R/continue_beast2.R

In beastier: Call 'BEAST2'

#' Continue a BEAST2 run
#' @inheritParams default_params_doc
#' @return The text sent to \code{STDOUT} and \code{STDERR}.
#'   It will create the file with name \code{output_state_filenames}
#' @examples
#' check_empty_beaustier_folders()
#'
#' if (is_beast2_installed() && beautier::is_on_ci()) {
#'   beast2_options <- create_beast2_options(
#'     input_filename = get_beastier_path("2_4.xml")
#'   )
#'   run_beast2_from_options(beast2_options)
#'   continue_beast2(beast2_options)
#'   file.remove(beast2_options$output_state_filename)
#'   remove_beaustier_folders()
#' }
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
continue_beast2 <- function(
  beast2_options = create_beast2_options()
) {
  check_beast2_options(beast2_options)

  if (beast2_options$verbose) {
    print_beast2_options(beast2_options)
  }

  if (is_win_bin_path(beast2_options$beast2_path)) {
   stop("Cannot use the Windows executable BEAST2.exe in scripts")
  }
  ##############################################################################
  # Check files
  ##############################################################################
  check_input_filename(beast2_options$input_filename)
  check_beast2_path(beast2_options$beast2_path)
  check_beast2_options_do_not_overwrite_existing_files(beast2_options)
  check_input_filename_validity(beast2_options)
  check_can_create_dir_for_state_output_file(beast2_options)
  check_can_create_state_output_file(beast2_options)

  ##############################################################################
  # Create the BEAST2 command
  ##############################################################################
  cmd <- create_beast2_continue_cmd_from_options(
    beast2_options = beast2_options
  )
  if (beast2_options$verbose) {
    message(paste("cmd:", paste0(cmd, collapse = " ")))
  }

  # Create the folder to hold the file, without warning if it's already present
  output_folder <- dirname(beast2_options$output_state_filename)
  if (beast2_options$verbose) {
    message(
      "Creating folder '", output_folder, "'",
      "for BEAST2 .xml.state output file"
    )
  }
  dir.create(
    path = output_folder,
    recursive = TRUE,
    showWarnings = FALSE
  )
  # This assumpion should have been proven to be valid
  # by check_can_create_dir_for_state_output_file
  check_true(dir.exists(output_folder))

  ##############################################################################
  # Run BEAST2
  ##############################################################################
  output <- system2(
    command = cmd[1],
    args = cmd[-1],
    stdout = TRUE,
    stderr = TRUE
  )
  # If the output is only 1 line, this will probably be an error message
  check_true(
    length(output) != 1,
    info = paste0(
      "Command '", paste0(cmd, collapse = " "), "' failed ",
      "with error '", output, "'"
    )
  )

  ##############################################################################
  # The files as created by BEAST2
  ##############################################################################
  # This is only true if there has been one sampling event in the MCMC
  check_true(
    file.exists(beast2_options$output_state_filename),
    info = paste0(
      "BEAST2 state file not created after a continued run. \n",
      "Command '", paste0(cmd, collapse = " "), "' failed. ",
      "'beast2_options$output_state_filename': '",
        beast2_options$output_state_filename, "'\n",
      "Maybe no permission to write at that location?"
    )
  )
  output
}