list_guidelines

Instructions

Implementation Reference

• src/noctua_mcp/mcp_server.py:1879-1901 (handler)

  The main tool handler for 'list_guidelines' - an MCP tool decorated with @mcp.tool() that lists all available GO-CAM guideline documents. It calls _get_available_guidelines() helper and returns a dictionary with guidelines list, count, and a note about using get_guideline_content.

  @mcp.tool()
  async def list_guidelines() -> Dict[str, Any]:
      """List all available GO-CAM guideline documents.
  
      Returns a list of available guideline names that can be accessed
      using the get_guideline_content tool.
  
      Returns:
          Dictionary with 'guidelines' key containing list of available guidelines
  
      Examples:
          # List all available guidelines
          result = list_guidelines()
          for guide in result['guidelines']:
              print(guide)
      """
      guidelines = _get_available_guidelines()
  
      return {
          "guidelines": guidelines,
          "count": len(guidelines),
          "note": "Use get_guideline_content(guideline_name) to fetch any guideline"
      }

• src/noctua_mcp/mcp_server.py:1879-1879 (registration)

  Registration of the 'list_guidelines' tool via the @mcp.tool() decorator on the async function. This registers the function as an MCP tool with the FastMCP server.

  @mcp.tool()

• src/noctua_mcp/mcp_server.py:1793-1797 (helper)

  Helper function _get_available_guidelines() used by list_guidelines to scan the GUIDELINES_DIR for .md files and return sorted list of available guideline names (file stems).

  def _get_available_guidelines() -> List[str]:
      """Get list of available guideline files."""
      if not GUIDELINES_DIR.exists():
          return []
      return sorted([f.stem for f in GUIDELINES_DIR.glob("*.md")])

• src/noctua_mcp/mcp_server.py:1800-1820 (helper)

  Helper function _inject_guideline_list() used by resource handlers to append a formatted list of available guidelines to content.

  def _inject_guideline_list(content: str, title: str) -> str:
      """Inject list of available guidelines at the end of content."""
      guidelines = _get_available_guidelines()
      if not guidelines:
          return content
  
      # Create formatted list
      guideline_section = "\n\n## Available GO-CAM Guidelines\n\n"
      guideline_section += f"This is the '{title}' guideline. Other available guidelines include:\n\n"
  
      for guide in guidelines:
          # Skip the current one
          if guide == title:
              continue
          # Make the filename more readable
          readable_name = guide.replace("_", " ").replace("-", " ")
          guideline_section += f"- {readable_name}\n"
  
      guideline_section += "\nUse the `get_guideline_content` tool to access any specific guideline."
  
      return content + guideline_section

• src/noctua_mcp/mcp_server.py:1904-1957 (helper)

  Companion tool get_guideline_content() that pairs with list_guidelines to fetch specific guideline content by name.

  @mcp.tool()
  async def get_guideline_content(guideline_name: str) -> Dict[str, Any]:
      """Fetch specific GO-CAM guideline content.
  
      Args:
          guideline_name: Name of guideline file (without .md extension).
                         Use list_guidelines() to see available options.
  
      Returns:
          Dictionary with guideline content or error message
  
      Examples:
          # Get a specific guideline
          content = get_guideline_content("E3_ubiquitin_ligases")
  
          # Get transcription factor guidelines
          content = get_guideline_content("DNA-binding_transcription_factor_activity_annotation_guidelines")
      """
      file_path = GUIDELINES_DIR / f"{guideline_name}.md"
  
      if not file_path.exists():
          available = _get_available_guidelines()
          return {
              "success": False,
              "error": f"Guideline '{guideline_name}' not found",
              "available_guidelines": available,
              "hint": "Use one of the available guideline names listed above"
          }
  
      try:
          with open(file_path) as f:
              content = f.read()
  
          # Extract first heading as description
          lines = content.split('\n')
          description = ""
          for line in lines:
              if line.strip():
                  description = line.strip('#').strip()
                  break
  
          return {
              "success": True,
              "guideline_name": guideline_name,
              "description": description,
              "content": content,
              "length": len(content)
          }
      except Exception as e:
          return {
              "success": False,
              "error": f"Failed to read guideline: {str(e)}",
              "guideline_name": guideline_name
          }