#' Download GEO .CEL files

#'

#' Function for downloading the CEL files of a GEO dataset and prepare it for

#' preprocessing.

#' The function uses \code{getGEOSuppFiles} which downloads the data. The

#' function then unzips the data files in the GEO series.

#'

#' @param geo_nbr The GEO ascession number.

#' @param destdir The destination dir of the downloaded files.

#' @param clean Should the strictly unnessesary files be deleted?

#' @param verbose Signal the process.

#' @note The function will overwrite existing files in the \code{destdir}.

#' @author

#'   Anders Ellern Bilgrau,

#'   Steffen Falgreen Larsen

#' @examples

#' \dontrun{

#' downloadAndPrepareCELFiles(geo_nbr = "GSE18376",

#'                           destdir = tempdir())

#' }

#' @importFrom GEOquery getGEOSuppFiles gunzip

#' @keywords internal

#' @export

downloadAndPrepareCELFiles <- function(geo_nbr,

                                       destdir = getwd(),

                                       clean = FALSE,

                                       verbose = TRUE) {

  options("timeout" = 240) # Increase timeout (in seconds)

  on.exit(options("timeout" = 60)) # Reset to standard timeout on exit

  if (verbose) message("Preparing GEO ", geo_nbr, " data")

  dl_dir <- file.path(destdir, geo_nbr)

  # Download data if nessesary

  raw_file <- paste0(file.path(dl_dir, geo_nbr), "_RAW.tar")

  if (!file.exists(raw_file)) {

    if (verbose) message("Downloading .CEL files...\n")

    dir.create(dl_dir, showWarnings = FALSE)

    getGEOSuppFiles(GEO = geo_nbr, makeDirectory = FALSE, baseDir = dl_dir)

  } else {

    if (verbose) message("Compressed .CEL files already downloaded...")

  }

  # List celfiles (if any)

  cel_files <- list.files(dl_dir, pattern = "\\.cel$",

                          ignore.case = TRUE, full.names = TRUE)

  if (identical(cel_files, character(0))) {

    # Untar the file bundle

    if (verbose) message("Untaring the RAW file...\n")

    tar_file <- list.files(path = dl_dir, pattern = "RAW.tar$", full.names = TRUE)

    untar(tarfile = tar_file, exdir = dl_dir)

    # Unzip the files

    if (verbose) message("Unzipping the .CEL files...\n")

    gz_files <- list.files(dl_dir, pattern = "\\.cel.gz$", ignore.case = TRUE,

                           full.names = TRUE)

    for (file in gz_files) {

      gunzip(file, overwrite = TRUE, remove = TRUE)

    }

    # List celfiles

    cel_files <- list.files(dl_dir, pattern = "\\.cel$",

                            ignore.case = TRUE, full.names = TRUE)

  } else {

    message("(Some) .CEL files already unpacked...\n")

  }

  # Clean-up if wanted

  if (clean) {

    if (verbose) message("Removing all non CEL files...\n")

    file.remove(setdiff(list.files(dl_dir, full.names = TRUE), cel_files))

  }

  cel_files <- normalizePath(cel_files)

  if (verbose) message("Download and preparation of CEL files done.\n")

  return(invisible(cel_files))

}