PubMed MCP Server

""" Citation formatting module for different academic citation styles. This module provides functionality to format PubMed articles into various citation formats including BibTeX, APA, MLA, Chicago, Vancouver, EndNote, and RIS. """ import logging import re from typing import List from .models import Article, Author, CitationFormat logger = logging.getLogger(__name__) class CitationFormatter: """Citation formatter for various academic styles.""" @staticmethod def format_citation(article: Article, format_type: CitationFormat) -> str: """ Format an article citation in the specified format. Args: article: The article to format format_type: The citation format to use Returns: Formatted citation string Raises: ValueError: If format type is not supported """ formatters = { CitationFormat.APA: CitationFormatter._format_apa, CitationFormat.MLA: CitationFormatter._format_mla, CitationFormat.CHICAGO: CitationFormatter._format_chicago, CitationFormat.VANCOUVER: CitationFormatter._format_vancouver, CitationFormat.BIBTEX: CitationFormatter._format_bibtex, CitationFormat.ENDNOTE: CitationFormatter._format_endnote, CitationFormat.RIS: CitationFormatter._format_ris, } formatter = formatters.get(format_type) if not formatter: raise ValueError(f"Unsupported citation format: {format_type}") return formatter(article) @staticmethod def format_multiple_citations( articles: List[Article], format_type: CitationFormat ) -> List[str]: """Format multiple articles as citations. Args: articles: List of articles to format format_type: The citation format to use Returns: List of formatted citation strings """ return [CitationFormatter.format_citation(article, format_type) for article in articles] @staticmethod def _clean_text(text: str) -> str: """Clean text for citation formatting.""" if not text: return "" # Remove HTML tags and extra whitespace text = re.sub(r"<[^>]+>", "", text) text = re.sub(r"\s+", " ", text) return text.strip() @staticmethod def _format_authors_apa(authors: List[Author]) -> str: """Format authors for APA style.""" if not authors: return "" formatted_authors = [] authors_to_process = authors[:20] if len(authors) <= 20 else authors[:19] for author in authors_to_process: if isinstance(author, str): # Handle string authors (legacy format) parts = author.split() if len(parts) >= 2: # Check if this looks like a real name (LastName should be alphabetic) last_name = parts[-1] if last_name.isalpha() and len(last_name) > 1: # Last, F. M. format for real names initials = " ".join([f"{name[0]}." for name in parts[:-1]]) formatted_authors.append(f"{last_name}, {initials}") else: # Keep as-is for things like "Author 24" formatted_authors.append(author) else: formatted_authors.append(author) else: # Handle Author objects if author.last_name: author_str = author.last_name if author.initials: # Ensure initials have periods initials = author.initials if not initials.endswith("."): initials += "." author_str += f", {initials}" elif author.first_name: author_str += f", {author.first_name[0]}." formatted_authors.append(author_str) elif author.first_name: formatted_authors.append(author.first_name) if len(authors) > 20: # For more than 20 authors, show first 19, then "... & last_author" last_author = authors[-1] if isinstance(last_author, str): parts = last_author.split() if len(parts) >= 2: last_name = parts[-1] if last_name.isalpha() and len(last_name) > 1: # Format real names initials = " ".join([f"{name[0]}." for name in parts[:-1]]) last_formatted = f"{last_name}, {initials}" else: # Keep as-is for things like "Author 24" last_formatted = last_author else: last_formatted = last_author else: # Handle Author objects if last_author.last_name: last_formatted = last_author.last_name if last_author.initials: initials = last_author.initials if not initials.endswith("."): initials += "." last_formatted += f", {initials}" elif last_author.first_name: last_formatted += f", {last_author.first_name[0]}." else: last_formatted = last_author.first_name or "Unknown" return ", ".join(formatted_authors) + ", ... & " + last_formatted elif len(formatted_authors) > 1: return ", ".join(formatted_authors[:-1]) + ", & " + formatted_authors[-1] else: return formatted_authors[0] if formatted_authors else "" @staticmethod def _format_apa(article: Article) -> str: """Format citation in APA style.""" citation_parts = [] # Authors authors = CitationFormatter._format_authors_apa(article.authors) if authors: citation_parts.append(authors) # Year if article.pub_date: year = article.pub_date[:4] citation_parts.append(f"({year})") # Title if article.title: title = CitationFormatter._clean_text(article.title) # Remove period at end if present title = title.rstrip(".") citation_parts.append(f"{title}.") # Journal if article.journal: journal_part = f"*{article.journal.title}*" if article.journal.volume: journal_part += f", *{article.journal.volume}*" if article.journal.issue: journal_part += f"({article.journal.issue})" citation_parts.append(journal_part + ".") # DOI or PMID if article.doi: citation_parts.append(f"https://doi.org/{article.doi}") elif article.pmid: pmid_url = f"https://pubmed.ncbi.nlm.nih.gov/{article.pmid}/" citation_parts.append(pmid_url) return " ".join(citation_parts) @staticmethod def _format_mla(article: Article) -> str: """Format citation in MLA style.""" citation_parts = [] # Authors (Last, First format for first author) if article.authors: first_author = article.authors[0] if isinstance(first_author, str): parts = first_author.split() if len(parts) >= 2: mla_author = f"{parts[-1]}, {' '.join(parts[:-1])}" else: mla_author = first_author else: # Handle Author object if first_author.last_name and first_author.first_name: mla_author = f"{first_author.last_name}, {first_author.first_name}" elif first_author.last_name: mla_author = first_author.last_name else: mla_author = first_author.first_name or "Unknown Author" if len(article.authors) > 1: mla_author += ", et al" citation_parts.append(mla_author + ".") # Title if article.title: title = CitationFormatter._clean_text(article.title) title = title.rstrip(".") citation_parts.append(f'"{title}."') # Journal if article.journal: journal_part = f"*{article.journal.title}*" if article.journal.volume: journal_part += f", vol. {article.journal.volume}" if article.journal.issue: journal_part += f", no. {article.journal.issue}" if article.pub_date: year = article.pub_date[:4] journal_part += f", {year}" citation_parts.append(journal_part + ".") # Access information if article.pmid: pmid_url = f"https://pubmed.ncbi.nlm.nih.gov/{article.pmid}/" citation_parts.append(f"Web. {pmid_url}") elif article.doi: citation_parts.append(f"DOI: {article.doi}.") return " ".join(citation_parts) @staticmethod def _format_chicago(article: Article) -> str: """Format citation in Chicago style.""" citation_parts = [] # Authors if article.authors: first_author = article.authors[0] if isinstance(first_author, str): parts = first_author.split() if len(parts) >= 2: chicago_author = f"{parts[-1]}, {' '.join(parts[:-1])}" else: chicago_author = first_author else: # Handle Author object if first_author.last_name and first_author.first_name: chicago_author = f"{first_author.last_name}, {first_author.first_name}" elif first_author.last_name: chicago_author = first_author.last_name else: chicago_author = first_author.first_name or "Unknown Author" if len(article.authors) > 1: chicago_author += ", et al" citation_parts.append(chicago_author + ".") # Title if article.title: title = CitationFormatter._clean_text(article.title) title = title.rstrip(".") citation_parts.append(f'"{title}."') # Journal if article.journal: journal_part = f"*{article.journal.title}*" if article.journal.volume: journal_part += f" {article.journal.volume}" if article.journal.issue: journal_part += f", no. {article.journal.issue}" if article.pub_date: year = article.pub_date[:4] journal_part += f" ({year})" citation_parts.append(journal_part + ".") # DOI or PMID if article.doi: citation_parts.append(f"https://doi.org/{article.doi}.") elif article.pmid: pmid_url = f"https://pubmed.ncbi.nlm.nih.gov/{article.pmid}/" citation_parts.append(pmid_url) return " ".join(citation_parts) @staticmethod def _format_vancouver(article: Article) -> str: """Format citation in Vancouver style.""" citation_parts = [] # Authors (up to 6, then et al.) if article.authors: vancouver_authors = [] for i, author in enumerate(article.authors[:6]): if isinstance(author, str): parts = author.split() if len(parts) >= 2: # Last FM format last_name = parts[-1] initials = "".join([name[0] for name in parts[:-1]]) vancouver_authors.append(f"{last_name} {initials}") else: vancouver_authors.append(author) else: # Handle Author object if author.last_name: author_str = author.last_name if author.initials: author_str += f" {author.initials.replace('.', '')}" elif author.first_name: author_str += f" {author.first_name[0]}" vancouver_authors.append(author_str) if len(article.authors) > 6: vancouver_authors.append("et al") citation_parts.append(", ".join(vancouver_authors) + ".") # Title if article.title: title = CitationFormatter._clean_text(article.title) title = title.rstrip(".") citation_parts.append(f"{title}.") # Journal if article.journal: journal_part = article.journal.title if article.pub_date: year = article.pub_date[:4] journal_part += f" {year}" if article.journal.volume: journal_part += f";{article.journal.volume}" if article.journal.issue: journal_part += f"({article.journal.issue})" citation_parts.append(journal_part + ".") # PMID if article.pmid: citation_parts.append(f"PMID: {article.pmid}") return " ".join(citation_parts) @staticmethod def _format_bibtex(article: Article) -> str: """Format citation in BibTeX format.""" # Generate citation key key_parts = [] if article.authors: first_author = article.authors[0] if isinstance(first_author, str): key_parts.append(first_author.split()[-1].lower()) else: if first_author and first_author.last_name: key_parts.append(first_author.last_name.lower()) if article.pub_date: key_parts.append(article.pub_date[:4]) # Add a simple letter suffix for the first word if article.title: # Use first significant word from title title_words = article.title.split() for word in title_words: if len(word) > 0 and word.lower() not in [ "the", "and", "for", "with", "a", "an", "sample", # Skip "sample" as it's not meaningful "research", # Skip "research" as it's not meaningful ]: key_parts.append(word[0].lower()) break citation_key = "".join(key_parts) if key_parts else f"article_{article.pmid}" bibtex_lines = [f"@article{{{citation_key},"] # Title if article.title: title = CitationFormatter._clean_text(article.title) bibtex_lines.append(f" title = {{{title}}},") # Authors if article.authors: author_list = [] for author in article.authors: if isinstance(author, str): author_list.append(author) else: if author.first_name and author.last_name: author_list.append(f"{author.first_name} {author.last_name}") elif author.last_name: author_list.append(author.last_name) elif author.first_name: author_list.append(author.first_name) if author_list: authors_str = " and ".join(author_list) bibtex_lines.append(f" author = {{{authors_str}}},") # Journal if article.journal: bibtex_lines.append(f" journal = {{{article.journal.title}}},") if article.journal.volume: bibtex_lines.append(f" volume = {{{article.journal.volume}}},") if article.journal.issue: bibtex_lines.append(f" number = {{{article.journal.issue}}},") # Year if article.pub_date: year = article.pub_date[:4] bibtex_lines.append(f" year = {{{year}}},") # DOI if article.doi: bibtex_lines.append(f" doi = {{{article.doi}}},") # PMID if article.pmid: bibtex_lines.append(f" pmid = {{{article.pmid}}},") # Note: pages field removed since it's not available in Article model # Could be added later if journal provides page information bibtex_lines.append("}") return "\n".join(bibtex_lines) @staticmethod def _format_endnote(article: Article) -> str: """Format citation in EndNote format.""" endnote_lines = [] # Reference type (Journal Article) endnote_lines.append("%0 Journal Article") # Title if article.title: title = CitationFormatter._clean_text(article.title) endnote_lines.append(f"%T {title}") # Authors for author in article.authors: if isinstance(author, str): endnote_lines.append(f"%A {author}") else: if author.first_name and author.last_name: endnote_lines.append(f"%A {author.first_name} {author.last_name}") elif author.last_name: endnote_lines.append(f"%A {author.last_name}") elif author.first_name: endnote_lines.append(f"%A {author.first_name}") # Journal if article.journal: endnote_lines.append(f"%J {article.journal.title}") if article.journal.volume: endnote_lines.append(f"%V {article.journal.volume}") if article.journal.issue: endnote_lines.append(f"%N {article.journal.issue}") # Date if article.pub_date: endnote_lines.append(f"%D {article.pub_date}") # DOI if article.doi: endnote_lines.append(f"%R {article.doi}") # PMID if article.pmid: endnote_lines.append(f"%M {article.pmid}") # Note: pages field removed since it's not available in Article model return "\n".join(endnote_lines) @staticmethod def _format_ris(article: Article) -> str: """Format citation in RIS format.""" ris_lines = [] # Type of reference ris_lines.append("TY - JOUR") # Title if article.title: title = CitationFormatter._clean_text(article.title) ris_lines.append(f"TI - {title}") # Authors for author in article.authors: if isinstance(author, str): ris_lines.append(f"AU - {author}") else: if author.first_name and author.last_name: ris_lines.append(f"AU - {author.first_name} {author.last_name}") elif author.last_name: ris_lines.append(f"AU - {author.last_name}") elif author.first_name: ris_lines.append(f"AU - {author.first_name}") # Journal if article.journal: ris_lines.append(f"JO - {article.journal.title}") if article.journal.volume: ris_lines.append(f"VL - {article.journal.volume}") if article.journal.issue: ris_lines.append(f"IS - {article.journal.issue}") # Handle pages if hasattr(article.journal, "pages") and article.journal.pages: pages = article.journal.pages if "-" in pages: # Page range (e.g., "123-456") start_page, end_page = pages.split("-", 1) ris_lines.append(f"SP - {start_page.strip()}") ris_lines.append(f"EP - {end_page.strip()}") else: # Single page ris_lines.append(f"SP - {pages.strip()}") # Date if article.pub_date: # Try to format date properly date_parts = article.pub_date.split("-") if len(date_parts) >= 1: ris_lines.append(f"PY - {date_parts[0]}") ris_lines.append(f"DA - {article.pub_date}") # DOI if article.doi: ris_lines.append(f"DO - {article.doi}") # PMID if article.pmid: ris_lines.append(f"AN - {article.pmid}") # Note: pages field handling removed since it's not available # in Article model # End of reference ris_lines.append("ER - ") return "\n".join(ris_lines)