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