#' Installs brainarray CDF and probe information packages

#'

#' This package downloads, installs, and/or loads the brainarray CDF and probe

#' enviroments from the Brainarray website.

#'

#' @param array_type A character of length 1 giving the giving the name of the'

#'   array. (Preferably as returned by \code{affyio::read.celfile.header})

#' @param custom_cdf A charcter giving the annotation type.

#' @param version A character of length 1 giving the version to download.

#' @return Invisibly returns a list of the locations of the saved files.

#' @author

#'   Steffen Falgreen,

#'   Anders Ellern Bilgrau

#' @seealso \code{\link{tempdir}}, \code{\link{install.packages}}

#' @references

#'   See \url{http://brainarray.mbni.med.umich.edu}.

#' @examples

#' tmp.path <- requireBrainarray("hgu133a", custom_cdf = "enst",

#'                               version = "18.0.0")

#' print(tmp.path)

#' tmp.path2 <- requireBrainarray("hgu133a", custom_cdf = "enst")

#' print(tmp.path2)

#' @import AnnotationDbi

#' @export

requireBrainarray <- function(array_type,

                              custom_cdf = "enst",

                              version = getLatestVersion()) {

  output <- list()

  brain_dat <- output[["brain_dat"]] <-

    readBrainarrayTable(custom_cdf = custom_cdf, version = version)

  base_url <- attributes(brain_dat)$base_url

  if (getSubversion(version) >= 19) {

    base_url <- paste0("http://mbni.org/customcdf/", version, "/",

                       tolower(custom_cdf))

  }

  pkgs <- getBrainarrayPackages(brain_dat, array_type = array_type)

  for (pkg in pkgs) {

    loaded <- suppressWarnings(require(pkg, character.only = TRUE))

    if (!loaded || packageVersion(pkg) != version) {

      if (loaded) {

         message("Installed package version is not ", version,

                 ". Overwriting installed package.", sep = "")

      }

      file.pkg <- paste0(pkg, "_", version, ".tar.gz")

      # Construct url and download package

      pkg_url <- file.path(paste0(base_url, ".download"), file.pkg)

      pkg_dest <- output[[pkg]] <- file.path(tempdir(), file.pkg)

      download.file(url = pkg_url, destfile = pkg_dest)

      # Install and load package

      install.packages(pkgs = pkg_dest, repos = NULL, type = "source")

      require(pkg, character.only = TRUE)

    }

  }

  return(invisible(output))

}