#' Download GEO metadata

#'

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

#' analysis.

#' 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.

#' @return A \code{list} of \code{data.frame}s giving the clinical and metadata

#'   information for the GEO dataset.

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

#' @author

#'   Anders Ellern Bilgrau,

#'   Steffen Falgreen Larsen

#' @examples

#' \dontrun{

#' print(DLBCL_overview)

#' geo_nbr <- DLBCL_overview[6,1]

#' downloadAndPrepareMetadata(geo_nbr = geo_nbr, destdir = getwd())

#' }

#' @importFrom GEOquery getGEO

#' @importFrom Biobase pData

#' @keywords internal

#' @export

downloadAndPrepareMetadata <- function(geo_nbr,

                                       destdir = getwd(),

                                       clean = FALSE,

                                       verbose = TRUE) {

  if (verbose) message("Preparing ", geo_nbr, " metadata")

  # Download data if not already downloaded

  if (verbose) message("Downloading files...")

  dl_dir <- file.path(destdir, geo_nbr)

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

  dl <- getGEO(GEO = geo_nbr, destdir = dl_dir,

               GSEMatrix = TRUE, getGPL = FALSE)

  # Extract pheno data

  if (!is.list(dl)) {

    pd <- pData(dl)

  } else {

    pd <- lapply(dl, pData)

    # Merge the dataframes (if multiple)

    merge2 <- function(x, y) {

      merge(x, y, all = TRUE, sort = FALSE)

    }

    pd <- Reduce(merge2, pd)

  }

  # Set class

  class(pd) <- c(geo_nbr, class(pd))

  # Clean-up if wanted

  if (clean) {

    if (verbose) message("Removing unnessary files...")

    file.remove(file.path(destdir, geo_nbr, names(dl)))

  }

  if (verbose) message("Done.")

  return(invisible(pd))

}