R/experiment.env_cleanup.R

In qBioTurin/epimod: Epidemiological modelling (epimod)

#' @title Removes unnexessary files and directories
#' @description This is an internal function removing unnecessary files (and the running directory itself) from the running environment
#' @param id, a numeric identifier used to format the output's file name
#' @param run_dir, the directory to cleanup
#' @param out_fname, output filename prefix
#' @param out_dir, output directory specified by the user
#' @author Beccuti Marco, Castagno Paolo, Pernice Simone
#'
#' @export
#' @examples
#'\dontrun{
#' experiment.env_cleanup(id=1, run_dir="/run/directory", out_fname="simulation", out_dir="/out/directory",)
#' }

experiment.env_cleanup <- function(id, run_dir,
																	 out_fname, out_dir){
	print("[experiment.env_clenup] Start removing unneeded files")
	r_dir <- paste0(run_dir, id)
	## file.copy(from = paste0(r_dir, .Platform$file.sep, out_fname, "-", id,".trace"), to = out_dir)
	print(paste0("[experimen.env_cleanup] Saving file ",
							 list.files(path = r_dir,
							 					 pattern = paste0(out_fname, "(-[0-9]+)+(.trace){1}"))))
	file.copy(from = paste0(r_dir,
													.Platform$file.sep,
													list.files(path = r_dir,
																		 pattern = paste0(out_fname,
																		 								 "(-[0-9]+)+(.trace){1}")
													)
	),
	to = out_dir)

	# If FBA was used
	fbafiles = list.files(
		path = r_dir,
		pattern = paste0(out_fname, "(-[0-9]+)+(.flux){1}")
	)

	if(length(fbafiles)>0){
		print(
			paste0(
				"[experimen.env_cleanup] Saving flux file ",
				fbafiles
			)
		)
		file.copy(
			from = paste0(
				r_dir,
				.Platform$file.sep,
				fbafiles
			),
			to = out_dir
		)
	}

	##
	print(paste0("[experimen.env_cleanup] Removing directory ", r_dir))
	unlink(r_dir,
				 recursive = TRUE,
				 force = TRUE)
	print("[experimen.env_cleanup] Done removing unneeded files")
}