run.R

#!/usr/bin/env Rscript
library("optparse")

option_list <- list(
  make_option(c("-d", "--dataset"),
    type = "character", default = "https://zenodo.org/record/4634013/files/physionet.zip?download=1",
    help = "dataset url", metavar = "character"
  ),
  make_option(c("-r", "--run"),
    type = "logical", default = TRUE,
    help = "run target pipeline [default= %default]", metavar = "logical"
  )
)

opt_parser <- OptionParser(option_list = option_list)
opt <- parse_args(opt_parser)

if (is.null(opt$dataset)) {
  print_help(opt_parser)
  stop("At least one argument must be supplied (dataset).n", call. = FALSE)
}

# pull data from the internet
if (!dir.exists(here::here("inst/extdata/physionet"))) {
  dir.create(here::here("inst/extdata"), recursive = TRUE, showWarnings = FALSE)
  options(timeout = max(300, getOption("timeout")))
  download.file(opt$dataset, method = "libcurl", destfile = here::here("inst/extdata/data.zip"))

  # if less than this, probably download error
  if (file.size(here::here("inst/extdata/data.zip")) < 300000000) {
    stop("Error downloading the dataset, the file seems too small. Please check what happened.")
  }

  unzip(here::here("inst/extdata/data.zip"), exdir = here::here("inst/extdata"), setTimes = TRUE, overwrite = FALSE)
  file.remove(here::here("inst/extdata/data.zip"))
}

if (dir.exists(here::here("inst/extdata"))) {
  if (isTRUE(as.logical(Sys.getenv("CI")))) {
    Rcpp::compileAttributes()
    renv::install(".")
    targets::tar_prune()
  } else {
    tryCatch(
      {
        pkg_date <- packageDate("false.alarm")
        files_r <- paste0(here::here("R"), "/", list.files(here::here("R"), pattern = "*.R"))
        files_cpp <- paste0(here::here("R"), "/", list.files(here::here("src"), pattern = "*.cpp"))
        files_h <- paste0(here::here("R"), "/", list.files(here::here("src"), pattern = "*.h"))
        files <- c(files_r, files_cpp, files_h)
        changed <- na.omit(files[as.Date(file.mtime(files)) > (pkg_date)])

        if (length(changed) > 0) {
          message("false.alarm is outdated, trying to automatically resolve this.")
          Rcpp::compileAttributes()
          renv::install(".")
        }
        rm("pkg_date", "files_r", "files_cpp", "files_h", "files", "changed")
      },
      error = function(e) {
        message("false.alarm is not installed, trying to automatically resolve this.")
        Rcpp::compileAttributes()
        renv::install(".")
      },
      finally = {
        message("done.")
      }
    )
  }

  if (opt$run) {
    # run targets?
    targets::tar_watch(
      targets_only = TRUE, supervise = TRUE, seconds = 30, display = "graph", browse = TRUE, outdated = FALSE,
      label = c("time", "branches", "size"), port = 55444
    )


    Sys.setenv(TAR_WARN = "false")

    # Uncomment to run targets sequentially on your local machine.
    # targets::tar_make()
    # Uncomment to run targets in parallel
    targets::tar_make_future(workers = 4L)
    # on local processes or a Sun Grid Engine cluster.
    # targets::tar_make_clustermq(workers = 2L)

    # Finally create the output files what will be used on this current Workflowr release:
    tryCatch(
      {
        message("Creating the outputs for Workflowr.")

        network <- targets::tar_visnetwork(TRUE, label = c("time", "size", "branches"))
        tips <- stringr::str_split_fixed(network$x$nodes$label, pattern = "\n", n = 2)[, 2]
        tips <- stringr::str_replace_all(tips, "\n", "<br />")
        network$x$nodes$title <- tips
        network$x$nodes$label <- network$x$nodes$name
        network$x$options$nodes$physics <- TRUE
        saveRDS(network, file = here::here("output/network.rds"))
        rm(network)
        rm(tips)

        source(here::here("scripts/helpers/create_output.R"), encoding = "UTF-8")
        create_output(file = here::here("output/work_output.rds"), "regime_optimize")
        rm(create_output)
      },
      error = function(e) {
        message("Could not create the outputs for Workflowr.")
      },
      finally = {
        message("done.")
      }
    )
  }
} else {
  stop("Error installing dataset.")
}

# remove data before commit results
# if (dir.exists(here::here("inst/extdata"))) {
#   unlink(here::here("inst/extdata"), recursive = TRUE, force = TRUE)
# }