R/launchResultsExplorer.R

In mi-erasmusmc/TreatmentPatterns: A package to analyse real-world treatment patterns of a study population of interest

#' Processes the zipped result folder(s) and launch the shiny application.
#' 
#' @param saveSettings Settings object as created by createSaveSettings().
#' @param zipFolder Name of local folder containing zip file(s) to move to outputFolder.
#' @param outputFolder Name of local folder containing output.
#'
#' @return
#' @export
launchResultsExplorer <- function(saveSettings = NULL, zipFolder = NULL, outputFolder = NULL) {
  ensure_installed("shiny")
  ensure_installed("shinydashboard")
  ensure_installed("reshape2")
  ensure_installed("ggplot2")
  ensure_installed("data.table")
  ensure_installed("DT")
  
  # Check if inputs correct
  if (!is.null(saveSettings)) {
    if (!class(saveSettings)%in%c('saveSettings')){
      stop('Incorrect class for saveSettings')
    } else {
      outputFolder <- stringr::str_remove(saveSettings$outputFolder, pattern = paste0("/", saveSettings$databaseName))
    }
  } else if (!is.null(zipFolder)) {
    if (length(list.dirs(file.path(zipFolder, "output"), recursive = FALSE, full.names = FALSE))==0) {
      print("Unzip files in zipFolder and move to /output")
      unzipFiles(zipFolder, unzipMainFolder = file.path(zipFolder, "output"))
      outputFolder <- file.path(zipFolder, "output")
    } else if (dir.exists(file.path(zipFolder, "output"))) {
      print("Files already unzipped, use existing results in /output")
      outputFolder <- file.path(zipFolder, "output")
    } }
  else if (is.null(outputFolder) & is.null(zipFolder) & is.null(saveSettings)) {
    stop('Input outputFolder, zipFolder or saveSettings')
  }
  
  outputFolder <- stringr::str_replace(outputFolder, pattern =  "^[.]", replacement = getwd())
  
  shinySettings <- list(outputFolder = outputFolder)
  
  .GlobalEnv$shinySettings <- shinySettings
  on.exit(rm("shinySettings", envir = .GlobalEnv))
  
  appDir <- file.path(system.file(package = "TreatmentPatterns"), "shiny")
  shiny::runApp(appDir = appDir)
}

# Borrowed and adapted function from CohortDiagnostics.
unzipFiles <- function(rootFolder, unzipMainFolder) {
  zipFiles <-
    dplyr::tibble(
      zipFile = list.files(
        rootFolder,
        pattern = ".zip",
        full.names = TRUE,
        recursive = TRUE
      ),
      unzipFolder = ""
    )
  ParallelLogger::logInfo("Merging ", nrow(zipFiles), " zip files.")
  
  if (!file.exists(unzipMainFolder))
    dir.create(path = unzipMainFolder, recursive = TRUE)
  
  for (i in 1:nrow(zipFiles)) {
    ParallelLogger::logInfo("- Unzipping ", basename(zipFiles$zipFile[i]))
    unzipFolder <-
      file.path(unzipMainFolder, sub(".zip", "", basename(zipFiles$zipFile[i])))
    if (!file.exists(unzipFolder))
      dir.create(unzipFolder)
    zip::unzip(zipFiles$zipFile[i], exdir = unzipFolder)
    zipFiles$unzipFolder[i] <- unzipFolder
  }
}