##' Download Datasets from UCSC Xena Hubs

##'

##' Avaliable datasets list: <https://xenabrowser.net/datapages/>

##'

##' @author Shixiang Wang <w_shixiang@163.com>

##' @param xquery a tibble object generated by [XenaQuery] function.

##' @param destdir specify a location to store download data. Default is system temp directory.

##' @param download_probeMap if `TRUE`, also download ProbeMap data, which used for id mapping.

##' @param trans_slash logical, default is `FALSE`. If `TRUE`, transform slash '/' in dataset id

##' to '__'. This option is for backwards compatibility.

##' @param max_try time limit to try downloading the data.

##' @param force logical. if `TRUE`, force to download data no matter whether files exist.

##'  Default is `FALSE`.

##' @param ... other argument to `download.file` function

##' @return a `tibble`

##' @export

##' @importFrom utils download.file

##' @importFrom dplyr filter

##' @examples

##' \dontrun{

##' xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")

##' hosts(xe)

##' xe_query = XenaQuery(xe)

##' xe_download = XenaDownload(xe_query)

##' }

XenaDownload <- function(xquery,

                         destdir = tempdir(),

                         download_probeMap = FALSE,

                         trans_slash = FALSE,

                         force = FALSE,

                         max_try = 3L,

                         ...) {

  stopifnot(is.data.frame(xquery), c("url") %in% names(xquery), is.logical(download_probeMap))

  if (download_probeMap) {

    xquery_probe <- UCSCXenaTools::XenaData %>%

      dplyr::filter(XenaDatasets %in% xquery$datasets) %>%

      XenaGenerate() %>%

      XenaQueryProbeMap()

    xquery <- dplyr::bind_rows(xquery, xquery_probe)

  }

  if (trans_slash) {

    xquery$fileNames <- gsub(

      pattern = "/",

      replacement = "__",

      x = xquery$datasets

    )

  } else {

    xquery$fileNames <- xquery$datasets

  }

  xquery$fileNames <- ifelse(grepl("\\.gz", xquery$url),

    paste0(xquery$fileNames, ".gz"),

    xquery$fileNames

  )

  # destdir = paste0(destdir,"/")

  xquery$destfiles <- file.path(destdir, xquery$fileNames)

  if (!dir.exists(destdir)) {

    dir.create(destdir, recursive = TRUE, showWarnings = FALSE)

  }

  message("All downloaded files will under directory ", destdir, ".")

  if (!trans_slash) {

    dir_names <- dirname(xquery$destfiles)

    message("The 'trans_slash' option is FALSE, keep same directory structure as Xena.")

    message("Creating directories for datasets...")

    for (i in dir_names) {

      dir.create(i, recursive = TRUE, showWarnings = FALSE)

    }

  }

  # Make sure the order is right

  xquery <- dplyr::select(xquery, c("hosts", "datasets", "url", "fileNames", "destfiles"), dplyr::everything())

  download_dataset <- function(x) { # nocov start

    tryCatch(

      {

        if (!file.exists(x[5]) | force) {

          message("Downloading ", x[4])

          download.file2(x[3], destfile = x[5], max_try = max_try, ...)

        } else {

          message(x[5], ", the file has been download!")

        }

      },

      error = function(e) {

        message(

          "Can not find file",

          x[4],

          ", this file maybe not compressed."

        )

        x[3] <- gsub(pattern = "\\.gz$", "", x[3])

        x[4] <- gsub(pattern = "\\.gz$", "", x[4])

        x[5] <- gsub(pattern = "\\.gz$", "", x[5])

        message("Try downloading file", x[4], "...")

        tryCatch(

          {

            download.file2(x[3], destfile = x[5], max_try = max_try, ...)

          },

          error = function(e) {

            message("Your network is bad (try again) or the data source is invalid (report to the developer).")

            invisible(NULL)

          }

        )

      }

    )

  }

  apply(xquery, 1, download_dataset) # nocov end

  if (trans_slash) {

    message(

      "Note file names inherit from names in datasets column\n  and '/' all changed to '__'."

    )

  }

  invisible(xquery)

}

download.file2 <- function(url, destfile,

                           max_try = 3L,

                           ...) {

  Sys.sleep(0.01)

  tryCatch(

    {

      if (abs(max_try - 4L) > 1) {

        message("==> Trying #", abs(max_try - 4L))

      }

      download.file(url, destfile, ...)

    },

    error = function(e) {

      if (max_try == 1) {

        message("Tried 3 times but failed, please check your internet connection!")

        invisible(NULL)

      } else {

        download.file2(url, destfile, max_try = max_try - 1L, ...)

      }

    }

  )

}