--- a
+++ b/R/downloadAndPrepareCELFiles.R
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+#' 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))
+}