script for importing publications from a "bibtex" file to a hugo-academic website

bibtex_2academic.R

#' @title bibtex_2academic
#' @description import publications from a bibtex file to a hugo-academic website
#' @author Lorenzo Busetto, phD (2017) <[email protected]>

bibtex_2academic <- function(bibfile,
                             outfold,
                             abstract = FALSE,
                             overwrite = FALSE) {

  require(RefManageR)
  require(dplyr)
  require(stringr)
  require(anytime)

  # Import the bibtex file and convert to data.frame
  mypubs   <- ReadBib(bibfile, check = "warn", .Encoding = "UTF-8") %>%
    as.data.frame()

  # assign "categories" to the different types of publications
  mypubs   <- mypubs %>%
    dplyr::mutate(
      pubtype = dplyr::case_when(document_type == "Article" ~ "2",
                                 document_type == "Article in Press" ~ "2",
                                 document_type == "InProceedings" ~ "1",
                                 document_type == "Proceedings" ~ "1",
                                 document_type == "Conference" ~ "1",
                                 document_type == "Conference Paper" ~ "1",
                                 document_type == "MastersThesis" ~ "3",
                                 document_type == "PhdThesis" ~ "3",
                                 document_type == "Manual" ~ "4",
                                 document_type == "TechReport" ~ "4",
                                 document_type == "Book" ~ "5",
                                 document_type == "InCollection" ~ "6",
                                 document_type == "InBook" ~ "6",
                                 document_type == "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 by appending date and start of title
    if (!is.na(x[["year"]])) {
      x[["date"]] <- paste0(x[["year"]], "-01-01")
    } else {
      x[["date"]] <- "2999-01-01"
    }

    filename <- paste(x[["date"]], x[["title"]] %>%
                        str_replace_all(fixed(" "), "_") %>%
                        str_remove_all(fixed(":")) %>%
                        str_sub(1, 20) %>%
                        paste0(".md"), sep = "_")
    # start writing
    if (!file.exists(file.path(outfold, filename)) | overwrite) {
      fileConn <- file.path(outfold, filename)
      write("+++", fileConn)

      # Title and date
      write(paste0("title = \"", x[["title"]], "\""), fileConn, append = T)
      write(paste0("date = \"", anydate(x[["date"]]), "\""), fileConn, append = T)

      # Authors. Comma separated list, e.g. `["Bob Smith", "David Jones"]`.
      auth_hugo <- str_replace_all(x["author"], " and ", "\", \"")
      auth_hugo <- stringi::stri_trans_general(auth_hugo, "latin-ascii")
      write(paste0("authors = [\"", auth_hugo,"\"]"), 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)

      # Publication details: journal, volume, issue, page numbers and doi link
      publication <- x[["journal"]]
      if (!is.na(x[["volume"]])) publication <- paste0(publication,
                                                       ", (", x[["volume"]], ")")
      if (!is.na(x[["number"]])) publication <- paste0(publication,
                                                       ", ", x[["number"]])
      if (!is.na(x[["pages"]])) publication <- paste0(publication,
                                                      ", _pp. ", x[["pages"]], "_")
      if (!is.na(x[["doi"]])) publication <- paste0(publication,
                                                    ", ", paste0("https://doi.org/",
                                                                 x[["doi"]]))

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

      # Abstract and optional shortened version.
      if (abstract) {
        write(paste0("abstract = \"", 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)
    }
  }
  # apply the "create_md" function over the publications list to generate
  # the different "md" files.

  apply(mypubs, FUN = function(x) create_md(x), MARGIN = 1)
}

That's really helpful, thanks!

sorry @bshor, I moved my site. in case that's still useful, the file is now here.
http://www.pik-potsdam.de/~pichler/blog/post/set-this-up/setting-up-this-site/

@pppichler, my url_pdf always renders as NA. Would you mind posting your bibtex file so i can see what I'm doing wrong?
thanks!

@pppichler, my url_pdf always renders as NA. Would you mind posting your bibtex file so i can see what I'm doing wrong?
thanks!

hi, does it only render as NA or is the "url_pdf" property empty in the generated index.md file empty? The url_pdf is taken from the "url" property in the bib file. I have just noticed that things can go wrong with better bibtex exports so you might want to try standard bibtex export if you are using zotero or another reference manager. my entries look like this, for example:

@Article{lenzenEnvironmentalFootprintHealth2020,
title = {The environmental footprint of health care: a global assessment},
issn = {2542-5196},
url = {https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(20)30121-2/abstract},
doi = {10.1016/S2542-5196(20)30121-2},
language = {English},
urldate = {2020-08-06},
journal = {The Lancet Planetary Health},
author = {Manfred Lenzen and Arunima Malik and Mengyu Li and Jacob Fry and Helga Weisz and Peter-Paul Pichler and Leonardo Suveges Moreira Chaves and Anthony Capon and David Pencheon},
year = {2020},
volume = {4},
number = {7},
month = {jul},
pages = {e271--e279},
pmid = {32681898},
shorttitle = {The environmental footprint of health care},
pubtype = {2},
date = {2020-01-01},
}

hope this helps
paul

thanks! i had url_pdf as an entry in the bib file, but if i switch to url it works.

…

On Wed, Sep 2, 2020 at 11:09 AM pppichler ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ @pppichler <https://github.com/pppichler>, my url_pdf always renders as NA. Would you mind posting your bibtex file so i can see what I'm doing wrong? thanks! hi, does it only render as NA or is the "url_pdf" property empty in the generated index.md file empty? The url_pdf is taken from the "url" property in the bib file. I have just noticed that things can go wrong with better bibtex exports so you might want to try standard bibtex export if you are using zotero or another reference manager. my entries look like this, for example: @Article <https://github.com/Article> {lenzenEnvironmentalFootprintHealth2020, title = {The environmental footprint of health care: a global assessment}, issn = {2542-5196}, url = { https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(20)30121-2/abstract} , doi = {10.1016/S2542-5196(20)30121-2}, language = {English}, urldate = {2020-08-06}, journal = {The Lancet Planetary Health}, author = {Manfred Lenzen and Arunima Malik and Mengyu Li and Jacob Fry and Helga Weisz and Peter-Paul Pichler and Leonardo Suveges Moreira Chaves and Anthony Capon and David Pencheon}, year = {2020}, volume = {4}, number = {7}, month = {jul}, pages = {e271--e279}, pmid = {32681898}, shorttitle = {The environmental footprint of health care}, pubtype = {2}, date = {2020-01-01}, } hope this helps paul — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://gist.github.com/da7b1fba4345e03192a450226a17636e#gistcomment-3439859>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAM5U6VPET5LYJBYY4M7IV3SDZNY7ANCNFSM4OOCHTAQ> .