keywords_bibliography.R

library(tidyverse)


## This gist allows to add keywords to bibentries
## It checks whether the keyword exists and if it doesn't
## it adds it. It does this by parsing all entries from a file,
## matchin these entries to the .bib file and adding the keyword
## only to those keywords that matched. This is handy when wanting
## to create a new chapter and add that chapters keyword only for the authors
## actually cited in that chapter

## Only specify three arguments
keyword  <-"conclusion"
where <- "back"
path_bib <- "./main_file/bibliography.bib"
path_chapter <- "./conclusion/conclusion.Rnw"



which_citations <- function(x) {
  raw_cits <- unlist(str_extract_all(x, "cite\\{[:alnum:]+\\}"))
  all_citations <- unique(str_replace_all(raw_cits, "\\{|\\}|cite", ""))
  all_citations
}

extract_bib_entries <- function(x) {
  #Criteria for a bib entry is whther starts with @
  bib_entries <- split(x, cumsum(str_detect(all_bib, "^@")) + 1)
  # Why +1 ? because cumsum starts at zero and this messes up indexing
  # later on by one number, i.e. pos 125 in the name of the list
  # is actually 126 in the index.
  bib_entries
}

matching_entries <- function(citations, bib_entries) {
  all_bibtex <- map(bib_entries, ~ str_extract_all(.x[1], "\\{.+,")[[1]])
  cleaned_index <- str_replace_all(all_bibtex, "\\{|,", "")
  
  entries_to_fix <- bib_entries[cleaned_index %in% citations]
  
  
  entries_to_fix
}

replace_keywords <- function(x, chosen_keyword, .where = c("front", "back")) {
  .where <- match.arg(.where)
  keywords <- str_detect(x, "keywords")
  
  if (any(keywords)) {
    
    extracted_keywords <- str_extract(x[keywords], "\\{.+\\}")
    splitted_entry <- str_split(str_replace_all(extracted_keywords, "\\{|\\}", ""), ",")[[1]]
    
    # If chosen keyword is not already in the keyword field, then write it
    if (!chosen_keyword %in% splitted_entry) {
      
      position <- switch(.where,
                         "front" = paste0("{", chosen_keyword,", \\1}"),
                         "back" = paste0("{\\1, ", chosen_keyword,"}"))
      
      new_keyword <- str_replace_all(x[keywords], "\\{(.+)\\}", position)
      x[keywords] <- new_keyword
    }
  } else {
    closing_brace <- max(which(str_detect(x, "\\}")))
    
    first_part <- x[1:(closing_brace - 2)]
    new_keyword <- paste0("  keywords={", chosen_keyword,"},")
    
    x <- c(first_part, new_keyword, x[(closing_brace - 1):length(x)])
  }
  x
}

all_lines <- read_lines(path_chapter)
all_bib <- read_lines(path_bib)

all_citations <- which_citations(all_lines)
all_bib_entries <- extract_bib_entries(all_bib)
entries_matched <- matching_entries(all_citations, all_bib_entries)
# Change keyword here!
correct_entries <- map(entries_matched, replace_keywords, keyword, where)


all_bib_entries[as.numeric(names(correct_entries))] <- correct_entries
final_bib_file <- reduce(all_bib_entries, `c`)
write_lines(final_bib_file, path_bib)