R/app_run.R

In earnaud/MetaShARK-v2: metashark

#' @title Run MetaShARK
#'
#' @description
#' Main function for launching the MetaShARK application.
#'
#' @usage
#' runMetashark(...)
#'
#' @param ...
#' options to pass to the application, ignored if missing or mistyped.
#' \describe{
#'   \item{wip}{logical. Shows WIP parts of the app. (default to FALSE)}
#'   \item{dev}{logical. Add development elements in the GUI.
#'   (default to FALSE)}
#'   \item{reactlog}{logical. Use reactlog? (default to TRUE)}
#'   \item{use_profvis}{logical. Profile the app with {profvis}?
#'   (default to FALSE)}
#'   \item{use_test}{logical. Lanch the app with its testing environment?
#'   (default to FALSE). Shall not be used by end-users.}
#' }
#'
#' @details
#' MetaShARK (METAdata SHiny Automated Resource & Knowledge) is a web app
#' which is designed to help its user as much as possible for filling ecological
#' metadata. It uses the EML standard (cf. NCEAS work) to allow a full and
#' precise description of input datasets.
#'
#' @author
#' Elie Arnaud <elie.arnaud@mnhn.fr>
#'
#' @examples
#'
#' ## Not run:
#'
#' library(MetaShARK)
#'
#' # run this to launch MetaShARK
#' runMetashark()
#'
#' ## End (Not run)
#'
#' @import shiny
#'
#' @include about_module_functions.R about_module.R app_header.R app_server.R
#' app_ui.R clean_modules.R documentation_module.R eal_1_SelectDP.R
#' eal_2_DataFiles_helpers.R eal_2_DataFiles.R eal_3_Attributes_dates.R
#' eal_3_Attributes_helpers.R eal_3_Attributes.R eal_4_CatVars_helpers.R
#' eal_4_CatVars.R eal_5_GeoCov_custom.R eal_5_GeoCov_helpers.R eal_5_GeoCov.R
#' eal_6_TaxCov.R eal_7_ORCID_helpers.R eal_7_Personnel_helpers.R
#' eal_7_Personnel.R eal_7_roleInput.R eal_8_Misc_helpers.R eal_8_Misc.R
#' eal_9_MakeEML.R eal_x_Annotations_helpers.R eal_x_Annotations.R
#' fill_module_saves.R fill_module_setup.R fill_module.R fill_pages.R metafin.R
#' runMetashark.R settings_rightSideBar.R template_functions.R
#' upload_module_functions.R upload_module.R utils_additional_HTML.R
#' utils_collapsible.R utils_devmsg.R utils_followPath.R utils_grep.R
#' utils_insertModule.R utils_isContentTruthy.R utils_listReactiveValues.R
#' utils_listToStructure.R utils_listToXML.R utils_reactiveDirReader.R
#' utils_reactiveTrigger.R utils_readDataTable.R utils_readHTMLFromMD.R
#' utils_readPlaintext.R utils_rebuild.R utils_urlInput.R utils_writeText.R
#' utils_xml_handling.R welcome_module.R
#'
#' @export
runMetashark <- function(...) {
  # Required -- dot not remove
  require(shinyTree)
  require(shinyBS)

  # Set args ====
  # in .GlobalEnv = local options
  args <- list(...)
  args$launch_browser <- isTRUE(args$launch_browser)

  # Dev - debug options
  args$dev <- isTRUE(args$dev)
  args$wip <- isTRUE(args$wip) || isTRUE(args$dev) # needed for some UI
  args$reactlog <- isTRUE(args$reactlog) || isTRUE(args$dev)
  args$use_profvis <- isTRUE(args$use_profvis)
  args$use_test <- isTRUE(args$use_test)

  # Set args in environment
  assign("metashark_args", args, envir = .GlobalEnv)

  # Settings =====
  # Set resourcePaths
  addResourcePath("media", system.file("media/", package = "MetaShARK"))
  on.exit(removeResourcePath("media"))

  # Ensure correct encoding
  options(encoding = "UTF-8")
  Sys.setlocale("LC_ALL", "en_US.utf8")

  # Set max flow at 2 Go
  options(shiny.maxRequestSize = 2 * 1024^3)

  # Set window values
  if (isFALSE(args$use_test)) {
    options(shiny.port = 3838)
  }

  # Launch ====
  if (isTRUE(args$use_profvis)) {
    profvis::profvis({
      runApp(
        shinyApp(ui = ui, server = server),
        launch_browser = args$launch_browser
      )
    })
  } else if (isTRUE(args$use_test)) {
    options("shiny.testmode" = TRUE)
    shinyApp(ui = ui, server = server)
  } else {
    runApp(
      shinyApp(ui = ui, server = server),
      launch.browser = args$launch_browser
    )
  }
}