R/utilities.R

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

#' @name utilities
#'
#' @title Utilities for managing library paths
#'
#' @description `add_libpaths()`: Add local library paths to
#'     `.libPaths()`.
#'
#' @param paths `character()`: vector of directories to add to
#'     `.libPaths()`. Paths that do not exist will be created.
#'
#' @return `add_libpaths()`: updated .libPaths(), invisibly.
#'
#' @examples
#' \dontrun{add_libpaths("/tmp/host-site-library")}
#'
#' @export
add_libpaths <-
    function(paths)
{
    stopifnot(is.character(paths))

    ## make sure all paths exist
    exist <- vapply(paths, dir.exists, logical(1))
    ok <- vapply(paths[!exist], dir.create, logical(1))
    if (!all(ok))
        stop(
            "'add_libpaths()' failed to create directories:\n",
            "  '", paste(paths[!exist][!ok], collapse="'\n  '"), "'"
        )

    .libPaths(c(paths, .libPaths()))
}

isScalarCharacter_or_NULL <- function(x, na.ok = FALSE, zchar = FALSE)
    isScalarCharacter(x, na.ok, zchar) || is.null(x)

.is_local_directory <- function(x)
    isScalarCharacter(x) && dir.exists(x)

.is_https <- function(x)
    isCharacter(x) & startsWith(x, "https://")

.is_workspace <-
    function(x)
{
    isScalarCharacter(x) &&
        ## exactly 1 `/`
        identical(lengths(regmatches(x, gregexpr("/", x, fixed = TRUE))), 1L)
}

#' @importFrom dplyr full_join
.tbl_with_template <-
    function(tbl, tmpl)
{
    result <- as_tibble(tmpl)
    if (nrow(tbl)) {
        have <- intersect(names(tbl), names(tmpl))
        tbl <- select(tbl, have)
        result <-
            full_join(tbl, result, by = have) |>
            select(names(tmpl))
    }
    result
}

#' @importFrom utils head
.pretty <- function(x, indent = 2, exdent = 0, some=FALSE) {
    len <- length(x)
    if (some && len > 6)
        x <- head(x, 5)
    pad <- paste0(rep(" ", indent), collapse="")
    paste(c(
        strwrap(paste(x, collapse=", "), indent = indent, exdent = exdent),
        if (some && len > 6)
            paste0(pad, "# ... with ", len, " more elements")
    ), collapse = "\n")
}

.pretty_text <- function(..., indent = 0L, exdent = 0L) {
    text <- paste(..., collapse = " ")
    paste(strwrap(text, indent = indent, exdent = exdent), collapse = "\n")
}