr(),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_mappoly"), "Submit MAPpoly", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              tags$p("Object of class `mappoly.map`."),
              fileInput(ns("mappoly_in"), label = h6("File: my_mappoly_list.RData"), multiple = F)
            ),
            box(
              id = ns("box_polymap"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload polymapR output"),
              tags$p(
                "Access further information about how to build a linkage maps with polymapR ",
                tags$a(href = "https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using polymapR functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_linkage_map_files", "here")
              ),
              hr(),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_polymapR"), "Submit polymapR", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              p("Indicates whether the genotype input is discrete or probabilistic."),
              prettyRadioButtons(
                inputId = ns("input.type"),
                label = "Data type:",
                choices = c("discrete" = "discrete", "probabilistic" = "probabilistic"),
                selected = "discrete",
                inline = TRUE,
                status = "info",
                fill = TRUE
              ), br(),
              p("Indicates the dataset specie ploidy."),
              prettyRadioButtons(
                inputId = ns("ploidy"),
                label = "Ploidy:",
                choices = c(4, 6),
                selected = 4,
                inline = TRUE,
                status = "info",
                fill = TRUE
              ), br(),
              fileInput(ns("polymapR.dataset"), label = h6("File: polymapR.dataset.RData"), multiple = F),
              fileInput(ns("polymapR.map"), label = h6("File: polymapR.map.RData"), multiple = F)
            ),
            box(
              id = ns("box_onemap"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload OneMap output"),
              tags$p(
                "Access further information about how to build a linkage maps for diploid outcrossing populations with OneMap ",
                tags$a(href = "https://cristianetaniguti.github.io/Tutorials/onemap/vignettes_highres/Outcrossing_Populations.html", "here")
              ), br(),
              tags$p(
                "Access further information about how to build a linkage maps for diploid inbred based populations with OneMap ",
                tags$a(href = "https://cristianetaniguti.github.io/Tutorials/onemap/vignettes_highres/Inbred_Based_Populations.html", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using OneMap functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_linkage_map_files", "here")
              ),
              hr(),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_onemap"), "Submit OneMap", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              tags$p("Object of class `viewmap`."),
              fileInput(ns("onemap_in"), label = h6("File: my_onemap_map.RData"), multiple = F)
            ),
            box(
              id = ns("box_mapst"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload linkage map files with standard format (.csv, .tsv or .tsv.gz)"),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_map_custom"), "Submit map custom", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              fileInput(ns("dosages"), label = h6("File: dosages.tsv"), multiple = F),
              fileInput(ns("genetic_map"), label = h6("File: genetic_map.tsv"), multiple = F),
              fileInput(ns("phases"), label = h6("File: phases.tsv"), multiple = F),
              p("Upload here an TSV file with table with three columns: 1) marker ID; 2) genome position; 3) chromosome"),
              fileInput(ns("mks.pos"), label = h6("File: marker information"), multiple = F),
              "Check the input file formats with the example files:", br(),
              radioButtons(ns("downloadType_map"), "",
                choices = c(
                  "dosages.tsv" = "dosages",
                  "genetic_map.tsv" = "genetic_map",
                  "phases.tsv" = "phases"
                ),
                inline = TRUE
              ), br(), br(),
              downloadButton(ns("downloadData_map"), "Download")
            )
          )
        )
      ), br(),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_qtl"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = TRUE, status = "info", title = tags$b("Upload QTL analysis files"),
            div(
              style = "position:absolute;right:1em;",
              actionButton(ns("reset_qtl"), "Reset", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE  ; border-color: #F2A7AE  ;")
            ), br(), br(),
            box(
              id = ns("box_qtlpoly"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload QTLpoly output"),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_qtlpoly"), "Submit QTLpoly", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              tags$p(
                "Access further information about how to perform QTL analysis with QTLpoly ",
                tags$a(href = "https://guilherme-pereira.github.io/QTLpoly/1-tutorial", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using QTLpoly functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_QTL_analysis_files", "here")
              ),
              hr(),
              fileInput(ns("qtlpoly_data"), label = h6("File: QTLpoly_data.RData", br(), br(), "Object of class: qtlpoly.data"), multiple = F),
              fileInput(ns("qtlpoly_remim.mod"), label = h6("File: QTLpoly_remim.mod.RData", br(), br(), "Object of class: qtlpoly.remim"), multiple = F),
              fileInput(ns("qtlpoly_est.effects"), label = h6("File: QTLpoly_est.effects.RData", br(), br(), "Object of class: qtlpoly.effects"), multiple = F),
              fileInput(ns("qtlpoly_fitted.mod"), label = h6("File: QTLpoly_fitted.mod.RData", br(), br(), "Object of class: qtlpoly.fitted"), multiple = F)
            ),
            box(
              id = ns("box_diaqtl"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload diaQTL output"),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_diaQTL"), "Submit diaQTL", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              tags$p(
                "Access further information about how to perform QTL analysis with diaQTL ",
                tags$a(href = "https://jendelman.github.io/diaQTL/diaQTL_Vignette.html", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using diaQTL functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_QTL_analysis_files", "here")
              ),
              hr(),
              fileInput(ns("diaQTL_scan1"), label = h6("File: diaQTL_scan1_list.RData"), multiple = F),
              fileInput(ns("diaQTL_scan1.summaries"), label = h6("File: diaQTL_scan1.summaries_list.RData"), multiple = F),
              fileInput(ns("diaQTL_BayesCI"), label = h6("File: diaQTL_BayesCI_list.RData"), multiple = F),
              fileInput(ns("diaQTL_fitQTL"), label = h6("File: diaQTL_fitQTL_list.RData"), multiple = F)
            ),
            box(
              id = ns("box_polyqtl"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload polyqtlR output"),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_polyqtlR"), "Submit polyqtlR", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              tags$p(
                "Access further information about how to perform QTL analysis with polyqtlR ",
                tags$a(href = "https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html", "here")
              ), br(),
              tags$p(
                "Access a example code of how to obtain these inputs using polyqtlR functions ",
                tags$a(href = "https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_QTL_analysis_files", "here")
              ),
              hr(),
              fileInput(ns("polyqtlR_effects"), label = h6("File: polyqtlR_effects.RData"), multiple = F), hr(),
              fileInput(ns("polyqtlR_qtl_info"), label = h6("File: polyqtlR_qtl_info.RData"), multiple = F),
              fileInput(ns("polyqtlR_QTLscan_list"), label = h6("File: polyqtlR_QTLscan_list.RData"), multiple = F)
            ),
            box(
              id = ns("box_qtlst"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload QTL analysis results with standard format (.csv, .tsv or .tsv.gz)"),
              div(
                style = "position:absolute;right:1em;",
                actionButton(ns("submit_qtl_custom"), "Submit QTL custom", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
              ), br(), br(),
              fileInput(ns("selected_mks"), label = h6("File: selected_mks.tsv"), multiple = F),
              fileInput(ns("qtl_info"), label = h6("File: qtl_info.tsv"), multiple = F),
              fileInput(ns("blups"), label = h6("File: blups.tsv"), multiple = F),
              fileInput(ns("beta.hat"), label = h6("File: beta.hat.tsv"), multiple = F),
              fileInput(ns("profile"), label = h6("File: profile.tsv"), multiple = F),
              fileInput(ns("effects"), label = h6("File: effects.tsv"), multiple = F),
              fileInput(ns("probs"), label = h6("File: probs.tsv"), multiple = F),
              "Check the input format with the example file:", br(), br(),
              radioButtons(ns("downloadType_qtl"), "",
                choices = c(
                  "selected_mks.tsv" = "selected_mks",
                  "qtl_info.tsv" = "qtl_info",
                  "blups.tsv" = "blups",
                  "beta.hat.tsv" = "beta.hat",
                  "profile.tsv" = "profile",
                  "effects.tsv" = "effects",
                  "probs.tsv" = "probs"
                ),
                inline = TRUE
              ), br(), br(),
              downloadButton(ns("downloadData_qtl"), "Download")
            )
          )
        )
      ), br(),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_genome"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = TRUE, status = "info", title = tags$b("Upload Genome Browser files"),
            tags$p(
              "Access further information about the files expected in this section ",
              tags$a(href = "https://gmod.github.io/JBrowseR/articles/creating-urls.html", "here")
            ), br(),
            fluidRow(
              column(
                6,
                tags$h5(tags$b("Upload genome information")),
                box(
                  width = NULL, background = "danger", solidHeader = FALSE, collapsible = FALSE,
                  "Warning! The uploaded .fasta, .gff3, .vcf, .bam, .cram, .wig genome version must be the same one used to build the genetic map"
                )
              ),
              column(
                6,
                div(
                  style = "text-align:right; padding-top:25px;",
                  actionButton(ns("reset_genome"), "Reset", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE  ; border-color: #F2A7AE  ;"), br(), br(),
                  actionButton(ns("submit_genome"), "Submit genome file", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8    ; border-color: #B5DDE8    ;")
                )
              )
            ), br(), br(),
            column(
              12,
              br(),
              tags$h5(tags$b("Upload .fasta/.fasta.gz and .fasta.fai/.fasta.gz.fai,.fasta.gz.gzi file with assembly information. Using this option, a local HTTP server will be generated.")),
              fileInput(ns("fasta"), label = h6("Files: genome_v2.fasta.gz, genome_v2.fasta.gz.fai, genome_v2.fasta.gz.gzi"), multiple = T),
              p("or"),
              tags$h5(tags$b("Add the URL of the hosted FASTA file location. The loading procedure is more efficient using this option.")),
              textInput(ns("fasta_server"), label = h6("https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz"), value = NULL),
              br(), hr(),
              tags$h5(tags$b("Upload .gff3/.gff3.gz and .gff3.tbi/.gff3.gz.tbi file with annotation information")),
              fileInput(ns("gff3"), label = h6("Files: genome_v2.gff3.gz, genome_v2.gff3.gz.tbi"), multiple = T),
              p("or"),
              tags$h5(tags$b("Add the URL of the hosted GFF3 file location. The loading procedure is more efficient using this option.")),
              textInput(ns("gff3_server"), label = h6("https://jbrowse.org/genomes/sars-cov2/sars-cov2-annotations.sorted.gff.gz"), value = NULL),
              br(), hr(),
              tags$h5(tags$b("Upload VCF file with variants information")),
              fileInput(ns("vcf"), label = h6("Files: markers.vcf, markers.vcf.tbi"), multiple = T),
              p("or"),
              tags$h5(tags$b("Add the URL of the hosted VCF file location. The loading procedure is more efficient using this option.")),
              textInput(ns("vcf_server"), label = h6("https://some/path/file.vcf"), value = NULL),
              br(), hr(),
              tags$h5(tags$b("Upload .bam and .bam.bai or .cram and .cram.crai file with alignment information")),
              fileInput(ns("align"), label = h6("Files: all_ind.bam, all_ind.bam.bai"), multiple = T),
              p("or"),
              tags$h5(tags$b("Add the URL of the hosted BAM or CRAM file location. The loading procedure is more efficient using this option.")),
              textInput(ns("align_server"), label = h6("https://some/path/file.bam"), value = NULL),
              br(), hr(),
              tags$h5(tags$b("Upload .wig file with bigWig information")),
              fileInput(ns("wig"), label = h6("File: data.wig"), multiple = F),
              p("or"),
              tags$h5(tags$b("Add the URL of the hosted WIG file location. The loading procedure is more efficient using this option.")),
              textInput(ns("wig_server"), label = h6("https://some/path/file.wig"), value = NULL),
            )
          )
        )
      ),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_hidecan"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = TRUE, status = "info", title = tags$b("Upload Hidecan files"),
            fluidRow(
              column(
                6,
                tags$p(
                  "Access further information about the files expected in this section ",
                  tags$a(href = "https://plantandfoodresearch.github.io/hidecan/", "here")
                ), br(),
              ),
              column(
                6,
                div(
                  style = "text-align:right; padding-top:25px;",
                  actionButton(ns("reset_hidecan"), "Reset", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE ; border-color: #F2A7AE ;"), br(), br(),
                  actionButton(ns("submit_hidecan"), "Submit HIDECAN file", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
                )
              )
            ), br(), br(),
            box(
              id = ns("box_gwaspoly"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload GWAS output"),
              div(style = "position:absolute;right:1em;", ), br(), br(),
              p("Object of class GWASpoly.thresh obtained with the GWASpoly::set.threshold():"), br(),
              fileInput(ns("gwaspoly"), label = h6("File: gwaspoly_res_thr.rda"), multiple = T),
              p("or"),
              fileInput(ns("gwas"), label = h6("File: gwas.csv"), multiple = T)
            ),
            box(
              id = ns("box_gwas_de"), width = 12, solidHeader = FALSE, collapsible = TRUE, collapsed = TRUE, status = "primary", title = tags$b("Upload differential expression (DE) and candidate genes (CAN) files"),
              div(style = "position:absolute;right:1em;", ), br(), br(),
              fileInput(ns("de"), label = h6("File: DE.csv"), multiple = T),
              fileInput(ns("can"), label = h6("File: CAN.csv"), multiple = T)
            )
          )
        )
      ),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_viewpoly"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = TRUE, status = "indigo", title = tags$b("Download VIEWpoly dataset"),
            p("The uploaded data are converted to the viewpoly format. It keeps the map and the QTL information. Genome information is not stored."), br(),
            textInput(ns("data.name"), label = p("Define the dataset name. Do not use spaces between words."), value = "dataset_name"), br(),
            tags$head(tags$style(".butt{background-color:#add8e6; border-color: #add8e6; color: #337ab7;}")),
            useShinyjs(),
            downloadButton(ns("export_viewpoly"), "Download", class = "butt")
          )
        )
      ),
      column(
        width = 12,
        fluidPage(
          box(
            id = ns("box_viewpolyup"), width = 12, solidHeader = TRUE, collapsible = TRUE, collapsed = FALSE, status = "indigo", title = tags$b("Upload VIEWpoly dataset"),
            fluidRow(
              column(
                8,
                radioButtons(ns("viewpoly_env"),
                  width = 500, label = "Check one of the availables datasets:",
                  choices = "There is no VIEWpoly object in your R environment. Load VIEWpoly object or convert other formats below.",
                  selected = "There is no VIEWpoly object in your R environment. Load VIEWpoly object or convert other formats below."
                )
              ),
              column(
                4,
                div(
                  style = "text-align:right; padding-top:25px;",
                  actionButton(ns("reset_viewpoly"), "Reset", icon("undo-alt", verify_fa = FALSE), style = "background-color: #F2A7AE ; border-color: #F2A7AE ;"), br(), br(),
                  actionButton(ns("submit_viewpoly"), "Submit VIEWpoly file", icon("share-square", verify_fa = FALSE), style = "background-color: #B5DDE8 ; border-color: #B5DDE8 ;")
                )
              )
            ),
            column(
              12,
              br(), hr(),
              p("Upload VIEWpoly RData file here:"),
              fileInput(ns("viewpoly_input"), label = h6("File: dataset_name.RData"), multiple = F)
            )
          )
        )
      )
    )
  )
}

#' upload Server Functions
#'
#' @import vroom
#' @importFrom shinyjs js
#' @importFrom utils packageVersion
#'
#' @noRd
mod_upload_server <- function(input, output, session, parent_session) {
  ns <- session$ns


  # Help links
  observeEvent(input$goPar, {
    # change to help tab
    updatebs4TabItems(
      session = parent_session, inputId = "MainMenu",
      selected = "help"
    )

    # select specific tab
    updateTabsetPanel(
      session = parent_session, inputId = "Inputs_tabset",
      selected = "Inputs_par"
    )
    # expand specific box
    updateBox(id = "Inputs_box", action = "toggle", session = parent_session)
  })

  observeEvent(input$goRes, {
    # change to help tab
    updatebs4TabItems(
      session = parent_session, inputId = "MainMenu",
      selected = "help"
    )

    # select specific tab
    updateTabsetPanel(
      session = parent_session, inputId = "Inputs_tabset",
      selected = "Inputs_results"
    )
    # expand specific box
    updateBox(id = "Inputs_box", action = "toggle", session = parent_session)
  })

  observeEvent(input$goCite, {
    # change to help tab
    updatebs4TabItems(
      session = parent_session, inputId = "MainMenu",
      selected = "help"
    )

    # select specific tab
    updateTabsetPanel(
      session = parent_session, inputId = "Inputs_tabset",
      selected = "Inputs_cite"
    )
    # expand specific box
    updateBox(id = "Inputs_box", action = "toggle", session = parent_session)
  })

  # Check environment
  observe({
    Objs <- Filter(function(x) inherits(get(x), "viewpoly"), ls(envir = .GlobalEnv))
    if (length(Objs) > 0) {
      dataset_choices <- as.list(Objs)
      names(dataset_choices) <- Objs
      updateRadioButtons(session, "viewpoly_env",
        label = "Check one of the availables datasets:",
        choices = dataset_choices,
        selected = character(0)
      )
    } else {
      updateRadioButtons(session, "viewpoly_env",
        label = "Check one of the availables datasets:",
        choices = "There is no viewpoly object in your R environment. Load view viewpoly object or convert formats below",
        selected = character(0)
      )
    }
  })

  # Format examples
  output$downloadData_map <- downloadHandler(
    filename = function() {
      paste0(input$downloadType_map, ".tsv")
    },
    content = function(file) {
      if (input$downloadType_map == "dosages") {
        filetemp <- vroom(system.file("ext/dosage.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_map == "phases") {
        filetemp <- vroom(system.file("ext/phases.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_map == "genetic_map") {
        filetemp <- vroom(system.file("ext/map.tsv.gz", package = "viewpoly"))
      }
      vroom_write(filetemp, file = file)
    }
  )

  output$downloadData_qtl <- downloadHandler(
    filename = function() {
      paste0(input$downloadType_qtl, ".tsv")
    },
    content = function(file) {
      if (input$downloadType_qtl == "qtl_info") {
        filetemp <- vroom(system.file("ext/qtl_info.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_qtl == "blups") {
        filetemp <- vroom(system.file("ext/blups.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_qtl == "beta.hat") {
        filetemp <- vroom(system.file("ext/beta.hat.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_qtl == "profile.hat") {
        filetemp <- vroom(system.file("ext/profile.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_qtl == "effects.hat") {
        filetemp <- vroom(system.file("ext/effects.tsv.gz", package = "viewpoly"))
      } else if (input$downloadType_qtl == "probs") {
        filetemp <- vroom(system.file("ext/probs.tsv.gz", package = "viewpoly"))
      }
      vroom_write(filetemp, file = file)
    }
  )

  observeEvent(input$goQTL, {
    updateTabsetPanel(
      session = parent_session, inputId = "MainMenu",
      selected = "qtl"
    )
  })

  observeEvent(input$goAbout, {
    updateTabsetPanel(
      session = parent_session, inputId = "MainMenu",
      selected = "welcome"
    )
  })

  # Reset buttons
  values <- reactiveValues(
    upload_state_map = 0,
    upload_state_mappoly = 0,
    upload_state_onemap = 0,
    upload_state_polymapR = 0,
    upload_state_map_custom = 0,
    upload_state_qtl = 0,
    upload_state_qtlpoly = 0,
    upload_state_diaQTL = 0,
    upload_state_polyqtlR = 0,
    upload_state_qtl_custom = 0,
    upload_state_genome = 0,
    upload_state_hidecan = 0
  )

  observeEvent(input$reset_all, {
    values$upload_state_viewpoly <- "reset"
    values$upload_state_map <- "reset"
    values$upload_state_mappoly <- 0
    values$upload_state_onemap <- 0
    values$upload_state_polymapR <- 0
    values$upload_state_map_custom <- 0
    values$upload_state_qtl <- "reset"
    values$upload_state_qtlpoly <- 0
    values$upload_state_diaQTL <- 0
    values$upload_state_polyqtlR <- 0
    values$upload_state_qtl_custom <- 0
    values$upload_state_genome <- "reset"
    values$upload_state_hidecan <- "reset"
  })

  observeEvent(input$reset_viewpoly, {
    values$upload_state_viewpoly <- "reset"
  })

  observeEvent(input$reset_map, {
    values$upload_state_map <- "reset"
    values$upload_state_mappoly <- 0
    values$upload_state_onemap <- 0
    values$upload_state_polymapR <- 0
    values$upload_state_map_custom <- 0
  })

  observeEvent(input$reset_qtl, {
    values$upload_state_qtl <- "reset"
    values$upload_state_qtlpoly <- 0
    values$upload_state_diaQTL <- 0
    values$upload_state_polyqtlR <- 0
    values$upload_state_qtl_custom <- 0
  })

  observeEvent(input$reset_genome, {
    values$upload_state_genome <- "reset"
  })

  observeEvent(input$reset_hidecan, {
    values$upload_state_hidecan <- "reset"
  })

  observeEvent(input$submit_viewpoly, {
    values$upload_state_viewpoly <- "uploaded"
  })

  observeEvent(input$submit_mappoly, {
    values$upload_state_mappoly <- "uploaded"
    values$upload_state_map <- 0
  })

  observeEvent(input$submit_onemap, {
    values$upload_state_onemap <- "uploaded"
    values$upload_state_map <- 0
  })

  observeEvent(input$submit_polymapR, {
    values$upload_state_polymapR <- "uploaded"
    values$upload_state_map <- 0
  })

  observeEvent(input$submit_map_custom, {
    values$upload_state_map_custom <- "uploaded"
    values$upload_state_map <- 0
  })

  observeEvent(input$submit_qtlpoly, {
    values$upload_state_qtlpoly <- "uploaded"
    values$upload_state_qtl <- 0
  })

  observeEvent(input$submit_diaQTL, {
    values$upload_state_diaQTL <- "uploaded"
    values$upload_state_qtl <- 0
  })

  observeEvent(input$submit_polyqtlR, {
    values$upload_state_polyqtlR <- "uploaded"
    values$upload_state_qtl <- 0
  })

  observeEvent(input$submit_qtl_custom, {
    values$upload_state_qtl_custom <- "uploaded"
    values$upload_state_qtl <- 0
  })

  observeEvent(input$submit_genome, {
    values$upload_state_genome <- "uploaded"
  })

  observeEvent(input$submit_hidecan, {
    values$upload_state_hidecan <- "uploaded"
  })

  input_map <- reactive({
    if (values$upload_state_map == 0 &
      values$upload_state_mappoly == 0 &
      values$upload_state_onemap == 0 &
      values$upload_state_polymapR == 0 &
      values$upload_state_map_custom == 0) {
      return(NULL)
    } else if (values$upload_state_map == "reset") {
      return(NULL)
    } else if (values$upload_state_mappoly == "uploaded") {
      validate(
        need(!is.null(input$mappoly_in), "Upload mappoly file before submit")
      )
      return(list(mappoly_in = input$mappoly_in))
    } else if (values$upload_state_onemap == "uploaded") {
      validate(
        need(!is.null(input$onemap_in), "Upload onemap file before submit")
      )
      return(list(onemap_in = input$onemap_in))
    } else if (values$upload_state_polymapR == "uploaded") {
      validate(
        need(!is.null(input$polymapR.dataset), "Upload polymapR dataset file before submit"),
        need(!is.null(input$polymapR.map), "Upload polymapR map file before submit")
      )
      return(list(
        polymapR.dataset = input$polymapR.dataset,
        polymapR.map = input$polymapR.map,
        input.type = input$input.type,
        ploidy = as.numeric(input$ploidy)
      ))
    } else if (values$upload_state_map_custom == "uploaded") {
      validate(
        need(!is.null(input$dosages), "Upload custom dosages file before submit"),
        need(!is.null(input$phases), "Upload custom phases file before submit"),
        need(!is.null(input$genetic_map), "Upload custom genetic map file before submit")
      )
      return(list(
        dosages = input$dosages,
        phases = input$phases,
        genetic_map = input$genetic_map
      ))
    }
  })

  input_qtl <- reactive({
    if (values$upload_state_qtl == 0 &
      values$upload_state_qtlpoly == 0 &
      values$upload_state_diaQTL == 0 &
      values$upload_state_polyqtlR == 0 &
      values$upload_state_qtl_custom == 0) {
      return(NULL)
    } else if (values$upload_state_qtl == "reset") {
      return(NULL)
    } else if (values$upload_state_qtl_custom == "uploaded") {
      validate(
        need(!is.null(input$dosages), "Upload custom selected markers file before submit"),
        need(!is.null(input$phases), "Upload custom QTL info file before submit"),
        need(!is.null(input$blups), "Upload custom BLUPs file before submit"),
        need(!is.null(input$beta.hat), "Upload custom beta hat file before submit"),
        need(!is.null(input$profile), "Upload custom QTL profile file before submit"),
        need(!is.null(input$effects), "Upload custom effects file before submit"),
        need(!is.null(input$probs), "Upload custom genotype probabilities file before submit")
      )
      return(list(
        selected_mks = input$selected_mks,
        qtl_info = input$qtl_info,
        blups = input$blups,
        beta.hat = input$beta.hat,
        profile = input$profile,
        effects = input$effects,
        probs = input$probs
      ))
    } else if (values$upload_state_qtlpoly == "uploaded") {
      validate(
        need(!is.null(input$qtlpoly_data), "Upload QTLpoly data file before submit"),
        need(!is.null(input$qtlpoly_remim.mod), "Upload QTLpoly remim.mod file before submit"),
        need(!is.null(input$qtlpoly_est.effects), "Upload QTLpoly estimated effects file before submit"),
        need(!is.null(input$qtlpoly_fitted.mod), "Upload QTLpoly fitted.mod file before submit")
      )
      return(list(
        qtlpoly_data = input$qtlpoly_data,
        qtlpoly_remim.mod = input$qtlpoly_remim.mod,
        qtlpoly_est.effects = input$qtlpoly_est.effects,
        qtlpoly_fitted.mod = input$qtlpoly_fitted.mod
      ))
    } else if (values$upload_state_diaQTL == "uploaded") {
      validate(
        need(!is.null(input$diaQTL_scan1), "Upload diaQTL scan1 file before submit"),
        need(!is.null(input$diaQTL_scan1.summaries), "Upload diaQTL scan1.summaries file before submit"),
        need(!is.null(input$diaQTL_fitQTL), "Upload diaQTL fitQTL file before submit"),
        need(!is.null(input$diaQTL_BayesCI), "Upload diaQTL BayesCI file before submit")
      )
      return(list(
        diaQTL_scan1 = input$diaQTL_scan1,
        diaQTL_scan1.summaries = input$diaQTL_scan1.summaries,
        diaQTL_fitQTL = input$diaQTL_fitQTL,
        diaQTL_BayesCI = input$diaQTL_BayesCI
      ))
    } else if (values$upload_state_polyqtlR == "uploaded") {
      validate(
        need(!is.null(input$qtlpoly_data), "Upload polyqtlR scan list file before submit"),
        need(!is.null(input$qtlpoly_remim.mod), "Upload polyqtlR QTL info file before submit"),
        need(!is.null(input$qtlpoly_est.effects), "Upload polyqtlR estimated effects file before submit")
      )
      return(list(
        polyqtlR_QTLscan_list = input$polyqtlR_QTLscan_list,
        polyqtlR_qtl_info = input$polyqtlR_qtl_info,
        polyqtlR_effects = input$polyqtlR_effects
      ))
    }
  })

  input_genome <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading fasta path..."))
      if (is.null(values$upload_state_genome)) {
        return(NULL)
      } else if (values$upload_state_genome == "reset") {
        return(NULL)
      } else if (values$upload_state_genome == "uploaded") {
        validate(
          need(!is.null(input$fasta) | !is.null(input$fasta_server), "Upload reference genome (FASTA) file before submit.")
        )
        return(list(
          fasta = input$fasta,
          fasta_server = input$fasta_server,
          gff3 = input$gff3,
          gff3_server = input$gff3_server,
          vcf = input$vcf,
          vcf_server = input$vcf_server,
          align = input$align,
          align_server = input$align_server,
          wig = input$wig,
          wig_server = input$wig_server
        ))
      }
    })
  })

  input_hidecan <- reactive({
    if (values$upload_state_hidecan == 0) {
      return(NULL)
    } else if (values$upload_state_hidecan == "reset") {
      return(NULL)
    } else if (values$upload_state_hidecan == "uploaded") {
      validate(
        need(!all(c(is.null(input$gwas), is.null(input$gwaspoly))), "Upload GWAS results file before submit")
      )

      if (!is.null(input$gwaspoly)) {
        for (i in 1:length(input$gwaspoly$datapath)) {
          temp123 <- load(input$gwaspoly$datapath[i])
          gwaspoly_temp <- get(temp123)
          gwaspoly_list <- GWAS_data_from_gwaspoly(gwaspoly_temp)

          if (i == 1) {
            gwaspoly <- gwaspoly_list
          } else {
            if (!all(gwaspoly$chrom_length == gwaspoly_list$chrom_length)) {
              # If same chromosome but different chromosomes length - keep the maximum
              if (all(gwaspoly$chrom_length$chromosome == gwaspoly_list$chrom_length$chromosome)) {
                idx <- which(gwaspoly$chrom_length$length < gwaspoly_list$chrom_length$length)
                if (length(idx) > 0) {
                  gwaspoly$chrom_length$length[idx] <- gwaspoly_list$chrom_length$length[idx]
                }
              } else {
                stop("Not same reference genome used")
              }
            }
            gwaspoly$gwas_data_list <- c(gwaspoly$gwas_data_list, gwaspoly_list$gwas_data_list)
            gwaspoly$gwas_data_thr_list <- c(gwaspoly$gwas_data_thr_list, gwaspoly_list$gwas_data_thr_list)
          }
        }
      } else {
        gwaspoly <- NULL
      }

      return(list(
        GWASpoly = gwaspoly,
        GWAS = {
          if (!is.null(input$gwas)) read_input_hidecan(input$gwas, GWAS_data) else list()
        },
        DE = {
          if (!is.null(input$de)) read_input_hidecan(input$de, DE_data) else list()
        },
        CAN = {
          if (!is.null(input$can)) read_input_hidecan(input$can, CAN_data) else list()
        }
      ))
    }
  })

  # Wait system for the uploads
  loadExample <- reactive({
    if (is.null(input_map()$dosages) & is.null(input_map()$phases) & is.null(input_map()$genetic_map) &
      is.null(input_map()$mappoly_in) &
      is.null(input_map()$onemap_in) &
      is.null(input_map()$polymapR.dataset) &
      is.null(input_map()$polymapR.map) &
      is.null(input_qtl()$selected_mks) &
      is.null(input_qtl()$qtl_info) &
      is.null(input_qtl()$blups) &
      is.null(input_qtl()$beta.hat) &
      is.null(input_qtl()$profile) &
      is.null(input_qtl()$effects) &
      is.null(input_qtl()$probs) &
      is.null(input_qtl()$qtlpoly_data) &
      is.null(input_qtl()$qtlpoly_remim.mod) &
      is.null(input_qtl()$qtlpoly_est.effects) &
      is.null(input_qtl()$qtlpoly_fitted.mod) &
      is.null(input_qtl()$diaQTL_data) &
      is.null(input_qtl()$diaQTL_scan1) &
      is.null(input_qtl()$diaQTL_scan1.summaries) &
      is.null(input_qtl()$diaQTL_fitQTL) &
      is.null(input_qtl()$diaQTL_BayesCI) &
      is.null(input_qtl()$polyqtlR_QTLscan_list) &
      is.null(input_qtl()$polyqtlR_qtl_info) &
      is.null(input_qtl()$polyqtlR_effects) &
      is.null(input_genome()$fasta) &
      is.null(input_genome()$fasta_server) &
      is.null(input_genome()$gff3) &
      is.null(input_genome()$gff3_server) &
      is.null(input_genome()$vcf) &
      is.null(input_genome()$vcf_server) &
      is.null(input_genome()$align) &
      is.null(input_genome()$align_server) &
      is.null(input_genome()$wig) &
      is.null(input_genome()$wig_server) &
      is.null(input$viewpoly_input) &
      is.null(input$viewpoly_env)) {
      withProgress(message = "Working:", value = 0, {
        incProgress(0.5, detail = paste("Uploading example map data..."))
        req(input$example_map)
        prepare_examples(input$example_map)
      })
    } else {
      NULL
    }
  })

  # Load hidecan example
  loadHidecanExample <- reactive({
    if (is.null(input_hidecan()$gwas) & is.null(input_hidecan()$de) & is.null(input_hidecan()$can)) {
      withProgress(message = "Working:", value = 0, {
        incProgress(0.5, detail = paste("Uploading example map data..."))
        x <- get_example_data()

        list(
          "GWAS" = list(GWAS_data(x[["GWAS"]])),
          "DE" = list(DE_data(x[["DE"]])),
          "CAN" = list(CAN_data(x[["CAN"]]))
        )
      })
    } else {
      NULL
    }
  })

  loadViewpoly <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading viewpoly file..."))
      if (is.null(values$upload_state_viewpoly)) {
        return(NULL)
      } else if (values$upload_state_viewpoly == "reset") {
        return(NULL)
      } else if (values$upload_state_viewpoly == "uploaded") {
        if (is.null(input$viewpoly_input) & is.null(input$viewpoly_env)) {
          warning("Upload a viewpoly dataset or select one available in your R environment before submit.")
          viewpoly.obj <- NULL
        } else if (!is.null(input$viewpoly_input)) {
          temp123 <- load(input$viewpoly_input$datapath)
          viewpoly.obj <- get(temp123)
        } else if (!is.null(input$viewpoly_env)) {
          viewpoly.obj <- get(input$viewpoly_env)
        }
        return(viewpoly.obj)
      }
    })
  })

  loadMap_custom <- reactive({
    if (!(is.null(input_map()$dosages) & is.null(input_map()$phases) & is.null(input_map()$genetic_map))) {
      req(input_map()$dosages, input_map()$phases, input_map()$genetic_map)
      withProgress(message = "Working:", value = 0, {
        incProgress(0.5, detail = paste("Uploading custom map data..."))
        prepare_map_custom_files(
          input_map()$dosages,
          input_map()$phases,
          input_map()$genetic_map
        )
      })
    } else {
      NULL
    }
  })

  loadMap_mappoly <- reactive({
    if (!is.null(input_map()$mappoly_in)) {
      withProgress(message = "Working:", value = 0, {
        incProgress(0.3, detail = paste("Uploading MAPpoly data..."))
        prepare_MAPpoly(input_map()$mappoly_in)
      })
    } else {
      NULL
    }
  })

  loadMap_onemap <- reactive({
    if (!is.null(input_map()$onemap_in)) {
      withProgress(message = "Working:", value = 0, {
        incProgress(0.3, detail = paste("Uploading OneMap data..."))
        temp123 <- load(input_map()$onemap_in$datapath)
        viewmap <- get(temp123)
        viewmap
      })
    } else {
      NULL
    }
  })

  loadMap_polymapR <- reactive({
    if (!(is.null(input_map()$polymapR.dataset) &
      is.null(input_map()$polymapR.map))) {
      req(input_map()$polymapR.dataset, input_map()$polymapR.map)
      withProgress(message = "Working:", value = 0, {
        incProgress(0.1, detail = paste("Uploading polymapR data..."))
        prepare_polymapR(
          input_map()$polymapR.dataset, input_map()$polymapR.map,
          input$input.type, as.numeric(input$ploidy)
        )
      })
    } else {
      NULL
    }
  })

  loadQTL_custom <- reactive({
    if (!(is.null(input_qtl()$selected_mks) &
      is.null(input_qtl()$qtl_info) &
      is.null(input_qtl()$blups) &
      is.null(input_qtl()$beta.hat) &
      is.null(input_qtl()$profile) &
      is.null(input_qtl()$effects) &
      is.null(input_qtl()$probs))) {
      req(
        input_qtl()$selected_mks, input_qtl()$qtl_info, input_qtl()$blups,
        input_qtl()$beta.hat, input_qtl()$profile, input_qtl()$effects,
        input_qtl()$probs
      )
      withProgress(message = "Working:", value = 0, {
        incProgress(0.5, detail = paste("Uploading custom QTL data..."))
        prepare_qtl_custom_files(
          input_qtl()$selected_mks,
          input_qtl()$qtl_info,
          input_qtl()$blups,
          input_qtl()$beta.hat,
          input_qtl()$profile,
          input_qtl()$effects,
          input_qtl()$probs
        )
      })
    } else {
      NULL
    }
  })

  loadQTL_qtlpoly <- reactive({
    if (!(is.null(input_qtl()$qtlpoly_data) &
      is.null(input_qtl()$qtlpoly_remim.mod) &
      is.null(input_qtl()$qtlpoly_est.effects) &
      is.null(input_qtl()$qtlpoly_fitted.mod))) {
      req(
        input_qtl()$qtlpoly_data,
        input_qtl()$qtlpoly_remim.mod,
        input_qtl()$qtlpoly_est.effects,
        input_qtl()$qtlpoly_fitted.mod
      )

      withProgress(message = "Working:", value = 0, {
        incProgress(0.3, detail = paste("Uploading QTLpoly data..."))
        prepare_QTLpoly(
          input_qtl()$qtlpoly_data,
          input_qtl()$qtlpoly_remim.mod,
          input_qtl()$qtlpoly_est.effects,
          input_qtl()$qtlpoly_fitted.mod
        )
      })
    } else {
      NULL
    }
  })

  loadQTL_diaQTL <- reactive({
    if (!(is.null(input_qtl()$diaQTL_scan1) &
      is.null(input_qtl()$diaQTL_scan1.summaries) &
      is.null(input_qtl()$diaQTL_fitQTL) &
      is.null(input_qtl()$diaQTL_BayesCI))) {
      req(
        input_qtl()$diaQTL_scan1,
        input_qtl()$diaQTL_scan1.summaries,
        input_qtl()$diaQTL_fitQTL,
        input_qtl()$diaQTL_BayesCI
      )

      withProgress(message = "Working:", value = 0, {
        incProgress(0.3, detail = paste("Uploading diaQTL data..."))
        prepare_diaQTL(
          input_qtl()$diaQTL_scan1,
          input_qtl()$diaQTL_scan1.summaries,
          input_qtl()$diaQTL_fitQTL,
          input_qtl()$diaQTL_BayesCI
        )
      })
    } else {
      NULL
    }
  })

  loadQTL_polyqtlR <- reactive({
    if (!(is.null(input_qtl()$polyqtlR_QTLscan_list) &
      is.null(input_qtl()$polyqtlR_qtl_info) &
      is.null(input_qtl()$polyqtlR_effects))) {
      req(
        input_qtl()$polyqtlR_QTLscan_list,
        input_qtl()$polyqtlR_qtl_info,
        input_qtl()$polyqtlR_effects
      )

      withProgress(message = "Working:", value = 0, {
        incProgress(0.3, detail = paste("Uploading polyqtlR data..."))
        prepare_polyqtlR(
          input_qtl()$polyqtlR_QTLscan_list,
          input_qtl()$polyqtlR_qtl_info,
          input_qtl()$polyqtlR_effects
        )
      })
    } else {
      NULL
    }
  })

  temp_dir <- reactive(tempdir())

  loadJBrowse_fasta <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading fasta path..."))
      if (!is.null(input_genome()$fasta) & !is.null(loadMap())) {
        # keep fasta name
        for (i in 1:length(input_genome()$fasta$datapath)) {
          print(file.path(temp_dir(), input_genome()$fasta$name))

          file.rename(
            input_genome()$fasta$datapath[i],
            file.path(temp_dir(), input_genome()$fasta$name[i])
          )
        }
        file.path(temp_dir(), sort(input_genome()$fasta$name)[1])
      } else if (!is.null(input_genome()$fasta_server) & !is.null(loadMap())) {
        input_genome()$fasta_server
      } else if (!is.null(input_genome()$fasta) | !is.null(input_genome()$fasta_server)) {
        warning("Load map data first to use this feature.")
      } else if (!is.null(loadExample())) {
        loadExample()$fasta
      } else {
        NULL
      }
    })
  })

  loadJBrowse_gff3 <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading gff3 path..."))
      if (!is.null(input_genome()$gff3)) {
        for (i in 1:length(input_genome()$gff3$datapath)) {
          file.rename(
            input_genome()$gff3$datapath[i],
            file.path(temp_dir(), input_genome()$gff3$name[i])
          )
        }
        file.path(temp_dir(), input_genome()$gff3$name[1])
      } else if (!is.null(input_genome()$gff3_server)) {
        input_genome()$gff3_server
      } else if (!is.null(loadExample())) {
        loadExample()$gff3
      } else {
        NULL
      }
    })
  })

  loadJBrowse_vcf <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading VCF path..."))
      if (!is.null(input_genome()$vcf)) {
        for (i in 1:length(input_genome()$vcf$datapath)) {
          file.rename(
            input_genome()$vcf$datapath[i],
            file.path(temp_dir(), input_genome()$vcf$name[i])
          )
        }
        file.path(temp_dir(), input_genome()$vcf$name[1])
      } else if (!is.null(input_genome()$vcf_server)) {
        input_genome()$vcf_server
      } else {
        NULL
      }
    })
  })

  loadJBrowse_align <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading BAM or CRAM alignment data path..."))
      if (!is.null(input_genome()$align)) {
        for (i in 1:length(input_genome()$align$datapath)) {
          file.rename(
            input_genome()$align$datapath[i],
            file.path(temp_dir(), input_genome()$align$name[i])
          )
        }
        file.path(temp_dir(), input_genome()$align$name[1])
      } else if (!is.null(input_genome()$align_server)) {
        input_genome()$align_server
      } else {
        NULL
      }
    })
  })

  loadJBrowse_wig <- reactive({
    withProgress(message = "Working:", value = 0, {
      incProgress(0.1, detail = paste("Uploading bigWig data path..."))
      if (!is.null(input_genome()$wig)) {
        for (i in 1:length(input_genome()$wig$datapath)) {
          file.rename(
            input_genome()$wig$datapath[i],
            file.path(temp_dir(), input_genome()$wig$name[i])
          )
        }
        file.path(temp_dir(), input_genome()$wig$name[1])
      } else if (!is.null(input_genome()$wig_server)) {
        input_genome()$wig_server
      } else {
        NULL
      }
    })
  })

  loadMap <- reactive({

    req(
      !is.null(loadExample()) |
      !is.null(loadMap_custom()) |
      !is.null(loadMap_mappoly()) |
      !is.null(loadMap_onemap()) |
      !is.null(loadMap_polymapR()) |
      !is.null(loadViewpoly())
    )
    
    if (!is.null(loadViewpoly())) {
      return(loadViewpoly()$map)
    } else if (!is.null(loadMap_custom())) {
      return(loadMap_custom())
    } else if (!is.null(loadMap_mappoly())) {
      return(loadMap_mappoly())
    } else if (!is.null(loadMap_onemap())) {
      return(loadMap_onemap())
    } else if (!is.null(loadMap_polymapR())) {
      return(loadMap_polymapR())
    } else if (!is.null(loadExample())) {
      return(loadExample()$map)
    }
  })

  loadQTL <- reactive({
    req(
      !is.null(loadExample()) |
      !is.null(loadQTL_custom()) |
      !is.null(loadQTL_qtlpoly()) |
      !is.null(loadQTL_diaQTL()) |
      !is.null(loadQTL_polyqtlR()) |
      !is.null(loadViewpoly())
    )
    
    if (!is.null(loadViewpoly())) {
      return(loadViewpoly()$qtl)
    } else if (!is.null(loadQTL_custom())) {
      return(loadQTL_custom())
    } else if (!is.null(loadQTL_qtlpoly())) {
      return(loadQTL_qtlpoly())
    } else if (!is.null(loadQTL_diaQTL())) {
      return(loadQTL_diaQTL())
    } else if (!is.null(loadQTL_polyqtlR())) {
      return(loadQTL_polyqtlR())
    } else if (!is.null(loadExample())) {
      return(loadExample()$qtl)
    }
  })

  loadHidecan <- reactive({
    if (is.null(loadHidecanExample()) &
      is.null(input_hidecan()) &
      is.null(loadViewpoly())) {
      warning("Select one of the options in `upload` session")
      return(NULL)
    } else if (!is.null(loadViewpoly())) {
      return(loadViewpoly()$hidecan)
    } else if (!is.null(input_hidecan())) {
      return(input_hidecan())
    } else if (!is.null(loadHidecanExample())) {
      return(loadHidecanExample())
    }
  })

  observe({
    if (!is.null(loadMap()) | !is.null(loadQTL())) {
      Sys.sleep(1)
      # enable the download button
      shinyjs::enable("export_viewpoly")
    } else {
      shinyjs::disable("export_viewpoly")
    }
  })

  output$export_viewpoly <- downloadHandler(
    filename = function() {
      paste0("viewpoly.RData")
    },
    content = function(file) {
      withProgress(message = "Working:", value = 0, {
        incProgress(0.1, detail = paste("Saving viewpoly object..."))
        validate(
          need(!is.null(loadMap()) | !is.null(loadQTL()), "For exporting VIEWpoly dataset it is required to load
               linkage map or QTL data in the above boxes.")
        )
        obj <- structure(
          list(
            map = loadMap(),
            qtl = loadQTL(),
            fasta = NULL, # It would save only the temporary path
            gff3 = NULL,
            vcf = NULL,
            align = NULL,
            wig = NULL,
            hidecan = loadHidecan(),
            version = packageVersion("viewpoly")
          ),
          class = "viewpoly"
        )
        assign(input$data.name, obj)
        incProgress(0.5, detail = paste("Saving viewpoly object..."))
      })
      save(list = input$data.name, file = file)
    }
  )

  return(list(
    loadMap = reactive(loadMap()),
    loadQTL = reactive(loadQTL()),
    loadJBrowse_fasta = reactive(loadJBrowse_fasta()),
    loadJBrowse_gff3 = reactive(loadJBrowse_gff3()),
    loadJBrowse_vcf = reactive(loadJBrowse_vcf()),
    loadJBrowse_align = reactive(loadJBrowse_align()),
    loadJBrowse_wig = reactive(loadJBrowse_wig()),
    loadHidecan = reactive(loadHidecan())
  ))
}

## To be copied in the UI
# mod_upload_ui("upload_ui_1")

## To be copied in the server
# mod_upload_server("upload_ui_1")