R/scdoc.r

In larmarange/scdoc: Long document with R Studio, knitr, pandoc and prince XML

#' Initialize scdoc or knit and convert a Rmd file using scdoc
#' 
#' @param file file to knit and convert using scdoc, if NULL initialize scdoc in R Studio
#' @details Use the command \code{scdoc()} to define scdoc() as the command to 
#' apply when clicking on \strong{Knit HTML} button in R Studio. Alternativaly,
#' you can also specify a file to knit and convert into HTML/PDF.
#' @export scdoc

scdoc <- function(file = NULL) {
  if (is.null(file))
    options(rstudio.markdownToHTML = scdoc.md2html)
  else {
    mdfile <- paste0(sub("\\.[a-zA-Z]*$","", file),".md")
    htmlfile <- paste0(sub("\\.[a-zA-Z]*$","", file),".html")
    knit(file, mdfile)
    scdoc.md2html(mdfile, htmlfile)
  }
}

#' Convert an md file to HTML/PDF
#' 
#' @param inputFile input file name (md file)
#' @param outputFile output file name (html file)
#' @details the output pdf file name will be derivated from \code{outputFile}.
#' @export scdoc.md2html


scdoc.md2html <- function(inputFile, outputFile) {
  path <- paste0(installed.packages()["scdoc","LibPath"],"/scdoc/scdoc/")
  if (!require(yaml)) {
    install.packages("yaml")
    library("yaml")
  }
  f <- readLines(inputFile, encoding="UTF-8")
  if (!is.na(b <- which(f == "---")[1]) & !is.na(e <- which(f == "...")[1]))
    opt <- yaml.load(paste(f[(b+1):(e-1)], collapse="\n"))
  else
    opt <- list()
  if (!is.null(opt$zotxt)) zotxt <- "--filter=pandoc-zotxt"
  else zotxt <- ""
  system(paste("pandoc", 
    shQuote(inputFile), 
    "-t html5 -s -o", 
    shQuote(outputFile),
    paste0("--template=", path, "scdoc-template.html5"),
    paste0("--include-in-header=", path, "scdoc-head.html"),
    "--self-contained",
    paste0("--data-dir=", path),
    "--smart",
    "--number-sections",
    "--mathml",
    zotxt,
    "--filter=pandoc-citeproc",
    "-S"))
  if (!is.null(opt$pdf)) if (opt$pdf == 'prince')
    system(paste("prince",
      shQuote(outputFile),
      "--javascript"))
}

#' Extract references from a Rmd/md file with Zotxt and create a JSON file
#' 
#' @param file file to parse
#' @param json name of the JSON file to produce (if NULL automatically determined)
#' @param return.file.name if TRUE, return the name of the JSON file
#' @note Zotero should be opened for this function to work.
#' @export zotxt2json

zotxt2json <- function (file, json = NULL, return.file.name = FALSE) {
  if (is.null(json)) {
    base.file <- sub("\\.[a-zA-Z]*$","", file)
    json <- paste0(base.file,".json")  
  }
  json.code <- system(paste(
    paste0("python ", system.file("scdoc/extractcites.py", package="scdoc")),
    shQuote(file)
  ), intern = TRUE)
  cat(json.code, file=json, sep="\n")
  if (return.file.name) return(json)
}

#' Extract references from a Rmd/md file with Zotxt and convert it to YAML
#' 
#' @param file file to parse
#' @param keep if TRUE, keep the json and YAML files produced
#' @param display if TRUE, display the result in the console
#' @note Zotero should be opened for this function to work.
#' @export zotxt2yaml

zotxt2yaml <- function (file, keep = FALSE, display = TRUE) {
  base.file <- sub("\\.[a-zA-Z]*$","", file)
  json.file <- paste0(base.file,".json")
  yaml.file <- paste0(base.file,".yaml")
  zotxt2json(file, json.file)
  yaml <- system(paste(
    "biblio2yaml",
    shQuote(json.file)
    ), intern = TRUE)
  Encoding(yaml) <- "UTF-8"
  if (keep)
    cat(yaml, file=yaml.file, sep="\n")
  else
    file.remove (json.file)
  if (display)
    cat(yaml, sep="\n")
}