@synsci/cli-darwin-arm64 1.1.71 → 1.1.73

package/bin/skills/citation-management/scripts/doi_to_bibtex.py

@@ -0,0 +1,182 @@
+#!/usr/bin/env python3
+"""
+DOI to BibTeX Converter
+Quick utility to convert DOIs to BibTeX format using CrossRef API.
+"""
+
+import argparse
+import json
+import sys
+import time
+from typing import List, Optional
+
+import requests
+
+
+class DOIConverter:
+    """Convert DOIs to BibTeX entries using CrossRef API."""
+
+    def __init__(self):
+        self.session = requests.Session()
+        self.session.headers.update(
+            {'User-Agent': 'DOIConverter/1.0 (Citation Management Tool; mailto:support@example.com)'}
+        )
+
+    def doi_to_bibtex(self, doi: str) -> Optional[str]:
+        """
+        Convert a single DOI to BibTeX format.
+
+        Args:
+            doi: Digital Object Identifier
+
+        Returns:
+            BibTeX string or None if conversion fails
+        """
+        # Clean DOI (remove URL prefix if present)
+        doi = doi.strip()
+        if doi.startswith('https://doi.org/'):
+            doi = doi.replace('https://doi.org/', '')
+        elif doi.startswith('http://doi.org/'):
+            doi = doi.replace('http://doi.org/', '')
+        elif doi.startswith('doi:'):
+            doi = doi.replace('doi:', '')
+
+        # Request BibTeX from CrossRef content negotiation
+        url = f'https://doi.org/{doi}'
+        headers = {'Accept': 'application/x-bibtex', 'User-Agent': 'DOIConverter/1.0 (Citation Management Tool)'}
+
+        try:
+            response = self.session.get(url, headers=headers, timeout=15)
+
+            if response.status_code == 200:
+                bibtex = response.text.strip()
+                # CrossRef sometimes returns entries with @data type, convert to @misc
+                if bibtex.startswith('@data{'):
+                    bibtex = bibtex.replace('@data{', '@misc{', 1)
+                return bibtex
+            elif response.status_code == 404:
+                print(f'Error: DOI not found: {doi}', file=sys.stderr)
+                return None
+            else:
+                print(f'Error: Failed to retrieve BibTeX for {doi} (status {response.status_code})', file=sys.stderr)
+                return None
+
+        except requests.exceptions.Timeout:
+            print(f'Error: Request timeout for DOI: {doi}', file=sys.stderr)
+            return None
+        except requests.exceptions.RequestException as e:
+            print(f'Error: Request failed for {doi}: {e}', file=sys.stderr)
+            return None
+
+    def convert_multiple(self, dois: List[str], delay: float = 0.5) -> List[str]:
+        """
+        Convert multiple DOIs to BibTeX.
+
+        Args:
+            dois: List of DOIs
+            delay: Delay between requests (seconds) for rate limiting
+
+        Returns:
+            List of BibTeX entries (excludes failed conversions)
+        """
+        bibtex_entries = []
+
+        for i, doi in enumerate(dois):
+            print(f'Converting DOI {i + 1}/{len(dois)}: {doi}', file=sys.stderr)
+            bibtex = self.doi_to_bibtex(doi)
+
+            if bibtex:
+                bibtex_entries.append(bibtex)
+
+            # Rate limiting
+            if i < len(dois) - 1:  # Don't delay after last request
+                time.sleep(delay)
+
+        return bibtex_entries
+
+
+def main():
+    """Command-line interface."""
+    parser = argparse.ArgumentParser(
+        description='Convert DOIs to BibTeX format using CrossRef API',
+        epilog='Example: python doi_to_bibtex.py 10.1038/s41586-021-03819-2',
+    )
+
+    parser.add_argument('dois', nargs='*', help='DOI(s) to convert (can provide multiple)')
+
+    parser.add_argument('-i', '--input', help='Input file with DOIs (one per line)')
+
+    parser.add_argument('-o', '--output', help='Output file for BibTeX (default: stdout)')
+
+    parser.add_argument('--delay', type=float, default=0.5, help='Delay between requests in seconds (default: 0.5)')
+
+    parser.add_argument(
+        '--format', choices=['bibtex', 'json'], default='bibtex', help='Output format (default: bibtex)'
+    )
+
+    args = parser.parse_args()
+
+    # Collect DOIs from command line and/or file
+    dois = []
+
+    if args.dois:
+        dois.extend(args.dois)
+
+    if args.input:
+        try:
+            with open(args.input, 'r', encoding='utf-8') as f:
+                file_dois = [line.strip() for line in f if line.strip()]
+                dois.extend(file_dois)
+        except FileNotFoundError:
+            print(f'Error: Input file not found: {args.input}', file=sys.stderr)
+            sys.exit(1)
+        except Exception as e:
+            print(f'Error reading input file: {e}', file=sys.stderr)
+            sys.exit(1)
+
+    if not dois:
+        parser.print_help()
+        sys.exit(1)
+
+    # Convert DOIs
+    converter = DOIConverter()
+
+    if len(dois) == 1:
+        bibtex = converter.doi_to_bibtex(dois[0])
+        if bibtex:
+            bibtex_entries = [bibtex]
+        else:
+            sys.exit(1)
+    else:
+        bibtex_entries = converter.convert_multiple(dois, delay=args.delay)
+
+    if not bibtex_entries:
+        print('Error: No successful conversions', file=sys.stderr)
+        sys.exit(1)
+
+    # Format output
+    if args.format == 'bibtex':
+        output = '\n\n'.join(bibtex_entries) + '\n'
+    else:  # json
+        output = json.dumps({'count': len(bibtex_entries), 'entries': bibtex_entries}, indent=2)
+
+    # Write output
+    if args.output:
+        try:
+            with open(args.output, 'w', encoding='utf-8') as f:
+                f.write(output)
+            print(f'Successfully wrote {len(bibtex_entries)} entries to {args.output}', file=sys.stderr)
+        except Exception as e:
+            print(f'Error writing output file: {e}', file=sys.stderr)
+            sys.exit(1)
+    else:
+        print(output)
+
+    # Summary
+    if len(dois) > 1:
+        success_rate = len(bibtex_entries) / len(dois) * 100
+        print(f'\nConverted {len(bibtex_entries)}/{len(dois)} DOIs ({success_rate:.1f}%)', file=sys.stderr)
+
+
+if __name__ == '__main__':
+    main()