R/bib2acad.R

In petzi53/bib2acad: Convert Bibtex to Markdown for the Hugo Academic Theme

#' Convert .bib Files to .md Files for the Hugo Academic Theme
#'
#' \code{bib2acad} takes a .bib file and generates for each record a .md file
#' suitable for the publication folder of the Hugo Academic theme
#' (\url{https://sourcethemes.com/academic/}).
#'
#' @param bibfile A string in the format "path/to/bibfile": required
#' @param copybib   Logical, optional, default = TRUE
#' @param abstract  Logical, optional, default = TRUE
#' @param overwrite Logical, optional, default = FALSE
#'
#' @return NULL
#'
#' @importFrom dplyr mutate case_when
#' @importFrom RefManageR ReadBib WriteBib as.BibEntry
#' @importFrom pbapply startpb closepb
#' @importFrom stringr str_replace_all str_squish
#' @importFrom stringi stri_trans_general
#' @importFrom utils menu
#'
################################################################################

#' @export
bib2acad <- function(bibfile = "",
                     copybib = TRUE,
                     abstract = TRUE,
                     overwrite = FALSE) {

    ############################################################################
    # check files and permissions
    msg1 <- "You must specify a .bib file as input for the conversion."
    msg2 <- paste0("Cannot find file '", bibfile,
                   "'. Check path and/or file name.")
    msg3 <- "Aborted by user"

    if (bibfile == "") {return(message(msg1))}
    if (!file.exists(bibfile)) {return(message(msg2))}


    outfold <- paste0(tempdir(), "/my-md-folder")
    bibfold <- paste0(tempdir(), "/my-bib-folder")


    question1 <- paste0("The package will create a temporary new folder '",
                        outfold, "'. OK?")
    question2 <- paste0("The package will create a temporary new folder '",
                        bibfold, "'. OK?")
    question3 <- paste0("Overwrite files in '", outfold, "' and/or in '",
                        bibfold, "'. OK?")

    if (!dir.exists(file.path(outfold))) {
        choice_outfold <- menu(c("Yes", "No"), title = question1)
        if (choice_outfold == 2) {return(message(msg3))}
    }


    if ((copybib) &&  (!dir.exists(file.path(bibfold)))) {
        choice_bibfold <- menu(c("Yes", "No"), title = question2)
        if (choice_bibfold == 2) {return(message(msg3))}
    }


    if ((overwrite) && ((dir.exists(file.path(outfold))) ||
                         (dir.exists(file.path(bibfold))))) {
        choice_overwrite <- menu(c("Yes", "No"), title = question3)
        if (choice_overwrite == 2) {return(message(msg3))}
    }


    # create folders the brutal way; do not worry if they alreday exist
    dir.create(outfold, showWarnings = FALSE)
    dir.create(bibfold, showWarnings = FALSE)

    ############################################################################
    # Import the bibtex file and convert it to a data.frame
    mypubs   <- RefManageR::ReadBib(bibfile, check = "warn", .Encoding = "UTF-8")
    mypubs <- as.data.frame(mypubs)
    mypubs$key <- rownames(mypubs)

    ############################################################################
    # assign "categories" to the different types of publications
    mypubs   <- dplyr::mutate(mypubs,
            pubtype = dplyr::case_when(bibtype == "Article" ~ "2",
                                       bibtype == "Article in Press" ~ "2",
                                       bibtype == "InProceedings" ~ "1",
                                       bibtype == "Proceedings" ~ "1",
                                       bibtype == "Conference" ~ "1",
                                       bibtype == "Conference Paper" ~ "1",
                                       bibtype == "MastersThesis" ~ "3",
                                       bibtype == "PhdThesis" ~ "3",
                                       bibtype == "Manual" ~ "4",
                                       bibtype == "TechReport" ~ "4",
                                       bibtype == "Book" ~ "5",
                                       bibtype == "InCollection" ~ "6",
                                       bibtype == "InBook" ~ "6",
                                       bibtype == "Misc" ~ "0",
                                       TRUE ~ "0")
                            )

    ############################################################################
    # create a function which populates the md template based on the info
    # about a publication

    create_md <- function(x) {
        # define a date and create filename_md by appending date and bibtex key
        if (!is.na(x[["year"]])) {
            x[["date"]] <- paste0(x[["year"]], "-01-01")
        } else {
            x[["date"]] <- "2999-01-01"
        }

        filename_md <- paste0(x[["date"]], "_", x[["key"]], ".md")

        # start writing

        if (!file.exists(file.path(outfold, filename_md)) | overwrite) {
            fileConn <- file.path(outfold, filename_md)
            write("+++", fileConn)

            # title and date
            # title has sometimes with older bibtex files special characters "{}"
            # escape " and \ (e.g. the "ampersand"\&) with funtion escapeStr

            write(paste0("title = \"", cleanStr(x[["title"]]), "\""),
                  fileConn, append = T)
            write(paste0("date = \"", x[["date"]], "\""),
                  fileConn, append = T)

            # Publication type. Legend:
            # 0 = Uncategorized, 1 = Conference paper, 2 = Journal article
            # 3 = Manuscript, 4 = Report, 5 = Book,  6 = Book section
            write(paste0("publication_types = [\"", x[["pubtype"]],"\"]"),
                  fileConn, append = T)


            if (!is.na(x[["author"]])) {
                # Authors. Comma separated list, e.g.
                # `["Bob Smith", "David Jones"]`.
                authors <- stringr::str_replace_all(
                    stringr::str_squish(x["author"]), " and ", "\", \"")
                authors <- stringi::stri_trans_general(authors, "latin-ascii")
                write(paste0("authors = [\"", authors,"\"]"),
                      fileConn, append = T)
            } else {
                # Editors. Comma separated list, e.g.
                # `["Bob Smith", "David Jones"]`.
                editors <- stringr::str_replace_all(
                    stringr::str_squish(x["editor"]), " and ", "\", \"")
                editors <- stringi::stri_trans_general(editors, "latin-ascii")
                write(paste0("editors = [\"", editors,"\"]"),
                      fileConn, append = T)
            }


            # Publication details:
            # start with title: every bib entry has a title field!
            # then check if field booktitle or journal
            # if booktitle, then: booktitle, year and maybe pages
            # if journal, then: journal, check if volume, number, pages
            # check first if field is available and then if it is.na
            # only if both conditions are satiesfied: write field content
            # NOTE: This will not generate a complete citation record
            # NOTE: Only summary information providing links to detailed infos
            # NOTE: One of these infos is to see & copy the complete bib record


            publication <- NULL # variable to collect data and to write it to file

            if ("booktitle" %in% names(x) && !is.na(x[["booktitle"]])) {
                publication <- paste0(publication,
                                      "In: ", cleanStr(x[["booktitle"]]))
                if ("publisher" %in% names(x) && !is.na(x[["publisher"]])) {
                    publication <- paste0(publication, ", ",
                                          cleanStr(x[["publisher"]]))
                }
                if ("address" %in% names(x) && !is.na(x[["address"]])) {
                    publication <- paste0(publication, ", ",
                                          cleanStr(x[["address"]]))
                }
                if ("pages" %in% names(x) && !is.na(x[["pages"]])) {
                    publication <- paste0(publication, ", _pp. ",
                                          cleanStr(x[["pages"]]), "_")
                }
            }

            if ("journal" %in% names(x) && !is.na(x[["journal"]])) {
                publication <- paste0(publication, "In: ",
                                      cleanStr(x[["journal"]]))
                if ("volume" %in% names(x) && !is.na(x[["volume"]])) {
                    publication <- paste0(publication, ", (",
                                          cleanStr(x[["volume"]]), ")")
                }
                if ("number" %in% names(x) && !is.na(x[["number"]])) {
                    publication <- paste0(publication, ", ",
                                          cleanStr(x[["number"]]))
                }
                if ("pages" %in% names(x) && !is.na(x[["pages"]])) {
                    publication <- paste0(publication, ", _pp. ",
                                          cleanStr(x[["pages"]]), "_")
                }
                if ("doi" %in% names(x) && !is.na(x[["doi"]])) {
                    publication <- paste0(publication, ", ",
                                          paste0("https://doi.org/",
                                                 cleanStr(x[["doi"]])))
                }
                if ("url" %in% names(x) && !is.na(x[["url"]])) {
                    publication <- paste0(publication, ", ",
                                          cleanStr(x[["url"]]))
                }


            }

            write(paste0("publication = \"", publication, "\""),
                  fileConn, append = T)

            # Abstract and optional shortened version.
            if ((abstract) && "abstract" %in% names(x)
                && !is.na(x[["abstract"]]))
            {
                write(paste0("abstract = \"", cleanStr(x[["abstract"]]), "\""),
                      fileConn, append = T)
            } else {
                write("abstract = \"\"", fileConn, append = T)
            }
            write(paste0("abstract_short = \"","\""),
                  fileConn, append = T)


            # other possible fields are kept empty.
            # They can be customized later by editing the created md

            write("image_preview = \"\"", fileConn, append = T)
            write("selected = false", fileConn, append = T)
            write("projects = []", fileConn, append = T)
            write("tags = []", fileConn, append = T)
            #links
            write("url_pdf = \"\"", fileConn, append = T)
            write("url_preprint = \"\"", fileConn, append = T)
            write("url_code = \"\"", fileConn, append = T)
            write("url_dataset = \"\"", fileConn, append = T)
            write("url_project = \"\"", fileConn, append = T)
            write("url_slides = \"\"", fileConn, append = T)
            write("url_video = \"\"", fileConn, append = T)
            write("url_poster = \"\"", fileConn, append = T)
            write("url_source = \"\"", fileConn, append = T)
            #other stuff
            write("math = true", fileConn, append = T)
            write("highlight = true", fileConn, append = T)
            # Featured image
            write("[header]", fileConn, append = T)
            write("image = \"\"", fileConn, append = T)
            write("caption = \"\"", fileConn, append = T)

            write("+++", fileConn, append = T)



        }
        # write bibtex Data into separate file
        # these bib files can be stored under "static/files/citations"
        # then a button "cite" is generated automatically
        # in the academic framework
        if (copybib) {
            filename_bib <- (gsub(".md", ".bib", filename_md))
            y <- as.list(x)
            y["pubtype"] <- NULL
            y <- RefManageR::as.BibEntry(y)
            if (!file.exists(file.path(bibfold, filename_bib)) | overwrite) {
                RefManageR::WriteBib(y,
                        file = file.path(bibfold, filename_bib),
                        verbose = FALSE)
            }
        }
    }

    ############################################################################
    # apply the "create_md" function over the publications list to generate
    # the different "md" files.

    pb <- pbapply::startpb(min = 0, max = nrow(mypubs))
    pbapply::pbapply(mypubs, FUN = function(x) create_md(x), MARGIN = 1)
    pbapply::closepb(pb)

    opendir(tempdir())

    return(message("Conversion finished!"))

}

cleanStr <- function(str) {
    # if special character has in front a "\": replace it with "\\\\"
    str <- gsub('\\', '\\\\', str, fixed = TRUE)
    # delete all "{" and "}" in old bibtex files
    str <- gsub("[{}]", '', str)
    # replace all inline quotes '"' with "four '\\\\"'
    str <- gsub('"', '\\\\"', str)
    # delete extra lines, tabs and spaces
    # (especially important with field 'abstract')
    # and return the cleaned string
    return(stringr::str_squish(str))
}

opendir <- function(dir = getwd()){
    if (.Platform['OS.type'] == "windows"){
        shell.exec(dir)
    } else {
        system(paste(Sys.getenv("R_BROWSER"), dir))
    }
}