parse_bib_file.py

#! /usr/bin/env python3
# -*- coding: utf-8 -*-
"""
parse_bib_file.py: Convert raw bibtex file to yml format and md pages. 
"""

import os

import bibtexparser as bb
import yaml


def get_link(entry):
    if "url" in entry.keys():
        return entry["url"]
    elif "doi" in entry.keys():
        return f"https://doi.org/{entry['doi']}"
    else:
        print("Warning: no link in", entry["ID"])
        return ""


def get_journal(entry):
    if entry.get("ENTRYTYPE") == "article":
        return entry.get("journal")
    elif entry.get("ENTRYTYPE") == "inproceedings":
        return entry.get("booktitle")
    else:
        print("Warning: unknown entry type in", entry)
        return ""


def clean(list_of_string):
    replace = [
        ['{\\"u}', "ü"],
        ['{\\"o}', "ö"],
        ['{\\"a}', "ä"],
        ["{", ""],
        ["}", ""],
    ]
    if not isinstance(list_of_string, list):
        list_of_string = [list_of_string]

    clean_list = []
    for a in list_of_string:
        for r in replace:
            a = a.replace(*r)
        clean_list.append(a)
    return clean_list


def check_for_overwrite(fname):
    answer = ""
    if os.path.exists(fname):
        while answer not in ["y", "n", "Y"]:
            answer = (
                input(f"{fname} exists, overwrite? (y/[n], Y to overwrite all)") or "n"
            )
    return answer


if __name__ == "__main__":
    import sys

    in_name_bib = "_data/mendeley-export.bib"
    out_name_data = "_data/mendeley-export.yml"
    out_folder_pages = "_publications"

    with open(in_name_bib, "r") as f:
        bib_db = bb.load(f)

    general_dict = {
        "layout": "publication",
        "ref-code": "",
        "ref-link": "",
        "ref-video": "",
    }

    categories = {"inproceedings": "Conference", "article": "Journal"}

    answer = "n"
    all_dicts = []
    for entry in bib_db.entries:
        try:
            author_tuples = [a.split(", ") for a in entry["author"].split(" and ")]
            author_names = [f"{a[1].strip()[0]}. {a[0]}" for a in author_tuples]
            author_names = clean(author_names)
        except Exception as e:
            print("Error reading authors:", e)
            print(entry)
            author_names = []

        dict_to_write = {}
        dict_to_write["ref-authors"] = author_names
        dict_to_write["title"] = clean(entry["title"])[0]
        dict_to_write["ref-year"] = int(entry["year"])
        dict_to_write["ref-journal"] = get_journal(entry)
        dict_to_write["ref-link"] = get_link(entry)
        dict_to_write["categories"] = categories.get(entry["ENTRYTYPE"], "Other")

        all_dicts.append(dict_to_write)

        fname = os.path.join(out_folder_pages, entry["ID"] + ".md")

        if answer != "Y":
            answer = check_for_overwrite(fname)

        if answer == "n":
            continue

        with open(fname, "w") as f:
            f.write("---\n")
            f.write("layout: publication\n")
            f.write(yaml.dump(dict_to_write))
            f.write("---\n\n\n")
            f.write(entry.get("abstract", ""))
            f.write("\n")
        print("wrote", fname)

    if not check_for_overwrite(out_name_data):
        sys.exit(0)  # successful termination

    with open(out_name_data, "w") as f:
        f.write(yaml.dump(all_dicts))
    print("wrote", out_name_data)