R/gtoxConf.R

In GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxConf: Configure the gtox options
#-------------------------------------------------------------------------------

#' @rdname config_funcs
#' 
#' @examples
#' 
#' ## Configure database
#' sqlite <- file.path(system.file(package="GladiaTOX"),
#'     "sql",
#'     "gladiatoxdb.sqlite")
#' gtoxConf(db=sqlite, user=NA, host=NA, drvr="SQLite")
#' 
#' @export

gtoxConf <- function (drvr=NULL, user=NULL, pass=NULL, host=NULL, db=NULL) {

    ## Variable-binding to pass R CMD Check
    Value <- NULL

    if (!is.null(user)) options("TCPL_USER"=user)
    if (!is.null(pass)) options("TCPL_PASS"=pass)
    if (!is.null(host)) options("TCPL_HOST"=host)
    if (!is.null(db))   options("TCPL_DB"=db)

    if (!is.null(drvr)) {

        if (!drvr %in% c("SQLite", "MySQL")) {
            stop(
                drvr,
                " is not a supported database driver. Must be 'SQLite' or ",
                "'MySQL'."
            )
        }

        if (drvr == "SQLite") {
            options("TCPL_DRVR"="SQLite")
        }

        if (drvr == "MySQL") {
            options("TCPL_DRVR"="MySQL")
            mxp <- gtoxQuery(
                "SHOW VARIABLES LIKE 'max_allowed_packet'")[ , Value]
            mxp <- as.numeric(mxp)
            if (mxp < 1073741824) {
                warning(
                    "The 'max_allowed_packet' MySQL server setting is set to ",
                    mxp, " bytes. It is recommended that you increase it to ",
                    "1073741824 bytes to ensure larger queries run without ",
                    "error."
                )
            }
        }

    }

}

#-------------------------------------------------------------------------------