R/registerMthd.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.                    ##
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#-------------------------------------------------------------------------------
# registerMthd: Add new analysis method
#-------------------------------------------------------------------------------

#' @title Add a new analysis method
#'
#' @description
#' \code{registerMthd} registers a new analysis method to the gtox
#' databases.
#'
#' @param lvl Integer of length 1, the level for the analysis method
#' @param mthd Character, the name of the method
#' @param desc Character, same length as mthd, the method description
#' @param nddr Integer, 0 or 1, 1 if the method requires loading the dose-
#'             response data
#' @param type Character of length 1, the data type, "sc" or "mc"
#'
#' @details
#' 'mthd' must match a corresponding function name in the functions that load
#' the methods, ie. \code{mc2_mthds}. 'nddr' only applies to level 6
#' methods.
#' 
#' @keywords internal
#' 
#' @return None
#'
#' @import data.table

registerMthd <- function(lvl, mthd, desc, nddr=0L, type) {

    nddr <- NULL

    if (length(mthd) != length(desc)) {
        stop("length of mthd must equal length of desc.")
    }

    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.")

    mb <- paste(
        Sys.info()[c(
            "login",
            "user",
            "effective_user"
            )],
        collapse="."
    )

    dat <- data.table(modified_by=rep(mb, length(mthd)))
    dat[ , (c(
            paste0(type, lvl, "_mthd"),
            "desc"
        )) := list(mthd, desc)]

    if (lvl == 6L) dat[ , nddr := nddr]

    gtoxAppend(
        dat=dat,
        tbl=paste0(type, lvl, "_methods"),
        db=getOption("TCPL_DB")
    )

}

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