R/bib_scrp.R

In fawda123/Jabbrev: Convert Journal Names From Long to Short Formats

#' Find bibtex tags in a document, scrape entries from external bib file, save new
#'
#' @param rmd_in chr string of path to Rmd file
#' @param bib_new path for output .bib file
#' @param ext_bib chr string of url for external bib file to scrape
#'
#' @details Currently only works for .Rmd files with the Rmarkdown format of bibtex tags, e.g., \code{[@Jones18]}.  The user must also check the external bib file to make sure all tags in the .Rmd file are present.
#'
#' @return A new bib file is saved, nothing is returned to the console
#'
#' @export
#'
#' @import dplyr
#'
#' @examples
#' \dontrun{
#' bib_scrp('document.Rmd', 'refs.bib')
#' }
bib_scrp <- function(rmd_in, bib_new = 'refs.bib', ext_bib = 'https://fawda123.github.io/refs/refs.bib'){

  # rmd tags
  tgs <- readLines(rmd_in) %>%
    .[grep("\\[.*@", .)] %>%
    regmatches(., gregexpr("@.*?[^a-zA-Z0-9]", .)) %>% # gregexpr gets starting index and length of all matches, regmatches returns text indexed by gregexpr
    unlist %>%
    .[!grepl('^@ref\\($', .)] %>% # remove bookdown ref tags
    gsub('[^a-zA-Z0-9]', '', .) %>%
    unique %>%
    sort

  # references to scrape
  refs <- try({readLines(ext_bib)})
  if(inherits(refs, 'try-error'))
    stop('Unable to pull external bib from ', ext_bib)

  # extract bib entries from bib_fl using keys from bbl_fl
  ext <- sapply(tgs, function(x){

    # start index (NA if not found)
    str <- grep(paste0(x, ','), refs)
    if(length(str) == 0) return(NA)

    # stop index
    stp <- grep('@', refs[str:length(refs)])[2]

    # get chrs in start to stop
    out <- try({refs[str:(str + stp - 2)] %>%
        .[. != '']
    })

    out

  }, simplify = FALSE) %>%
  do.call('c', .)

  # check NA
  nachk <- ext[is.na(ext)]
  if(length(nachk) > 0){
    stop('Bib tags not found in .bib file: ', paste(names(nachk), collapse = ', '))
  }

  # add preamble for non-standard year
  ext <- c('@preamble{ " \\newcommand{\\noop}[1]{} " }', ext)

  # save
  writeLines(ext, bib_new)

}