R/mod-edit-annotations.R

In Sage-Bionetworks/dccmonitor: Monitor Data Validation

#' @title Edit annotations module UI
#'
#' @description UI function for the edit annotations module.
#'
#' @noRd
#' @inheritParams mod_main_ui
edit_annotations_ui <- function(id) {
  ns <- NS(id)

  tagList(
    div(
      h4("Instructions"),
      # nolint start
      tags$ol(
        tags$li("Click on 'Get Annotations' to join all metadata to the manifest."),
        tags$li("Select the desired annotation columns and verify annotations do not contain PII/PHI."),
        tags$li("Below the annotations table, give the name to upload the file as and click on 'Upload' to save the annotations as a csv file in Synapse.")
      ),
      h4("Important:"),
      tags$ul(
        tags$li("In order to save to Synapse, the annotations file is first downloaded to a local, temporary file. Double-check that PII/PHI data has not been included."),
        tags$li("All metadata files listed in the table above are joined to the manifest. Verify that only files relevant to the current data release are present.")
      ),
      # nolint end
      dccvalidator::with_busy_indicator_ui(
        actionButton(ns("get_annots"), "Get annotations")
      ),
      br(),
      br(),
      shinyWidgets::multiInput(
        ns("annot_keys"),
        label = "Choose Annotation Keys",
        choices = ""
      ),
      br(),
      h4("Annotations table"),
      reactable::reactableOutput(ns("annot_table")),
      textOutput(ns("no_annots")),
      br(),
      textInput(ns("file_name"), "Enter file name to upload as:"),
      shinyjs::disabled(
        dccvalidator::with_busy_indicator_ui(
          actionButton(ns("upload"), "Upload")
        )
      )
    )
  )
}

#' @title Edit annotations module server
#'
#' @description Server function for the edit annotations module.
#'
#' @noRd
#' @param id Module id.
#' @param fileview The fileview for a specific study.
#' @param annots_folder Synapse synID folder to upload annotation table to.
#' @param syn Synapse client object
edit_annotations_server <- function(id, fileview, annots_folder,
                                    syn) {
  moduleServer(
    id,
    function(input, output, session) {
      all_metadata <- NULL
      observeEvent(input$get_annots, {
        dccvalidator::with_busy_indicator_server("get_annots", {
          all_metadata <<- combine_all_metadata(fileview)
          annot_keys <- names(all_metadata)
          disallowed_keys <- get_golem_config("annotation_keys")
          annot_keys_subset <- setdiff(annot_keys, disallowed_keys)

          if (!is.null(all_metadata)) {
            shinyWidgets::updateMultiInput(
              session = session,
              "annot_keys",
              label = "Choose Annotation Keys",
              choices = annot_keys,
              selected = annot_keys_subset
            )
          }
        })
      })

      observe({
        if (is.null(input$annot_keys)) {
          output$annot_table <- reactable::renderReactable(NULL)
        } else {
          metadata_subset <- all_metadata[, input$annot_keys]
          output$annot_table <- reactable::renderReactable({
            reactable::reactable(
              metadata_subset,
              highlight = TRUE,
              searchable = TRUE,
              resizable = TRUE,
              showPageSizeOptions = TRUE,
              pageSizeOptions = c(1, 5, 10, 25, 50, 100),
              outlined = TRUE
            )
          })
        }
      })

      # Require important info to be able to push upload button
      observe({
        if (input$file_name == "" || is.null(input$file_name) ||
          input$annot_keys == "" || is.null(input$annot_keys)) {
          shinyjs::disable("upload")
        } else {
          shinyjs::enable("upload")
        }
      })

      # Upload handling
      observeEvent(input$upload, {
        dccvalidator::with_busy_indicator_server("upload", {
          metadata_subset <- all_metadata[, input$annot_keys]
          temp <- tempfile(pattern = input$file_name, fileext = ".csv")
          utils::write.csv(metadata_subset, file = temp, row.names = FALSE)
          file_to_upload <- synapse$File(
            temp,
            parent = annots_folder,
            name = input$file_name,
            annotations = list(
              study = unique(fileview$study[!is.na(fileview$study)])
            )
          )
          syn$store(file_to_upload)
        })
      })
    }
  )
}