find_markers

Instructions

Implementation Reference

• src/millimap_mcp/server.py:275-289 (handler)

  The `find_markers` tool registered with `@mcp.tool()`. Delegates to the MilliMap desktop app by POSTing to its /tool endpoint with name='find_markers' and the groupby/method arguments.

  @mcp.tool()
  def find_markers(groupby: str = "clusters", method: str = "wilcoxon") -> str:
      """Run rank_genes_groups in MilliMap to find marker genes per cluster.
  
      After this completes, the MilliMap snapshot refreshes with the top
      markers per cluster — subsequent calls to get_cluster_markers or
      genes_for_cell_type will see them.
  
      Args:
          groupby: obs column to group by. Default 'clusters'.
          method: 'wilcoxon' (default), 't-test', or 'logreg'.
      """
      return _fmt_json(_post_tool("find_markers", {
          "groupby": groupby, "method": method,
      }))

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

  Helper function that sends the tool request to the MilliMap desktop app's HTTP endpoint. Used by `find_markers` and all other write-path tools.

  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}"}

• src/millimap_mcp/server.py:77-78 (helper)

  Helper that formats the response dict as a pretty-printed JSON string. Used by `find_markers` to return its result.

  def _fmt_json(payload: Any) -> str:
      return json.dumps(payload, indent=2, default=str)

• src/millimap_mcp/server.py:275-276 (registration)

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

  @mcp.tool()
  def find_markers(groupby: str = "clusters", method: str = "wilcoxon") -> str: