R/standardizeCall.R

In acidgenomics/acidbase: Acid Genomics Base Functions

#' Standardize call
#'
#' This function adds matching support for S4 methods with formals that aren't
#' identical to the generic, and use a nested `.local` call.
#'
#' @export
#' @note Updated 2020-01-09.
#'
#' @inheritParams base::sys.call
#' @inheritParams AcidRoxygen::params
#'
#' @param defaults `logical(1)`.
#' Include default arguments in the call.
#'
#' @param expandDots `logical(1)`.
#' Should arguments matching `...` in the call be included or left as a
#' `...` argument?
#'
#' @return
#' - `call`: Matched call.
#' - `list`: Verbose list that includes additional information about how the
#' call was standardized. Recommended for debugging purposes only.
#'
#' @seealso
#' - `match.call()`.
#' - `sys.call()`.
#' - `sys.parent()`.
#' - `pryr::standardise_call()`.
#' - `stackoverflow::match.call.defaults()`.
#'
#' @examples
#' aaa <- "AAA"
#' bbb <- "BBB"
#'
#' ## Standard function.
#' testing <- function(a, b) {
#'     standardizeCall()
#' }
#' testing(aaa, bbb)
#'
#' ## Inside S4 method.
#' setGeneric(
#'     name = "testing",
#'     def = function(a, ...) {
#'         standardGeneric("testing")
#'     }
#' )
#' setMethod(
#'     f = "testing",
#'     signature = signature(a = "character"),
#'     definition = function(a, b, ...) {
#'         standardizeCall()
#'     }
#' )
#' testing(aaa, bbb)
standardizeCall <-
    function(which = sys.parent(n = 1L),
             defaults = TRUE,
             expandDots = TRUE,
             return = c("call", "list"),
             verbose = getOption(x = "verbose", default = FALSE)) {
        assert(
            isInt(which),
            isTRUE(which >= 0L),
            isTRUE(which < length(sys.calls())),
            isFlag(defaults),
            isFlag(expandDots),
            isFlag(verbose)
        )
        return <- match.arg(return)
        ## Don't allow a `which` value less than 1.
        if (which < 1L) {
            which <- 1L
        }
        ## Determine where the call is in the stack that we want to standardize.
        ## Note that this differs for S4 methods containing a nested `.local`.
        .local <- .isLocalCall(sys.call(which = which))
        if (isTRUE(.local) && which > 1L) {
            which <- which - 1L
        }
        ## Local the parameters we need to sanitize call.
        definition <- sys.function(which = which)
        call <- sys.call(which = which)
        envir <- sys.frame(which = which)
        list <- list(
            sys.status = sys.status(),
            sys.nframe = sys.nframe(),
            sys.parent = sys.parent(),
            .local = .local,
            which = which,
            definition = definition,
            call = call,
            envir = envir
        )
        ## Extract the definition from `.local`, if necessary.
        if (isTRUE(.local)) {
            assert(!isTRUE(.isLocalCall(call)))
            ## Update definition.
            if (is(definition, "MethodDefinition")) {
                definition <- .extractLocal(definition)
                list[["definition"]] <- definition
            }
        }
        if (isTRUE(verbose)) {
            print(list)
        }
        ## Now ready to match the call.
        call <- match.call(
            definition = definition,
            call = call,
            expand.dots = expandDots,
            envir = envir
        )
        ## Expand the call to include default arguments, if desired.
        ## Inspired by `stackoverflow::match.call.defaults()`.
        if (isTRUE(defaults)) {
            formals <- formals(definition)
            if (isTRUE(expandDots) && "..." %in% names(formals)) {
                formals[["..."]] <- NULL
            }
            for (i in setdiff(names(formals), names(call))) {
                call[i] <- list(formals[[i]])
            }
            call <- match.call(
                definition = definition,
                call = call,
                expand.dots = TRUE,
                envir = envir
            )
        }
        list[["match.call"]] <- call
        if (isTRUE(verbose)) {
            print(list(match.call = call))
        }
        assert(is.call(call))
        switch(EXPR = return,
            call = call,
            list = list
        )
    }



## Detect `.local()` inside an S4 method.
## Updated 2019-10-21.
.isLocalCall <- function(x) {
    ok <- is.call(x)
    if (!isTRUE(ok)) {
        return(FALSE)
    }
    ok <- identical(x[[1L]], as.symbol(".local"))
    if (!isTRUE(ok)) {
        return(FALSE)
    }
    TRUE
}