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Zhongwei Li
204
skills/citation-management/scripts/doi_to_bibtex.py
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204
skills/citation-management/scripts/doi_to_bibtex.py
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#!/usr/bin/env python3
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"""
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DOI to BibTeX Converter
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Quick utility to convert DOIs to BibTeX format using CrossRef API.
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"""
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import sys
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import requests
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import argparse
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import time
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import json
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from typing import Optional, List
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class DOIConverter:
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"""Convert DOIs to BibTeX entries using CrossRef API."""
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def __init__(self):
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self.session = requests.Session()
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self.session.headers.update({
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'User-Agent': 'DOIConverter/1.0 (Citation Management Tool; mailto:support@example.com)'
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})
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def doi_to_bibtex(self, doi: str) -> Optional[str]:
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"""
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Convert a single DOI to BibTeX format.
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Args:
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doi: Digital Object Identifier
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Returns:
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BibTeX string or None if conversion fails
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"""
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# Clean DOI (remove URL prefix if present)
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doi = doi.strip()
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if doi.startswith('https://doi.org/'):
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doi = doi.replace('https://doi.org/', '')
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elif doi.startswith('http://doi.org/'):
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doi = doi.replace('http://doi.org/', '')
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elif doi.startswith('doi:'):
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doi = doi.replace('doi:', '')
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# Request BibTeX from CrossRef content negotiation
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url = f'https://doi.org/{doi}'
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headers = {
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'Accept': 'application/x-bibtex',
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'User-Agent': 'DOIConverter/1.0 (Citation Management Tool)'
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}
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try:
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response = self.session.get(url, headers=headers, timeout=15)
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if response.status_code == 200:
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bibtex = response.text.strip()
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# CrossRef sometimes returns entries with @data type, convert to @misc
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if bibtex.startswith('@data{'):
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bibtex = bibtex.replace('@data{', '@misc{', 1)
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return bibtex
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elif response.status_code == 404:
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print(f'Error: DOI not found: {doi}', file=sys.stderr)
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return None
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else:
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print(f'Error: Failed to retrieve BibTeX for {doi} (status {response.status_code})', file=sys.stderr)
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return None
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except requests.exceptions.Timeout:
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print(f'Error: Request timeout for DOI: {doi}', file=sys.stderr)
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return None
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except requests.exceptions.RequestException as e:
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print(f'Error: Request failed for {doi}: {e}', file=sys.stderr)
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return None
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def convert_multiple(self, dois: List[str], delay: float = 0.5) -> List[str]:
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"""
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Convert multiple DOIs to BibTeX.
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Args:
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dois: List of DOIs
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delay: Delay between requests (seconds) for rate limiting
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Returns:
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List of BibTeX entries (excludes failed conversions)
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"""
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bibtex_entries = []
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for i, doi in enumerate(dois):
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print(f'Converting DOI {i+1}/{len(dois)}: {doi}', file=sys.stderr)
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bibtex = self.doi_to_bibtex(doi)
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if bibtex:
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bibtex_entries.append(bibtex)
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# Rate limiting
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if i < len(dois) - 1: # Don't delay after last request
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time.sleep(delay)
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return bibtex_entries
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def main():
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"""Command-line interface."""
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parser = argparse.ArgumentParser(
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description='Convert DOIs to BibTeX format using CrossRef API',
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epilog='Example: python doi_to_bibtex.py 10.1038/s41586-021-03819-2'
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)
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parser.add_argument(
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'dois',
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nargs='*',
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help='DOI(s) to convert (can provide multiple)'
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)
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parser.add_argument(
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'-i', '--input',
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help='Input file with DOIs (one per line)'
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)
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parser.add_argument(
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'-o', '--output',
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help='Output file for BibTeX (default: stdout)'
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)
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parser.add_argument(
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'--delay',
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type=float,
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default=0.5,
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help='Delay between requests in seconds (default: 0.5)'
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)
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parser.add_argument(
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'--format',
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choices=['bibtex', 'json'],
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default='bibtex',
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help='Output format (default: bibtex)'
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)
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args = parser.parse_args()
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# Collect DOIs from command line and/or file
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dois = []
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if args.dois:
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dois.extend(args.dois)
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if args.input:
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try:
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with open(args.input, 'r', encoding='utf-8') as f:
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file_dois = [line.strip() for line in f if line.strip()]
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dois.extend(file_dois)
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except FileNotFoundError:
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print(f'Error: Input file not found: {args.input}', file=sys.stderr)
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sys.exit(1)
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except Exception as e:
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print(f'Error reading input file: {e}', file=sys.stderr)
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sys.exit(1)
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if not dois:
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parser.print_help()
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sys.exit(1)
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# Convert DOIs
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converter = DOIConverter()
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if len(dois) == 1:
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bibtex = converter.doi_to_bibtex(dois[0])
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if bibtex:
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bibtex_entries = [bibtex]
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else:
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sys.exit(1)
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else:
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bibtex_entries = converter.convert_multiple(dois, delay=args.delay)
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if not bibtex_entries:
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print('Error: No successful conversions', file=sys.stderr)
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sys.exit(1)
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# Format output
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if args.format == 'bibtex':
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output = '\n\n'.join(bibtex_entries) + '\n'
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else: # json
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output = json.dumps({
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'count': len(bibtex_entries),
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'entries': bibtex_entries
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}, indent=2)
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# Write output
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if args.output:
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try:
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with open(args.output, 'w', encoding='utf-8') as f:
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f.write(output)
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print(f'Successfully wrote {len(bibtex_entries)} entries to {args.output}', file=sys.stderr)
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except Exception as e:
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print(f'Error writing output file: {e}', file=sys.stderr)
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sys.exit(1)
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else:
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print(output)
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# Summary
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if len(dois) > 1:
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success_rate = len(bibtex_entries) / len(dois) * 100
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print(f'\nConverted {len(bibtex_entries)}/{len(dois)} DOIs ({success_rate:.1f}%)', file=sys.stderr)
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if __name__ == '__main__':
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main()
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