Academic MCP Server

""" bioRxiv/medRxiv Adapter Provides access to bioRxiv and medRxiv preprint servers """ import requests from typing import List, Dict, Any, Optional from datetime import datetime, timedelta from .base_adapter import BaseAdapter class BioRxivAdapter(BaseAdapter): """Adapter for bioRxiv and medRxiv preprint servers""" def __init__(self, server: str = "biorxiv"): """ Initialize adapter Args: server: "biorxiv" or "medrxiv" """ if server not in ["biorxiv", "medrxiv"]: raise ValueError("server must be 'biorxiv' or 'medrxiv'") self.server = server self.base_url = f"https://api.biorxiv.org" def get_source_name(self) -> str: return self.server def search_by_keywords(self, keywords: str, num_results: int = 10) -> List[Dict[str, Any]]: """ Search bioRxiv/medRxiv by keywords Note: bioRxiv API doesn't support keyword search directly, so we fetch recent papers and filter by keywords Args: keywords: Search query string num_results: Number of results to return Returns: List of standardized paper dictionaries """ try: # Fetch papers from the last year and filter end_date = datetime.now() start_date = end_date - timedelta(days=365) date_range = f"{start_date.strftime('%Y-%m-%d')}/{end_date.strftime('%Y-%m-%d')}" all_results = [] cursor = 0 keywords_lower = keywords.lower() # Fetch in batches until we have enough results while len(all_results) < num_results and cursor < 10000: url = f"{self.base_url}/details/{self.server}/{date_range}/{cursor}" response = requests.get(url, timeout=30) if response.status_code != 200: break data = response.json() collection = data.get("collection", []) if not collection: break # Filter by keywords in title or abstract for item in collection: title = item.get("title", "").lower() abstract = item.get("abstract", "").lower() if keywords_lower in title or keywords_lower in abstract: all_results.append(self._format_biorxiv_result(item)) if len(all_results) >= num_results: break cursor += len(collection) return all_results[:num_results] except Exception as e: print(f"Error searching {self.server}: {e}") return [] def search_advanced(self, **kwargs) -> List[Dict[str, Any]]: """ Advanced search in bioRxiv/medRxiv Args: title: Search in title author: Author name start_date: Start date (YYYY-MM-DD) end_date: End date (YYYY-MM-DD) num_results: Number of results Returns: List of standardized paper dictionaries """ try: start_date = kwargs.get('start_date') end_date = kwargs.get('end_date') title_query = kwargs.get('title', '').lower() author_query = kwargs.get('author', '').lower() num_results = kwargs.get('num_results', 10) # Default to last year if no dates provided if not end_date: end_date = datetime.now().strftime('%Y-%m-%d') if not start_date: start_obj = datetime.strptime(end_date, '%Y-%m-%d') - timedelta(days=365) start_date = start_obj.strftime('%Y-%m-%d') date_range = f"{start_date}/{end_date}" all_results = [] cursor = 0 while len(all_results) < num_results and cursor < 10000: url = f"{self.base_url}/details/{self.server}/{date_range}/{cursor}" response = requests.get(url, timeout=30) if response.status_code != 200: break data = response.json() collection = data.get("collection", []) if not collection: break for item in collection: # Filter by title and author title_match = not title_query or title_query in item.get("title", "").lower() author_match = not author_query or author_query in item.get("authors", "").lower() if title_match and author_match: all_results.append(self._format_biorxiv_result(item)) if len(all_results) >= num_results: break cursor += len(collection) return all_results[:num_results] except Exception as e: print(f"Error in advanced {self.server} search: {e}") return [] def get_metadata(self, identifier: str) -> Dict[str, Any]: """ Get metadata for a bioRxiv/medRxiv article by DOI Args: identifier: DOI of the article (e.g., "10.1101/2024.01.001") Returns: Standardized metadata dictionary """ try: # Extract DOI suffix if full DOI provided doi = identifier.replace("10.1101/", "") url = f"{self.base_url}/details/{self.server}/{doi}" response = requests.get(url, timeout=30) if response.status_code != 200: return {"error": f"Could not retrieve metadata for DOI: {identifier}"} data = response.json() collection = data.get("collection", []) if collection: return self._format_biorxiv_result(collection[0]) return {"error": f"No metadata found for DOI: {identifier}"} except Exception as e: return {"error": f"Error fetching metadata: {str(e)}"} def download_pdf(self, identifier: str) -> str: """ Download PDF for a bioRxiv/medRxiv article Args: identifier: DOI of the article Returns: Status message """ try: # bioRxiv/medRxiv DOI format: 10.1101/YYYY.MM.DD.XXXXXX doi = identifier.replace("10.1101/", "") # PDF URL format pdf_url = f"https://www.{self.server}.org/content/{doi}v1.full.pdf" response = requests.get(pdf_url, timeout=30) if response.status_code != 200: return f"Error: Unable to download PDF (status code: {response.status_code})" # Save PDF filename = f"{self.server}_{doi.replace('/', '_')}.pdf" with open(filename, 'wb') as f: f.write(response.content) return f"PDF downloaded successfully as {filename}" except Exception as e: return f"Error downloading PDF: {str(e)}" def _format_biorxiv_result(self, item: Dict[str, Any]) -> Dict[str, Any]: """ Convert bioRxiv/medRxiv format to standardized format Args: item: Result from bioRxiv API Returns: Standardized result dictionary """ doi = item.get("doi", "") return { "id": doi, "title": item.get("title", ""), "authors": item.get("authors", ""), "abstract": item.get("abstract", ""), "publication_date": item.get("date", ""), "journal": f"{self.server} (preprint)", "url": f"https://www.{self.server}.org/content/{doi}", "pdf_url": f"https://www.{self.server}.org/content/{doi}v1.full.pdf", "source": self.server }