@synsci/cli-darwin-x64 1.1.71 → 1.1.72

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

@@ -0,0 +1,570 @@
+#!/usr/bin/env python3
+"""
+Metadata Extraction Tool
+Extract citation metadata from DOI, PMID, arXiv ID, or URL using various APIs.
+"""
+
+import argparse
+import json
+import os
+import re
+import sys
+import time
+import xml.etree.ElementTree as ET
+from typing import Dict, List, Optional, Tuple
+from urllib.parse import urlparse
+
+import requests
+
+
+class MetadataExtractor:
+    """Extract metadata from various sources and generate BibTeX."""
+
+    def __init__(self, email: Optional[str] = None):
+        """
+        Initialize extractor.
+
+        Args:
+            email: Email for Entrez API (recommended for PubMed)
+        """
+        self.session = requests.Session()
+        self.session.headers.update({'User-Agent': 'MetadataExtractor/1.0 (Citation Management Tool)'})
+        self.email = email or os.getenv('NCBI_EMAIL', '')
+
+    def identify_type(self, identifier: str) -> Tuple[str, str]:
+        """
+        Identify the type of identifier.
+
+        Args:
+            identifier: DOI, PMID, arXiv ID, or URL
+
+        Returns:
+            Tuple of (type, cleaned_identifier)
+        """
+        identifier = identifier.strip()
+
+        # Check if URL
+        if identifier.startswith('http://') or identifier.startswith('https://'):
+            return self._parse_url(identifier)
+
+        # Check for DOI
+        if identifier.startswith('10.'):
+            return ('doi', identifier)
+
+        # Check for arXiv ID
+        if re.match(r'^\d{4}\.\d{4,5}(v\d+)?$', identifier):
+            return ('arxiv', identifier)
+        if identifier.startswith('arXiv:'):
+            return ('arxiv', identifier.replace('arXiv:', ''))
+
+        # Check for PMID (8-digit number typically)
+        if identifier.isdigit() and len(identifier) >= 7:
+            return ('pmid', identifier)
+
+        # Check for PMCID
+        if identifier.upper().startswith('PMC') and identifier[3:].isdigit():
+            return ('pmcid', identifier.upper())
+
+        return ('unknown', identifier)
+
+    def _parse_url(self, url: str) -> Tuple[str, str]:
+        """Parse URL to extract identifier type and value."""
+        parsed = urlparse(url)
+
+        # DOI URLs
+        if 'doi.org' in parsed.netloc:
+            doi = parsed.path.lstrip('/')
+            return ('doi', doi)
+
+        # PubMed URLs
+        if 'pubmed.ncbi.nlm.nih.gov' in parsed.netloc or 'ncbi.nlm.nih.gov/pubmed' in url:
+            pmid = re.search(r'/(\d+)', parsed.path)
+            if pmid:
+                return ('pmid', pmid.group(1))
+
+        # arXiv URLs
+        if 'arxiv.org' in parsed.netloc:
+            arxiv_id = re.search(r'/abs/(\d{4}\.\d{4,5})', parsed.path)
+            if arxiv_id:
+                return ('arxiv', arxiv_id.group(1))
+
+        # Nature, Science, Cell, etc. - try to extract DOI from URL
+        doi_match = re.search(r'10\.\d{4,}/[^\s/]+', url)
+        if doi_match:
+            return ('doi', doi_match.group())
+
+        return ('url', url)
+
+    def extract_from_doi(self, doi: str) -> Optional[Dict]:
+        """
+        Extract metadata from DOI using CrossRef API.
+
+        Args:
+            doi: Digital Object Identifier
+
+        Returns:
+            Metadata dictionary or None
+        """
+        url = f'https://api.crossref.org/works/{doi}'
+
+        try:
+            response = self.session.get(url, timeout=15)
+
+            if response.status_code == 200:
+                data = response.json()
+                message = data.get('message', {})
+
+                metadata = {
+                    'type': 'doi',
+                    'entry_type': self._crossref_type_to_bibtex(message.get('type')),
+                    'doi': doi,
+                    'title': message.get('title', [''])[0],
+                    'authors': self._format_authors_crossref(message.get('author', [])),
+                    'year': self._extract_year_crossref(message),
+                    'journal': message.get('container-title', [''])[0] if message.get('container-title') else '',
+                    'volume': str(message.get('volume', '')) if message.get('volume') else '',
+                    'issue': str(message.get('issue', '')) if message.get('issue') else '',
+                    'pages': message.get('page', ''),
+                    'publisher': message.get('publisher', ''),
+                    'url': f'https://doi.org/{doi}',
+                }
+
+                return metadata
+            else:
+                print(f'Error: CrossRef API returned status {response.status_code} for DOI: {doi}', file=sys.stderr)
+                return None
+
+        except Exception as e:
+            print(f'Error extracting metadata from DOI {doi}: {e}', file=sys.stderr)
+            return None
+
+    def extract_from_pmid(self, pmid: str) -> Optional[Dict]:
+        """
+        Extract metadata from PMID using PubMed E-utilities.
+
+        Args:
+            pmid: PubMed ID
+
+        Returns:
+            Metadata dictionary or None
+        """
+        url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+        params = {'db': 'pubmed', 'id': pmid, 'retmode': 'xml', 'rettype': 'abstract'}
+
+        if self.email:
+            params['email'] = self.email
+
+        api_key = os.getenv('NCBI_API_KEY')
+        if api_key:
+            params['api_key'] = api_key
+
+        try:
+            response = self.session.get(url, params=params, timeout=15)
+
+            if response.status_code == 200:
+                root = ET.fromstring(response.content)
+                article = root.find('.//PubmedArticle')
+
+                if article is None:
+                    print(f'Error: No article found for PMID: {pmid}', file=sys.stderr)
+                    return None
+
+                # Extract metadata from XML
+                medline_citation = article.find('.//MedlineCitation')
+                article_elem = medline_citation.find('.//Article')
+                journal = article_elem.find('.//Journal')
+
+                # Get DOI if available
+                doi = None
+                article_ids = article.findall('.//ArticleId')
+                for article_id in article_ids:
+                    if article_id.get('IdType') == 'doi':
+                        doi = article_id.text
+                        break
+
+                metadata = {
+                    'type': 'pmid',
+                    'entry_type': 'article',
+                    'pmid': pmid,
+                    'title': article_elem.findtext('.//ArticleTitle', ''),
+                    'authors': self._format_authors_pubmed(article_elem.findall('.//Author')),
+                    'year': self._extract_year_pubmed(article_elem),
+                    'journal': journal.findtext('.//Title', ''),
+                    'volume': journal.findtext('.//JournalIssue/Volume', ''),
+                    'issue': journal.findtext('.//JournalIssue/Issue', ''),
+                    'pages': article_elem.findtext('.//Pagination/MedlinePgn', ''),
+                    'doi': doi,
+                }
+
+                return metadata
+            else:
+                print(f'Error: PubMed API returned status {response.status_code} for PMID: {pmid}', file=sys.stderr)
+                return None
+
+        except Exception as e:
+            print(f'Error extracting metadata from PMID {pmid}: {e}', file=sys.stderr)
+            return None
+
+    def extract_from_arxiv(self, arxiv_id: str) -> Optional[Dict]:
+        """
+        Extract metadata from arXiv ID using arXiv API.
+
+        Args:
+            arxiv_id: arXiv identifier
+
+        Returns:
+            Metadata dictionary or None
+        """
+        url = 'http://export.arxiv.org/api/query'
+        params = {'id_list': arxiv_id, 'max_results': 1}
+
+        try:
+            response = self.session.get(url, params=params, timeout=15)
+
+            if response.status_code == 200:
+                # Parse Atom XML
+                root = ET.fromstring(response.content)
+                ns = {'atom': 'http://www.w3.org/2005/Atom', 'arxiv': 'http://arxiv.org/schemas/atom'}
+
+                entry = root.find('atom:entry', ns)
+                if entry is None:
+                    print(f'Error: No entry found for arXiv ID: {arxiv_id}', file=sys.stderr)
+                    return None
+
+                # Extract DOI if published
+                doi_elem = entry.find('arxiv:doi', ns)
+                doi = doi_elem.text if doi_elem is not None else None
+
+                # Extract journal reference if published
+                journal_ref_elem = entry.find('arxiv:journal_ref', ns)
+                journal_ref = journal_ref_elem.text if journal_ref_elem is not None else None
+
+                # Get publication date
+                published = entry.findtext('atom:published', '', ns)
+                year = published[:4] if published else ''
+
+                # Get authors
+                authors = []
+                for author in entry.findall('atom:author', ns):
+                    name = author.findtext('atom:name', '', ns)
+                    if name:
+                        authors.append(name)
+
+                metadata = {
+                    'type': 'arxiv',
+                    'entry_type': 'misc' if not doi else 'article',
+                    'arxiv_id': arxiv_id,
+                    'title': entry.findtext('atom:title', '', ns).strip().replace('\n', ' '),
+                    'authors': ' and '.join(authors),
+                    'year': year,
+                    'doi': doi,
+                    'journal_ref': journal_ref,
+                    'abstract': entry.findtext('atom:summary', '', ns).strip().replace('\n', ' '),
+                    'url': f'https://arxiv.org/abs/{arxiv_id}',
+                }
+
+                return metadata
+            else:
+                print(f'Error: arXiv API returned status {response.status_code} for ID: {arxiv_id}', file=sys.stderr)
+                return None
+
+        except Exception as e:
+            print(f'Error extracting metadata from arXiv {arxiv_id}: {e}', file=sys.stderr)
+            return None
+
+    def metadata_to_bibtex(self, metadata: Dict, citation_key: Optional[str] = None) -> str:
+        """
+        Convert metadata dictionary to BibTeX format.
+
+        Args:
+            metadata: Metadata dictionary
+            citation_key: Optional custom citation key
+
+        Returns:
+            BibTeX string
+        """
+        if not citation_key:
+            citation_key = self._generate_citation_key(metadata)
+
+        entry_type = metadata.get('entry_type', 'misc')
+
+        # Build BibTeX entry
+        lines = [f'@{entry_type}{{{citation_key},']
+
+        # Add fields
+        if metadata.get('authors'):
+            lines.append(f'  author  = {{{metadata["authors"]}}},')
+
+        if metadata.get('title'):
+            # Protect capitalization
+            title = self._protect_title(metadata['title'])
+            lines.append(f'  title   = {{{title}}},')
+
+        if entry_type == 'article' and metadata.get('journal'):
+            lines.append(f'  journal = {{{metadata["journal"]}}},')
+        elif entry_type == 'misc' and metadata.get('type') == 'arxiv':
+            lines.append('  howpublished = {arXiv},')
+
+        if metadata.get('year'):
+            lines.append(f'  year    = {{{metadata["year"]}}},')
+
+        if metadata.get('volume'):
+            lines.append(f'  volume  = {{{metadata["volume"]}}},')
+
+        if metadata.get('issue'):
+            lines.append(f'  number  = {{{metadata["issue"]}}},')
+
+        if metadata.get('pages'):
+            pages = metadata['pages'].replace('-', '--')  # En-dash
+            lines.append(f'  pages   = {{{pages}}},')
+
+        if metadata.get('doi'):
+            lines.append(f'  doi     = {{{metadata["doi"]}}},')
+        elif metadata.get('url'):
+            lines.append(f'  url     = {{{metadata["url"]}}},')
+
+        if metadata.get('pmid'):
+            lines.append(f'  note    = {{PMID: {metadata["pmid"]}}},')
+
+        if metadata.get('type') == 'arxiv' and not metadata.get('doi'):
+            lines.append('  note    = {Preprint},')
+
+        # Remove trailing comma from last field
+        if lines[-1].endswith(','):
+            lines[-1] = lines[-1][:-1]
+
+        lines.append('}')
+
+        return '\n'.join(lines)
+
+    def _crossref_type_to_bibtex(self, crossref_type: str) -> str:
+        """Map CrossRef type to BibTeX entry type."""
+        type_map = {
+            'journal-article': 'article',
+            'book': 'book',
+            'book-chapter': 'incollection',
+            'proceedings-article': 'inproceedings',
+            'posted-content': 'misc',
+            'dataset': 'misc',
+            'report': 'techreport',
+        }
+        return type_map.get(crossref_type, 'misc')
+
+    def _format_authors_crossref(self, authors: List[Dict]) -> str:
+        """Format author list from CrossRef data."""
+        if not authors:
+            return ''
+
+        formatted = []
+        for author in authors:
+            given = author.get('given', '')
+            family = author.get('family', '')
+            if family:
+                if given:
+                    formatted.append(f'{family}, {given}')
+                else:
+                    formatted.append(family)
+
+        return ' and '.join(formatted)
+
+    def _format_authors_pubmed(self, authors: List) -> str:
+        """Format author list from PubMed XML."""
+        formatted = []
+        for author in authors:
+            last_name = author.findtext('.//LastName', '')
+            fore_name = author.findtext('.//ForeName', '')
+            if last_name:
+                if fore_name:
+                    formatted.append(f'{last_name}, {fore_name}')
+                else:
+                    formatted.append(last_name)
+
+        return ' and '.join(formatted)
+
+    def _extract_year_crossref(self, message: Dict) -> str:
+        """Extract year from CrossRef message."""
+        # Try published-print first, then published-online
+        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 _extract_year_pubmed(self, article: ET.Element) -> str:
+        """Extract year from PubMed XML."""
+        year = article.findtext('.//Journal/JournalIssue/PubDate/Year', '')
+        if not year:
+            medline_date = article.findtext('.//Journal/JournalIssue/PubDate/MedlineDate', '')
+            if medline_date:
+                year_match = re.search(r'\d{4}', medline_date)
+                if year_match:
+                    year = year_match.group()
+        return year
+
+    def _generate_citation_key(self, metadata: Dict) -> str:
+        """Generate a citation key from metadata."""
+        # Get first author last name
+        authors = metadata.get('authors', '')
+        if authors:
+            first_author = authors.split(' and ')[0]
+            if ',' in first_author:
+                last_name = first_author.split(',')[0].strip()
+            else:
+                last_name = first_author.split()[-1] if first_author else 'Unknown'
+        else:
+            last_name = 'Unknown'
+
+        # Get year
+        year = metadata.get('year', '').strip()
+        if not year:
+            year = 'XXXX'
+
+        # Clean last name (remove special characters)
+        last_name = re.sub(r'[^a-zA-Z]', '', last_name)
+
+        # Get keyword from title
+        title = metadata.get('title', '')
+        words = re.findall(r'\b[a-zA-Z]{4,}\b', title)
+        keyword = words[0].lower() if words else 'paper'
+
+        return f'{last_name}{year}{keyword}'
+
+    def _protect_title(self, title: str) -> str:
+        """Protect capitalization in title for BibTeX."""
+        # Protect common acronyms and proper nouns
+        protected_words = [
+            'DNA',
+            'RNA',
+            'CRISPR',
+            'COVID',
+            'HIV',
+            'AIDS',
+            'AlphaFold',
+            'Python',
+            'AI',
+            'ML',
+            'GPU',
+            'CPU',
+            'USA',
+            'UK',
+            'EU',
+        ]
+
+        for word in protected_words:
+            title = re.sub(rf'\b{word}\b', f'{{{word}}}', title, flags=re.IGNORECASE)
+
+        return title
+
+    def extract(self, identifier: str) -> Optional[str]:
+        """
+        Extract metadata and return BibTeX.
+
+        Args:
+            identifier: DOI, PMID, arXiv ID, or URL
+
+        Returns:
+            BibTeX string or None
+        """
+        id_type, clean_id = self.identify_type(identifier)
+
+        print(f'Identified as {id_type}: {clean_id}', file=sys.stderr)
+
+        metadata = None
+
+        if id_type == 'doi':
+            metadata = self.extract_from_doi(clean_id)
+        elif id_type == 'pmid':
+            metadata = self.extract_from_pmid(clean_id)
+        elif id_type == 'arxiv':
+            metadata = self.extract_from_arxiv(clean_id)
+        else:
+            print(f'Error: Unknown identifier type: {identifier}', file=sys.stderr)
+            return None
+
+        if metadata:
+            return self.metadata_to_bibtex(metadata)
+        else:
+            return None
+
+
+def main():
+    """Command-line interface."""
+    parser = argparse.ArgumentParser(
+        description='Extract citation metadata from DOI, PMID, arXiv ID, or URL',
+        epilog='Example: python extract_metadata.py --doi 10.1038/s41586-021-03819-2',
+    )
+
+    parser.add_argument('--doi', help='Digital Object Identifier')
+    parser.add_argument('--pmid', help='PubMed ID')
+    parser.add_argument('--arxiv', help='arXiv ID')
+    parser.add_argument('--url', help='URL to article')
+    parser.add_argument('-i', '--input', help='Input file with identifiers (one per line)')
+    parser.add_argument('-o', '--output', help='Output file for BibTeX (default: stdout)')
+    parser.add_argument('--format', choices=['bibtex', 'json'], default='bibtex', help='Output format')
+    parser.add_argument('--email', help='Email for NCBI E-utilities (recommended)')
+
+    args = parser.parse_args()
+
+    # Collect identifiers
+    identifiers = []
+    if args.doi:
+        identifiers.append(args.doi)
+    if args.pmid:
+        identifiers.append(args.pmid)
+    if args.arxiv:
+        identifiers.append(args.arxiv)
+    if args.url:
+        identifiers.append(args.url)
+
+    if args.input:
+        try:
+            with open(args.input, 'r', encoding='utf-8') as f:
+                file_ids = [line.strip() for line in f if line.strip()]
+                identifiers.extend(file_ids)
+        except Exception as e:
+            print(f'Error reading input file: {e}', file=sys.stderr)
+            sys.exit(1)
+
+    if not identifiers:
+        parser.print_help()
+        sys.exit(1)
+
+    # Extract metadata
+    extractor = MetadataExtractor(email=args.email)
+    bibtex_entries = []
+
+    for i, identifier in enumerate(identifiers):
+        print(f'\nProcessing {i + 1}/{len(identifiers)}...', file=sys.stderr)
+        bibtex = extractor.extract(identifier)
+        if bibtex:
+            bibtex_entries.append(bibtex)
+
+        # Rate limiting
+        if i < len(identifiers) - 1:
+            time.sleep(0.5)
+
+    if not bibtex_entries:
+        print('Error: No successful extractions', 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:
+        with open(args.output, 'w', encoding='utf-8') as f:
+            f.write(output)
+        print(f'\nSuccessfully wrote {len(bibtex_entries)} entries to {args.output}', file=sys.stderr)
+    else:
+        print(output)
+
+    print(f'\nExtracted {len(bibtex_entries)}/{len(identifiers)} entries', file=sys.stderr)
+
+
+if __name__ == '__main__':
+    main()