R/simple_references.R

In muschellij2/leanbuild: Tools for Creating Automated Courses

#' Run Simple References
#'
#' @param x A filename of a markdown or Rmarkdown file, or the full output
#' from `readLines` on that file
#' @param bib_files bibliography files to use for pandoc
#' @param add_reference_header Should the `## References` header be added at the
#' end of the output?
#'
#' @return A character vector of the file, with references subbed in
#' @export
simple_references = function(x, bib_files, add_reference_header = FALSE) {
  if (length(x) == 1 && file.exists(x)) {
    x = readLines(x, warn = FALSE)
  }
  # indices = grepl("\\[\\s*[@]", x)
  indices = grepl("@", x)
  # [@bookdown2016 #bookdown2016]
  all_refs = x[indices]
  # out = x
  bad_string = "ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ"
  result = lapply(all_refs, function(out) {
    stopifnot(!any(grepl(bad_string, out)))
    out = c(out, "", bad_string)
    tfile = tempfile(fileext = ".md")
    writeLines(out, tfile, sep = "\n")
    pandoc_args = c(
      paste0("--bibliography=", path.expand(normalizePath(bib_files))),
      "--wrap=none")
    # o1 = tempfile(fileext = ".md")
    # rmarkdown::pandoc_convert(input = tfile,
    #                           to = "markdown_strict",
    #                           output = o1,
    #                           from = "markdown",
    #                           citeproc = FALSE,
    #                           options = NULL)
    o2 = tempfile(fileext = ".md")
    rmarkdown::pandoc_convert(input = tfile,
                              to = "markdown_strict",
                              output = o2,
                              citeproc = TRUE,
                              options = pandoc_args)
    o2_text = readLines(o2)
  })
  all_references = lapply(result, function(o2_text) {
    references = grep(bad_string, o2_text)
    stopifnot(length(references) == 1)
    if (references == length(o2_text)) {
      return(NULL)
    }
    references = o2_text[(references+1):length(o2_text)]
    references = references[!references %in% ""]
    references
  })
  # dangerous
  final_refs = unique(unlist(unique(all_references)))
  if (length(final_refs) > 0 && all(nchar(final_refs) > 0)) {
    final_refs = paste0(final_refs, "\n\n")
  }

  all_output = lapply(result, function(o2_text) {
    references = grep(bad_string, o2_text)
    stopifnot(length(references) == 1)
    stopifnot(o2_text[references-1] == "")
    out = o2_text[-((references-1):length(o2_text))]
  })
  all_output = mapply(function(x, y, z) {
    if (is.null(z)) {
      out = x
    } else {
      out = y
    }
    paste(out, collapse = "\n")
  }, all_refs, all_output, all_references, SIMPLIFY = TRUE)
  all_output = c(unlist(all_output))
  out_x = x
  out_x[indices] = all_output

  out_x = c(out_x, "",
            if (add_reference_header && length(final_refs) > 0) "## References",
            final_refs)
  out_x
}