R/settings.R

In FredHutch/fh.wdlR: Convenience Tools for Managing WDL Workflows via Cromwell

#' Cromwell Settings
#'
#' @name cromwell_settings
#'
#' @section Cromwell URL:
#' A URL for the Cromwell server you're interacting with is required.
#' The only way to do so is by setting the env var:
#'
#' `CROMWELLURL`
#'
#' You can set this env var in many different ways. From within R you can
#' do this with [cromwell_config()] like:
#'
#' `cromwell_config(url = "your/url")`
#'
#' Which is equivalent to
#'
#' `Sys.setenv(CROMWELLURL = "your/url")`
#'
#' Note that this only sets the url for the current R session and does
#' not persist among R sessions.
#'
#' Other options include:
#'
#' - Set `CROMWELLURL` env var in a `.bash_profile` file or equivalent
#' that will be picked up by R when it starts.
#' - Set `CROMWELLURL` env var in an IDE such as RStudio.
#' - Set `CROMWELLURL` env var by prefixing `R` on the command line, e.g.,
#' `CROMWELLURL=http://your/url R`
#'
#' @section Verbose messaging:
#'
#' You can set your preference for whether you get messages informing you
#' of various tasks `rcromwell` is performing. See [cromwell_config()]
NULL

#' Cromwell Configuration
#'
#' @export
#' @importFrom rlang is_character is_logical
#' @param cromwell_url (character) Cromwell server URL. The full url,
#' for example "http://localhost:8000" or "https://mycromwell.com"
#' @param verbose (logical) verbose messaging. default: `TRUE`. this
#' toggles on (`TRUE`) or off (`FALSE`) all messages throughout the package.
#' @details Note that although the default value for `cromwell_url` is
#' `NULL`, we fetch the current value of `CROMWELLURL` env var internally
#' if `cromwell_url=NULL` - thus, we retain a value for `CROMWELLURL` if
#' it is set even if this function is run without passing anything to
#' `cromwell_url`
#' @author Scott Chamberlain
#' @examples \dontrun{
#' cromwell_config()
#' cromwell_config("https://mycromwellinstance.com")
#' cromwell_config(verbose = FALSE)
#' }
cromwell_config <- function(cromwell_url = NULL, verbose = TRUE) {
  if (is.null(cromwell_url)) cromwell_url <- Sys.getenv("CROMWELLURL")
  rlang::is_character(cromwell_url)
  Sys.setenv(CROMWELLURL = cromwell_url)

  rlang::is_logical(verbose)
  pkg_env$verbose <- verbose

  list(
    rcromwell_settings =
      list(url = cromwell_url, verbose = pkg_env$verbose)
  )
}

crom_mssg <- function(...) {
  if (pkg_env$verbose) message(...)
}