Paper Search MCP

Instructions

Implementation Reference

• paper_search_mcp/academic_platforms/medrxiv.py:9-85 (handler)

  Implementation of the MedRxivSearcher class which performs the actual API calls to search for papers on medRxiv.

  class MedRxivSearcher(PaperSource):
      """Searcher for medRxiv papers"""
      BASE_URL = "https://api.biorxiv.org/details/medrxiv"
  
      def __init__(self):
          self.session = requests.Session()
          self.session.proxies = {'http': None, 'https': None}
          self.timeout = 30
          self.max_retries = 3
  
      def search(self, query: str, max_results: int = 10, days: int = 30) -> List[Paper]:
          """
          Search for papers on medRxiv by category within the last N days.
  
          Args:
              query: Category name to search for (e.g., "cardiovascular medicine").
              max_results: Maximum number of papers to return.
              days: Number of days to look back for papers.
  
          Returns:
              List of Paper objects matching the category within the specified date range.
          """
          # Calculate date range: last N days
          end_date = datetime.now().strftime('%Y-%m-%d')
          start_date = (datetime.now() - timedelta(days=days)).strftime('%Y-%m-%d')
          
          # Format category: lowercase and replace spaces with underscores
          category = query.lower().replace(' ', '_')
          
          papers = []
          cursor = 0
          while len(papers) < max_results:
              url = f"{self.BASE_URL}/{start_date}/{end_date}/{cursor}"
              if category:
                  url += f"?category={category}"
  
              tries = 0
              while tries < self.max_retries:
                  try:
                      response = self.session.get(url, timeout=self.timeout)
                      response.raise_for_status()
                      data = response.json()
                      collection = data.get('collection', [])
                      for item in collection:
                          try:
                              date = datetime.strptime(item['date'], '%Y-%m-%d')
                              papers.append(Paper(
                                  paper_id=item['doi'],
                                  title=item['title'],
                                  authors=item['authors'].split('; '),
                                  abstract=item['abstract'],
                                  url=f"https://www.medrxiv.org/content/{item['doi']}v{item.get('version', '1')}",
                                  pdf_url=f"https://www.medrxiv.org/content/{item['doi']}v{item.get('version', '1')}.full.pdf",
                                  published_date=date,
                                  updated_date=date,
                                  source="medrxiv",
                                  categories=[item['category']],
                                  keywords=[],
                                  doi=item['doi']
                              ))
                          except Exception as e:
                              print(f"Error parsing medRxiv entry: {e}")
                      if len(collection) < 100:
                          break  # No more results
                      cursor += 100
                      break  # Exit retry loop on success
                  except requests.exceptions.RequestException as e:
                      tries += 1
                      if tries == self.max_retries:
                          print(f"Failed to connect to medRxiv API after {self.max_retries} attempts: {e}")
                          break
                      print(f"Attempt {tries} failed, retrying...")
              else:
                  continue
              break
  
          return papers[:max_results]

• paper_search_mcp/server.py:404-418 (handler)

  MCP tool handler `search_medrxiv` that wraps the MedRxivSearcher service.

  async def search_medrxiv(query: str, max_results: int = 10) -> List[Dict]:
      """Search academic papers from medRxiv.
  
      Note: medRxiv API filters by category name within the last 30 days, not full-text
      keyword search. Use a category keyword such as 'infectious_diseases',
      'cardiovascular_medicine', 'oncology', etc.
  
      Args:
          query: Category name to filter by (e.g., 'infectious_diseases', 'oncology').
          max_results: Maximum number of papers to return (default: 10).
      Returns:
          List of paper metadata in dictionary format.
      """
      papers = await async_search(medrxiv_searcher, query, max_results)
      return papers if papers else []