R/rmd2md.R

In ivyleavedtoadflax/rmd2md: Prepare Rmarkdown files for publishing to github pages

#' This R script will process all R markdown files (those with in_ext file
#' extention, .rmd by default) in the current working directory. Files with a
#' status of 'processed' will be converted to markdown (with out_ext file
#' extention, '.markdown' by default). It will change the published parameter to
#' 'true' and change the status parameter to 'publish'.
#' 
#' @param path_site path to the local root storing the site files
#' @param dir_rmd directory containing R Markdown files (inputs)
#' @param dir_md directory containing markdown files (outputs)
#' @param figures where to store/get images created from plots directory +"/"
#'   (relative to path_site)
#' @param out_ext the file extention to use for processed files.
#' @param in_ext the file extention of input files to process.
#' @param recursive should rmd files in subdirectories be processed.
#' @return nothing.
#' @author Jason Bryer <jason@bryer.org> edited by Andy South and Matthew Upson
#'   <matthew.a.upson@gmail.com>
#' @export

rmd2md <- function(
  path_site = getwd(),
  dir_rmd = "_rmd",
  dir_md = "_posts",
  figures = 'figures',
  out_ext = '.md',
  in_ext = '.Rmd',
  recursive = FALSE
) {

  # Expand the dirs

  tryCatch({

    #suppressWarnings({

      dir_rmd <- file.path(path_site, dir_rmd)
      dir_md <- file.path(path_site, dir_md)

      # This is a horrible hack, but knitr will not seem to find this object if it
      # is not: <<-. See
      # http://stackoverflow.com/questions/8218196/object-not-found-error-when-passing-model-formula-to-another-function

      figures <- file.path(path_site, fig_path(figures))

      # Check that the dirs exist

      if (!file.exists(dir_rmd)) {

        stop('Input directory: ', dir_rmd ,' does not exist!')

      }

      if (!file.exists(dir_md)) {

        stop('Output directory: ', dir_md ,' does not exist!')

      }

      # if (!file.exists(file.path(path_site, figures))) {
      # 
      #   stop('Figures directory: ', figures ,' does not exist!')
      # 
      # }

      # List files to be converted

      files <- list.files(
        path = dir_rmd,
        pattern = in_ext,
        ignore.case = TRUE,
        recursive = recursive
      )

      # Check that there are files in the files directory

      if (length(files)==0) {

        stop('No files in specified input directory!')

      } else {

        message(length(files), ' files found in input folder.')
        message('Checking each file and processing if status: process')
        message()

      }

      # Loop through files and convert

      for(f in files) {

        # Read content from each of the files in turn

        content <- readLines(file.path(dir_rmd, f))

        if (parse_status(content) == 'process') {

          # This is a bit of a hack but if a line has zero length (i.e. a
          # black line), it will be removed in the resulting markdown file.
          # This will ensure that all line returns are retained.

          message(paste0('Processing ', f))

          content[nchar(content) == 0] <- ' '
          content <- change_status(content)

          # This is a horrible hack, but knitr will not seem to find this object
          # if it is not: <<-

          outFile <- file.path(
            dir_md, paste0(substr(f, 1, (nchar(f)-(nchar(in_ext)))), out_ext)
          )

          message()
          message("Writing file to:", outFile)
          message()

          # andy change to render for jekyll

          knitr::render_jekyll(highlight = "pygments")

          # render_jekyll(highlight = "prettify") #for javascript

          knitr::opts_knit$set(out.format = 'markdown')

          # andy BEWARE don't set base.dir!! it caused me problems
          # "base.dir is never used when composing the URL of the figures; it is
          # only used to save the figures to a different directory.
          # The URL of an image is always base.url + fig.path"
          # https://groups.google.com/forum/#!topic/knitr/18aXpOmsumQ

          knitr::opts_knit$set(base.url = '/')
          knitr::opts_chunk$set(fig.path = figures)

          knitr::knit(text = content, output = outFile)

          figs = list.files(
            path = figures,
            pattern = '*.jpg',
            full.names = TRUE
          )

          for (f in figs) remove_exifs(fig = f)

        } else {

          message("Ignoring ", f)

        }

        # Finally remove exifs from jpgs

      }

}
  #})
  ,
  warning = function() warning('Warning produced running rmd2md():', warnings()),
  error = function(e) stop('Error produced running rmd2md():', e),
  finally = {}
  )
}


# Last thing is to remove exif tags from jpgs in figures folder
# Requires linux tool exiv2. Check system is linux first...