example

network_failures        10.1145/2043164.2018477
comp_sci_ubiq           10.1145/159544.159617

PyBib

#!/usr/bin/env python3

import re
import os
import sys
import requests
import argparse

# This website allows information about a paper to be retrieved by accessing
# http://dx.doi.org/DOI
doi_database_url = "http://dx.doi.org/"

# Matches a valid DOI
doi_matcher = re.compile('(10\.\d{4}[\d\:\.\-\/a-z]+)')

# Matches a [citation_key DOI] pair
key_file_matcher = re.compile('(\w+)\s+(10\.\d{4}[\d\:\.\-\/a-z]+)')

# Matches the beginning of a BibTeX entry
bibtex_key_matcher = re.compile('@\w+{(\w+),')


def main(filename):
    """Convert a file in the format [citation_key doi_key]* into a valid bibtex file"""

    citation_key_to_doi = parse_file(filename)

    citation_key_to_bib = get_all_bibliography_data(citation_key_to_doi)

    bibtex_lines = replace_citation_keys(citation_key_to_bib)

    (root, ext) = os.path.splitext(filename)
    bibtex_file = root + ".bib"

    with open(bibtex_file, 'w') as bib:
        for citation in bibtex_lines:
            print(citation, file=bib)

    print("Wrote generated BibTeX file as {}".format(bibtex_file))

def parse_file(filename):
    """Parses a file in the format [citation_key doi_key]* into a dictionary {citation_key: doi_key}*"""

    citation_key_to_doi = {}

    f = open(filename)
    lines = f.readlines()
    f.close()

    for line_number, line in enumerate(lines, start=1):

        parsed_line = parse_line(line_number, line)

        if parsed_line is None:
            # Line was blank, or a comment
            continue

        citation_key, doi = parsed_line

        # Don't allow duplicate citation keys
        if citation_key in citation_key_to_doi:
            sys.exit("Duplicate citation key: {} on line number {}".format(citation_key, line_number))

        citation_key_to_doi[citation_key] = doi

    print("Found {} citations in {}".format(len(citation_key_to_doi), filename))

    return citation_key_to_doi

def parse_line(line_number, line):
    """Parses a single line, of the format [citation_key DOI]"""

    if line.isspace():
        return None

    if line.startswith("#"):
        # Found a comment
        return None

    parsed_line = key_file_matcher.match(line)

    if not parsed_line:
        sys.exit("Invalid line ({}) in file: {}".format(line_number, line.strip()))

    citation_key, doi = parsed_line.group(1, 2)

    # Limit the length of citation keys
    if len(citation_key) > 20:
        sys.exit("Citation key '{}' is over 20 characters".format(citation_key))

    if not doi_matcher.match(doi):
        sys.exit("Invalid doi key.")

    return citation_key, doi

def get_all_bibliography_data(citation_key_to_doi):
    """Takes a dict in the format {citation_key: doi_key}* and expands each doi key into its bibliography text"""

    print("Retrieving bibliography data... ", end="")

    key_to_bibliography = {}

    for citation_key, doi in citation_key_to_doi.items():
        bibliography_text = get_bibliography_text(doi)

        key_to_bibliography[citation_key] = bibliography_text

    print("Done")

    return key_to_bibliography

def get_bibliography_text(doi):
    """Takes a single doi and retrieves the bibtex entry for the corresponding paper"""

    full_url = doi_database_url + doi
    headers = {'Accept': 'text/bibliography; style=bibtex'}

    try:
        r = requests.get(full_url, headers=headers)
    except Exception as e:
        sys.exit("Network connection failed: {}".format(e))
    r.encoding = "utf-8"

    if r.status_code == 200:
        pass
    elif r.status_code == 404:
        sys.exit("Unknown doi key.")
    else:
        sys.exit("Unhandled http response code: {}".format(r.status_code))

    bibliography_text = r.text
    bibliography_text = bibliography_text.strip()

    return bibliography_text


def replace_citation_keys(key_to_bibliography):
    """Single the bibtex entry comes with a default citation key, we need to replace
    this with the key specified in the file"""

    bib_items = []

    for citation_key in key_to_bibliography:
        bib_text = key_to_bibliography[citation_key]

        citation_key_match = bibtex_key_matcher.match(bib_text)

        if not citation_key_match:
            sys.exit("Ill formatted bibtex entry:\n{}".format(bib_text))

        old_key = citation_key_match.group(1)

        new_bib = bib_text.replace(old_key, citation_key)

        bib_items.append(new_bib)

    return bib_items


parser = argparse.ArgumentParser(description='Turn a file of [cite-key: DOI]* into a valid bibtex file')
parser.add_argument('file', type=str, help="The filename to parse")

args = parser.parse_args()

main(args.file)