Academic MCP Server

""" PubMed Adapter Provides access to PubMed database using integrated utilities """ from typing import List, Dict, Any, Optional # Import PubMed utilities from local utils module from utils.pubmed_utils import ( search_key_words, search_advanced, get_pubmed_metadata, download_full_text_pdf, deep_paper_analysis as pubmed_deep_analysis ) from .base_adapter import BaseAdapter class PubMedAdapter(BaseAdapter): """Adapter for PubMed database using integrated PubMed utilities""" def get_source_name(self) -> str: return "pubmed" def search_by_keywords(self, keywords: str, num_results: int = 10) -> List[Dict[str, Any]]: """ Search PubMed using keywords Args: keywords: Search query string num_results: Number of results to return Returns: List of standardized paper dictionaries """ try: results = search_key_words(keywords, num_results) return [self._format_result(r) for r in results] except Exception as e: print(f"Error searching PubMed: {e}") return [] def search_advanced(self, **kwargs) -> List[Dict[str, Any]]: """ Advanced search in PubMed Args: title: Search in title author: Author name journal: Journal name start_date: Start date (YYYY/MM/DD) end_date: End date (YYYY/MM/DD) term: General search term num_results: Number of results Returns: List of standardized paper dictionaries """ try: term = kwargs.get('term') title = kwargs.get('title') author = kwargs.get('author') journal = kwargs.get('journal') start_date = kwargs.get('start_date') end_date = kwargs.get('end_date') num_results = kwargs.get('num_results', 10) results = search_advanced( term=term, title=title, author=author, journal=journal, start_date=start_date, end_date=end_date, num_results=num_results ) return [self._format_result(r) for r in results] except Exception as e: print(f"Error in advanced PubMed search: {e}") return [] def get_metadata(self, identifier: str) -> Dict[str, Any]: """ Get metadata for a PubMed article by PMID Args: identifier: PMID of the article Returns: Standardized metadata dictionary """ try: metadata = get_pubmed_metadata(str(identifier)) if metadata: return self._format_result(metadata) return {"error": f"No metadata found for PMID: {identifier}"} except Exception as e: return {"error": f"Error fetching metadata: {str(e)}"} def download_pdf(self, identifier: str) -> str: """ Attempt to download PDF for a PubMed article Args: identifier: PMID of the article Returns: Status message """ try: return download_full_text_pdf(str(identifier)) except Exception as e: return f"Error downloading PDF: {str(e)}" def deep_analysis(self, identifier: str) -> str: """ Generate deep analysis prompt for a PubMed article Args: identifier: PMID of the article Returns: Analysis prompt string """ try: metadata = get_pubmed_metadata(str(identifier)) if metadata: return pubmed_deep_analysis(metadata) return "Error: Could not retrieve metadata for analysis" except Exception as e: return f"Error generating analysis: {str(e)}" def _format_result(self, pubmed_result: Dict[str, Any]) -> Dict[str, Any]: """ Convert PubMed format to standardized format Args: pubmed_result: Result from PubMed API Returns: Standardized result dictionary """ if "error" in pubmed_result: return pubmed_result pmid = pubmed_result.get("PMID", "") return { "id": pmid, "title": pubmed_result.get("Title", "No title available"), "authors": pubmed_result.get("Authors", "No authors available"), "abstract": pubmed_result.get("Abstract", "No abstract available"), "publication_date": pubmed_result.get("Publication Date", ""), "journal": pubmed_result.get("Journal", ""), "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", "pdf_url": None, # PMC PDF URLs need to be determined separately "source": "pubmed" }