R/cache.R

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

.getCache <- function() {
    cache <- getOption("scmmCache", setCache(verbose = FALSE))
    BiocFileCache::BiocFileCache(cache)
}

#' @name scmmCache
#'
#' @title Manage cache / download directories for study data
#'
#' @description Managing data downloads is important to save disk space and
#' re-downloading data files. This can be done effortlessly via the integrated
#' `BiocFileCache` system.
#'
#' @section scmmCache:
#' Get the directory location of the cache. It will prompt the user to create
#' a cache if not already created. A specific directory can be used via
#' \code{setCache}.
#'
#' @section setCache:
#' Specify the directory location of the data cache. By default, it will
#' go into the user's home and package name directory as given by
#' \link[tools:userdir]{R_user_dir} (default: varies by system e.g., for Linux:
#' '$HOME/.cache/R/SingleCellMultiModal').
#'
#' @section removeCache:
#' Some files may become corrupt when downloading, this function allows
#' the user to delete the tarball associated with a study number in the
#' cache.
#'
#' @param directory character(1) The file location where the cache is located.
#' Once set, future downloads will go to this folder. See `setCache` section
#' for details.
#'
#' @param verbose Whether to print descriptive messages
#'
#' @param ask logical(1) (default TRUE when `interactive()`) Confirm the file
#' location of the cache directory
#'
#' @param accession character(1) A single string indicating the accession number
#' of the study
#'
#' @param ... For `scmmCache`, arguments passed to `setCache`
#'
#' @md
#'
#' @examples
#' getOption("scmmCache")
#' scmmCache()
#'
#' @return The directory / option of the cache location
#'
#' @export
scmmCache <- function(...) {
    getOption("scmmCache", setCache(..., verbose = FALSE))
}

#' @rdname scmmCache
#' @export
setCache <-
    function(directory = tools::R_user_dir("SingleCellMultiModal", "cache"),
        verbose = TRUE,
        ask = interactive())
{
    stopifnot(
        is.character(directory), length(directory) == 1L, !is.na(directory)
    )

    if (!dir.exists(directory)) {
        if (ask) {
            qtxt <- sprintf(
                "Create cBioPortalData cache at \n    %s? [y/n]: ",
                directory
            )
            answer <- .getAnswer(qtxt, allowed = c("y", "Y", "n", "N"))
            if ("n" == answer)
                stop("'cbioCache' directory not created. Use 'setCache'")
        }
        dir.create(directory, recursive = TRUE, showWarnings = FALSE)
    }
    options("cbioCache" = directory)

    if (verbose)
        message("cBioPortalData cache directory set to:\n    ",
                directory)
    invisible(directory)
}

#' @rdname scmmCache
#' @export
removeCache <- function(accession) {
    bfc <- .getCache()
    rid <- BiocFileCache::bfcquery(bfc, accession, "rname", exact = TRUE)$rid
    if (length(rid)) {
        BiocFileCache::bfcremove(bfc, rid)
        message("Cache record: ", accession, ".tar.gz removed")
    } else
        message("No record found: ", accession, ".tar.gz")
}