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Zhongwei Li
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skills/literature-review/scripts/verify_citations.py
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skills/literature-review/scripts/verify_citations.py
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#!/usr/bin/env python3
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"""
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Citation Verification Script
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Verifies DOIs, URLs, and citation metadata for accuracy.
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"""
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import re
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import requests
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import json
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from typing import Dict, List, Tuple
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from urllib.parse import urlparse
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import time
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class CitationVerifier:
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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': 'CitationVerifier/1.0 (Literature Review Tool)'
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})
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def extract_dois(self, text: str) -> List[str]:
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"""Extract all DOIs from text."""
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doi_pattern = r'10\.\d{4,}/[^\s\]\)"]+'
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return re.findall(doi_pattern, text)
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def verify_doi(self, doi: str) -> Tuple[bool, Dict]:
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"""
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Verify a DOI and retrieve metadata.
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Returns (is_valid, metadata)
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"""
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try:
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url = f"https://doi.org/api/handles/{doi}"
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response = self.session.get(url, timeout=10)
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if response.status_code == 200:
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# DOI exists, now get metadata from CrossRef
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metadata = self._get_crossref_metadata(doi)
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return True, metadata
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else:
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return False, {}
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except Exception as e:
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return False, {"error": str(e)}
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def _get_crossref_metadata(self, doi: str) -> Dict:
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"""Get metadata from CrossRef API."""
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try:
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url = f"https://api.crossref.org/works/{doi}"
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response = self.session.get(url, timeout=10)
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if response.status_code == 200:
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data = response.json()
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message = data.get('message', {})
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# Extract key metadata
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metadata = {
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'title': message.get('title', [''])[0],
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'authors': self._format_authors(message.get('author', [])),
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'year': self._extract_year(message),
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'journal': message.get('container-title', [''])[0],
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'volume': message.get('volume', ''),
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'pages': message.get('page', ''),
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'doi': doi
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}
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return metadata
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return {}
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except Exception as e:
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return {"error": str(e)}
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def _format_authors(self, authors: List[Dict]) -> str:
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"""Format author list."""
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if not authors:
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return ""
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formatted = []
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for author in authors[:3]: # First 3 authors
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given = author.get('given', '')
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family = author.get('family', '')
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if family:
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formatted.append(f"{family}, {given[0]}." if given else family)
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if len(authors) > 3:
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formatted.append("et al.")
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return ", ".join(formatted)
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def _extract_year(self, message: Dict) -> str:
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"""Extract publication year."""
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date_parts = message.get('published-print', {}).get('date-parts', [[]])
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if not date_parts or not date_parts[0]:
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date_parts = message.get('published-online', {}).get('date-parts', [[]])
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if date_parts and date_parts[0]:
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return str(date_parts[0][0])
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return ""
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def verify_url(self, url: str) -> Tuple[bool, int]:
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"""
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Verify a URL is accessible.
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Returns (is_accessible, status_code)
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"""
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try:
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response = self.session.head(url, timeout=10, allow_redirects=True)
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is_accessible = response.status_code < 400
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return is_accessible, response.status_code
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except Exception as e:
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return False, 0
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def verify_citations_in_file(self, filepath: str) -> Dict:
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"""
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Verify all citations in a markdown file.
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Returns a report of verification results.
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"""
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with open(filepath, 'r', encoding='utf-8') as f:
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content = f.read()
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dois = self.extract_dois(content)
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report = {
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'total_dois': len(dois),
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'verified': [],
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'failed': [],
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'metadata': {}
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}
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for doi in dois:
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print(f"Verifying DOI: {doi}")
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is_valid, metadata = self.verify_doi(doi)
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if is_valid:
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report['verified'].append(doi)
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report['metadata'][doi] = metadata
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else:
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report['failed'].append(doi)
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time.sleep(0.5) # Rate limiting
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return report
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def format_citation_apa(self, metadata: Dict) -> str:
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"""Format citation in APA style."""
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authors = metadata.get('authors', '')
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year = metadata.get('year', 'n.d.')
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title = metadata.get('title', '')
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journal = metadata.get('journal', '')
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volume = metadata.get('volume', '')
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pages = metadata.get('pages', '')
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doi = metadata.get('doi', '')
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citation = f"{authors} ({year}). {title}. "
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if journal:
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citation += f"*{journal}*"
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if volume:
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citation += f", *{volume}*"
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if pages:
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citation += f", {pages}"
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if doi:
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citation += f". https://doi.org/{doi}"
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return citation
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def format_citation_nature(self, metadata: Dict) -> str:
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"""Format citation in Nature style."""
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authors = metadata.get('authors', '')
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title = metadata.get('title', '')
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journal = metadata.get('journal', '')
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volume = metadata.get('volume', '')
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pages = metadata.get('pages', '')
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year = metadata.get('year', '')
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citation = f"{authors} {title}. "
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if journal:
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citation += f"*{journal}* "
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if volume:
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citation += f"**{volume}**, "
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if pages:
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citation += f"{pages} "
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if year:
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citation += f"({year})"
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return citation
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def main():
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"""Example usage."""
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import sys
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if len(sys.argv) < 2:
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print("Usage: python verify_citations.py <markdown_file>")
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sys.exit(1)
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filepath = sys.argv[1]
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verifier = CitationVerifier()
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print(f"Verifying citations in: {filepath}")
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report = verifier.verify_citations_in_file(filepath)
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print("\n" + "="*60)
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print("CITATION VERIFICATION REPORT")
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print("="*60)
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print(f"\nTotal DOIs found: {report['total_dois']}")
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print(f"Verified: {len(report['verified'])}")
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print(f"Failed: {len(report['failed'])}")
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if report['failed']:
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print("\nFailed DOIs:")
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for doi in report['failed']:
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print(f" - {doi}")
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if report['metadata']:
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print("\n\nVerified Citations (APA format):")
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for doi, metadata in report['metadata'].items():
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citation = verifier.format_citation_apa(metadata)
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print(f"\n{citation}")
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# Save detailed report
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output_file = filepath.replace('.md', '_citation_report.json')
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with open(output_file, 'w', encoding='utf-8') as f:
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json.dump(report, f, indent=2)
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print(f"\n\nDetailed report saved to: {output_file}")
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if __name__ == "__main__":
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main()
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