R/gtoxMthdLoad.R

In pmpsa-hpc/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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxMthdLoad: Load analysis method(s)
#-------------------------------------------------------------------------------

#' @rdname mthd_funcs
#' @export

gtoxMthdLoad <- function(lvl, id=NULL, type="mc") {

    if (length(lvl) > 1) stop("'lvl' must be an integer of length 1.")
    if (!type %in% c("mc", "sc")) stop("Invalid 'type' value.")
    if (type == "mc" & !lvl %in% c(2, 3, 5, 6)) stop("Invalid 'lvl' value.")
    if (type == "sc" & !lvl %in% seq_len(2)) stop("Invalid 'lvl' value.")

    id_name <- if (type == "mc" & lvl == 2) "acid" else "aeid"
    flds <- c(
        id_name,
        "b.%s_mthd AS mthd",
        "b.%s_mthd_id AS mthd_id"
    )
    if ((lvl < 4 & type == "mc") | (lvl == 1 & type == "sc")) {
        flds <- c(flds, "a.exec_ordr AS ordr")
    }
    if (lvl == 6) flds <- c(flds, "nddr")

    tbls <- c(paste0("%s_", id_name, " AS a"), "%s_methods AS b")

    qformat <- paste(
        "SELECT", paste(flds, collapse=","),
        "FROM", paste(tbls, collapse=","),
        "WHERE a.%s_mthd_id=b.%s_mthd_id"
    )
    qformat <- gsub("%s", paste0(type, lvl), qformat)

    if (!is.null(id)) {
        qformat <- paste(qformat, "AND", id_name, "IN (%s)")
        qformat <- sprintf(qformat, paste(id, collapse=","))
    }

    if ((lvl < 4 & type == "mc") | (lvl == 1 & type == "sc")) {
        qstring <- paste0(
            qformat, " ORDER BY ", id_name, ", a.exec_ordr"
        )
    } else {
        qstring <- qformat
    }

    dat <- gtoxQuery(query=qstring, db=getOption("TCPL_DB"))

    if (nrow(dat) == 0) {
        warning("The given id(s) do not have ", type, lvl, " methods.")
        return(dat[])
    }

    len_miss <- lw(!id %in% dat[[id_name]])
    if (len_miss > 0) {
        warning(
            len_miss, " of the given ids do not have ", type, lvl,
            " methods."
        )
    }

    dat[]

}

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