Paper Search MCP Server

Instructions

Args:
    paper_id: bioRxiv DOI.
    save_path: Directory to save PDF.

Returns:
    Full paper text in Markdown format.

Implementation Reference

• paper_find_mcp/server.py:351-362 (handler)

  MCP tool handler function for 'read_biorxiv_paper'. Defines input schema via type hints and docstring, and dispatches to the generic _read helper with 'biorxiv' key.

  @mcp.tool()
  async def read_biorxiv_paper(paper_id: str, save_path: Optional[str] = None) -> str:
      """Download and extract full text from bioRxiv paper.
      
      Args:
          paper_id: bioRxiv DOI.
          save_path: Directory to save PDF.
      
      Returns:
          Full paper text in Markdown format.
      """
      return await _read('biorxiv', paper_id, save_path)

• paper_find_mcp/server.py:137-157 (helper)

  Generic helper function _read that retrieves the platform-specific searcher from SEARCHERS dict and calls its read_paper method.

  async def _read(
      searcher_name: str, 
      paper_id: str, 
      save_path: Optional[str] = None
  ) -> str:
      """通用阅读函数"""
      if save_path is None:
          save_path = get_download_path()
      
      searcher = SEARCHERS.get(searcher_name)
      if not searcher:
          return f"Error: Unknown searcher {searcher_name}"
      
      try:
          return searcher.read_paper(paper_id, save_path)
      except NotImplementedError as e:
          return str(e)
      except Exception as e:
          logger.error(f"Read failed for {searcher_name}: {e}")
          return f"Error reading paper: {str(e)}"

• paper_find_mcp/academic_platforms/biorxiv.py:213-238 (helper)

  Core implementation in BioRxivSearcher.read_paper: downloads bioRxiv PDF if needed, then extracts full text as Markdown using pymupdf4llm.to_markdown.

  def read_paper(self, paper_id: str, save_path: str) -> str:
      """下载并提取论文文本
      
      Args:
          paper_id: bioRxiv DOI
          save_path: 保存目录
          
      Returns:
          提取的 Markdown 文本
      """
      pdf_path = os.path.join(save_path, f"{paper_id.replace('/', '_')}.pdf")
      
      if not os.path.exists(pdf_path):
          result = self.download_pdf(paper_id, save_path)
          if result.startswith("Error"):
              return result
          pdf_path = result
      
      try:
          text = pymupdf4llm.to_markdown(pdf_path, show_progress=False)
          logger.info(f"Extracted {len(text)} characters from {pdf_path}")
          return text
      except Exception as e:
          logger.error(f"Failed to extract text: {e}")
          return f"Error extracting text: {e}"

• paper_find_mcp/server.py:75-85 (registration)

  Global SEARCHERS dictionary initialization, instantiating and registering BioRxivSearcher() under 'biorxiv' key for use by _read.

  SEARCHERS = {
      'arxiv': ArxivSearcher(),
      'pubmed': PubMedSearcher(),
      'biorxiv': BioRxivSearcher(),
      'medrxiv': MedRxivSearcher(),
      'google_scholar': GoogleScholarSearcher(),
      'iacr': IACRSearcher(),
      'semantic': SemanticSearcher(),
      'crossref': CrossRefSearcher(),
      'repec': RePECSearcher(),
  }