score_gene_signature

Instructions

Implementation Reference

• src/millimap_mcp/server.py:308-321 (handler)

  The `score_gene_signature` tool handler function decorated with `@mcp.tool()`. It accepts a list of gene symbols and an optional score_name, then proxies the call to the MilliMap desktop app via `_post_tool`.

  @mcp.tool()
  def score_gene_signature(genes: list[str], score_name: str = "mcp_score") -> str:
      """Score a gene signature across all cells and add it as an obs column.
  
      Use this to apply a published signature (e.g. exhausted T cell markers,
      EMT genes) to the dataset. The score becomes a colorable field in MilliMap.
  
      Args:
          genes: List of gene symbols to score together.
          score_name: Name for the new obs column (default 'mcp_score').
      """
      return _fmt_json(_post_tool("score_gene_signature", {
          "genes": genes, "score_name": score_name,
      }))

• src/millimap_mcp/server.py:308-321 (registration)

  The `@mcp.tool()` decorator on line 308 registers `score_gene_signature` as an MCP tool on the FastMCP server instance.

  @mcp.tool()
  def score_gene_signature(genes: list[str], score_name: str = "mcp_score") -> str:
      """Score a gene signature across all cells and add it as an obs column.
  
      Use this to apply a published signature (e.g. exhausted T cell markers,
      EMT genes) to the dataset. The score becomes a colorable field in MilliMap.
  
      Args:
          genes: List of gene symbols to score together.
          score_name: Name for the new obs column (default 'mcp_score').
      """
      return _fmt_json(_post_tool("score_gene_signature", {
          "genes": genes, "score_name": score_name,
      }))

• src/millimap_mcp/server.py:319-321 (helper)

  The `score_gene_signature` handler calls `_post_tool` (defined at line 33) to send a POST request to the MilliMap desktop app's /tool endpoint with the tool name and args.

  return _fmt_json(_post_tool("score_gene_signature", {
      "genes": genes, "score_name": score_name,
  }))

• src/millimap_mcp/server.py:33-58 (helper)

  The `_post_tool` helper function that sends the tool call to the MilliMap desktop HTTP server. It reads the control file for host/port, posts the tool name and args as JSON, and returns the response.

  def _post_tool(name: str, args: dict, timeout: float = 600.0) -> dict:
      ctrl = _load_control()
      if not ctrl or not ctrl.get("port"):
          return {
              "ok": False,
              "error": (
                  f"MilliMap control endpoint not found at {CONTROL_PATH}. "
                  "Make sure MilliMap is running with a dataset loaded."
              ),
          }
      host = ctrl.get("host", "127.0.0.1")
      port = int(ctrl["port"])
      url = f"http://{host}:{port}/tool"
      data = json.dumps({"name": name, "args": args}).encode("utf-8")
      req = urllib.request.Request(
          url, data=data,
          headers={"Content-Type": "application/json"},
          method="POST",
      )
      try:
          with urllib.request.urlopen(req, timeout=timeout) as resp:
              return json.loads(resp.read().decode("utf-8"))
      except urllib.error.URLError as exc:
          return {"ok": False, "error": f"connection failed: {exc.reason}"}
      except Exception as exc:
          return {"ok": False, "error": f"HTTP call failed: {exc}"}