R/report_batch.R

In KWB-R/kwb.pilot: Importing, Aggregating and Visualising Data From KWB Pilot Plants

#' Report batch: creates batch file for report
#'
#' @param rmd_name name of Rmarkdown document to render (default: "report.Rmd")
#' @param output_dir outputDirectory (default: getwd())
#' @keywords internal
write_report <- function(rmd_name = "report.Rmd", output_dir = getwd()) {
  code <- 'if (!require("rmarkdown") || packageVersion("rmarkdown") < "1.3") {
    install.packages("rmarkdown", repos = "https://cloud.r-project.org")
  }
  print("Generating reports (HTML, PDF & WORD)")
  rmarkdown::render(
    input = "input/%s",
    output_format = paste0(c("html", "pdf", "word"), "_document"),
    output_dir = "output"
  )'

  file <- file.path(output_dir, "create_report.R")

  writeLines(sprintf(code, rmd_name), con = file)
}

#' Report batch: creates batch file for report
#'
#' @param batchDir path to report batch directory (default: tempdir())
#' @param batchName name for report batch file(default: "create_report.bat")
#' @param report_path (default: NULL)
#' @param report_config_path (default: NULL)
#' @param open_in_explorer open batchDir in Windows explorer (default: TRUE).
#' Only working on a Windows system!
#' @export
create_report_batch <- function(batchDir = file.path(tempdir(), "batch_report"),
                                batchName = "create_report.bat",
                                report_path = NULL,
                                report_config_path = NULL,
                                open_in_explorer = TRUE) {
  # Helper function
  force_copy <- function(from, to) file.copy(from, to, overwrite = TRUE)

  batchDir <- gsub(pattern = "\\\\", replacement = .Platform$file.sep, batchDir)

  if (!dir.exists(batchDir)) {
    dir.create(batchDir, showWarnings = FALSE)
  }

  owdir <- setwd(batchDir)
  on.exit(owdir)

  report_path <- kwb.utils::defaultIfNULL(
    report_path, package_file("shiny/haridwar/report/report.Rmd")
  )

  report_name <- basename(report_path)

  dir.create(path = file.path(batchDir, "input"), showWarnings = FALSE)

  force_copy(
    from = report_path,
    to = file.path(batchDir, "input", report_name)
  )

  write_report(rmd_name = report_name, output_dir = batchDir)

  if (!is.null(report_config_path)) {
    if (file.exists(report_config_path)) {
      force_copy(
        from = report_config_path,
        to = file.path(batchDir, "input", "report_config.txt")
      )
    }
  }

  batch_r_script <- paste0(
    kwb.utils::removeExtension(basename(batchName)), ".R"
  )

  r_path <- R.home("bin")

  r_script <- grep("Rscript", list.files(r_path), value = TRUE)

  r_exe <- normalizePath(file.path(r_path, r_script))

  batch_text <- sprintf(
    "%s%s%s%s%s",
    "set mypath=%cd%\n",
    "@echo \"Generating reports (HTML, PDF & WORD) and  saving to '\\output' folder .....\"\n",
    sprintf("\"%s\" \"%s\"\n", r_exe, batch_r_script),
    "@echo \"Report generation finished. Please check subfolder '\\output'!\"\n",
    "Pause"
  )

  batch_path <- file.path(batchDir, batchName)

  writeLines(batch_text, con = batch_path)

  cat("Batch file & data structure created at:", normalizePath(batch_path))

  if (open_in_explorer & .Platform$OS.type == "windows") {
    shell(paste("explorer", normalizePath(batchDir)))
  }

  list.files(getwd(), recursive = TRUE)
}