R/gtoxQuery.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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxQuery: Query the gtox databases
#-------------------------------------------------------------------------------

#' @rdname query_funcs
#'
#' @import DBI
#' @importFrom RSQLite SQLite
#' @import data.table
#' @importFrom RMySQL MySQL
#' @importMethodsFrom RMySQL dbConnect dbDisconnect
#' @export


gtoxQuery <- function(query, db=getOption("TCPL_DB"),
    drvr=getOption("TCPL_DRVR")) {

    if (is.null(db)) db <- getOption("TCPL_DB")
    if (is.null(drvr)) drvr <- getOption("TCPL_DRVR")

    ## Check for valid inputs
    if (length(query) != 1 || !is(query, "character")) {
        stop("The input 'query' must be a character of length one.")
    }
    if (length(db) != 1 || !is(db, "character")) {
        stop("The input 'db' must be a character of length one.")
    }

    db_pars <- NULL

    if (drvr == "SQLite") {

        db_pars <- list(drv=SQLite(), dbname=db)

    }

    if (drvr == "MySQL") {

        if (any(is.na(options()[c("TCPL_USER", "TCPL_HOST", "TCPL_PASS")]))) {
            stop(
                "Must configure TCPL_USER, TCPL_HOST, and TCPL_PASS options. ",
                "See ?gtoxConf for more details."
            )
        }

        db_pars <- list(
            drv=MySQL(),
            user=getOption("TCPL_USER"),
            password=getOption("TCPL_PASS"),
            host=getOption("TCPL_HOST"),
            dbname=db
        )

    }

    if (is.null(db_pars)) {

        stop(
            getOption("TCPL_DRVR"), " is not a supported database system. See ",
            "?gtoxConf for more details."
        )

    }

    dbcon <- do.call(dbConnect, db_pars)
    result <- dbGetQuery(dbcon, query)

    dbDisconnect(dbcon)

    result <- as.data.table(result)
    result[]

}

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