#' Retrieve path to a cached file.

#'

#' The function retrieves the path to a file that is cached in the archive

#' directory.

#'

#' @param filename Name of the file.

#'

#' @return String containing the path to the file.

archivePath <- function(filename) {

  ad <- archiveDir()

  filename <- paste0(filename, ".rds")

  return(file.path(ad, filename, fsep = .Platform$file.sep))

}

#' Retrieve the path to the cache directory.

#'

#' Retrieve the path to the cache directory for the multiGSEA package.

#' Create the cache directory if need be.

#'

#' @return String containing the path to the cache directory.

#'

#' @importFrom rappdirs user_cache_dir

archiveDir <- function() {

  ad <- rappdirs::user_cache_dir("multiGSEA")

  if (!file.exists(ad)) {

    if (!dir.create(ad, FALSE, TRUE)) {

      stop("An error occurred during creating the archive directory: ", ad,

        call. = FALSE

      )

    }

  }

  return(ad)

}

#' Read a local RDS file.

#'

#' Use the readRDS function to load the given file which should be in RDS

#' format.

#'

#' @param filename Path to the file to be read.

#'

#' @return Content of file.

#'

#' @importFrom methods is

loadLocal <- function(filename) {

  res <- try(readRDS(filename), silent = TRUE)

  if ("try-error" %in% methods::is(res)) {

    return(NULL)

  } else {

    return(res)

  }

}

#' Make a list of strings unique

#'

#' It might happen that there are duplicated strings in a list. With this

#' function we will rename those duplicated entries in a way that we simply add

#' the number of occurrences to the string. I.e., when the string foo occurs

#' three times in a list, it will be renamed to foo_1, foo_2, and foo_3,

#' respectively.

#'

#' @param names List of strings where duplicates should be renamed

#'

#' @return List where duplicates are renamed.

#'

#' @examples

#' l <- c("foo", "bar", "foo", "bars")

#' rename_duplicates(l)

#'

#' @export

rename_duplicates <- function(names) {

  tn <- table(names)

  for (name in names(tn[tn > 1])) {

    names[names == name] <- paste0(name, "_", 1:tn[names(tn) == name])

  }

  return(names)

}