Fix BibDesk file links

fix_bibdesk_file_links.py

#!/usr/bin/env python
"""
Fix file links in bibtex file used with BibDesk using bibtexparser.

To use, run the script then open the resulting bibtex file in BibDesk
and save it. This should fix all file links.

Daniel Mentiplay, 2019.
"""

import pathlib

import bibtexparser

# ------------------------------------------------------------------------------------ #

# EDIT THESE VARIABLES AS REQUIRED
# NOTE: BIBTEX_FILE and PDF_DIR must be pathlib.Path objects.

# Path to bibtex file.
BIBTEX_FILE = pathlib.Path('~/repos/phd/references/references.bib').expanduser()

# Path to PDFs.
PDF_DIR = pathlib.Path('~/Dropbox/references/astronomy').expanduser()

# New bibtex file name.
NEW_FILE = 'new.bib'

# ------------------------------------------------------------------------------------ #


def load_bibtex(path):
    with open(path) as bibtex_file:
        db = bibtexparser.bparser.BibTexParser(common_strings=True).parse_file(
            bibtex_file
        )
    return db


def cite_key_has_pdf(cite_key):
    return (PDF_DIR / f'{cite_key.replace(":", "")}.pdf').exists()


def update_cite_key_with_file_link(cite_key, reference_database):
    reference_database.entries_dict[cite_key]['bdsk-file-1'] = str(
        PDF_DIR / f'{cite_key.replace(":", "")}.pdf'
    )


def add_files_to_database(database):
    for entry in database.entries:
        if cite_key_has_pdf(entry['ID']):
            update_cite_key_with_file_link(entry['ID'], database)


if __name__ == '__main__':

    # Load bibtex database.
    print('Loading bibtex file with bibtexparser...')
    reference_database = load_bibtex(BIBTEX_FILE)

    # Add file links.
    print('Adding file links...')
    add_files_to_database(reference_database)

    # Write new .bib file.
    print(f'Writing {NEW_FILE} file with correct file links...')
    with open(NEW_FILE, 'w') as bibtex_file:
        bibtexparser.dump(reference_database, bibtex_file)