fix: cancel in-flight handlers when transport closes in server.run()

src/mcp/server/lowlevel/server.py

@@ -387,16 +387,23 @@ async def run(
                 await stack.enter_async_context(task_support.run())
 
             async with anyio.create_task_group() as tg:
-                async for message in session.incoming_messages:
-                    logger.debug("Received message: %s", message)
-
-                    tg.start_soon(
-                        self._handle_message,
-                        message,
-                        session,
-                        lifespan_context,
-                        raise_exceptions,
-                    )
+                try:
+                    async for message in session.incoming_messages:
+                        logger.debug("Received message: %s", message)
+
+                        tg.start_soon(
+                            self._handle_message,
+                            message,
+                            session,
+                            lifespan_context,
+                            raise_exceptions,
+                        )
+                finally:
+                    # Transport closed: cancel in-flight handlers. Without this the
+                    # TG join waits for them, and when they eventually try to
+                    # respond they hit a closed write stream (the session's
+                    # _receive_loop closed it when the read stream ended).
+                    tg.cancel_scope.cancel()
 
     async def _handle_message(
         self,
@@ -470,8 +477,14 @@ async def _handle_request(
             except MCPError as err:
                 response = err.error
             except anyio.get_cancelled_exc_class():
-                logger.info("Request %s cancelled - duplicate response suppressed", message.request_id)
-                return
+                if message.cancelled:
+                    # Client sent CancelledNotification; responder.cancel() already
+                    # sent an error response, so skip the duplicate.
+                    logger.info("Request %s cancelled - duplicate response suppressed", message.request_id)
+                    return
+                # Transport-close cancellation from the TG in run(); re-raise so the
+                # TG swallows its own cancellation.
+                raise
             except Exception as err:
                 if raise_exceptions:  # pragma: no cover
                     raise err

src/mcp/shared/session.py

@@ -105,7 +105,7 @@ def __exit__(
     ) -> None:
         """Exit the context manager, performing cleanup and notifying completion."""
         try:
-            if self._completed:  # pragma: no branch
+            if self._completed:
                 self._on_complete(self)
         finally:
             self._entered = False

tests/server/test_cancel_handling.py

@@ -6,12 +6,19 @@
 from mcp import Client
 from mcp.server import Server, ServerRequestContext
 from mcp.shared.exceptions import MCPError
+from mcp.shared.message import SessionMessage
 from mcp.types import (
+    LATEST_PROTOCOL_VERSION,
     CallToolRequest,
     CallToolRequestParams,
     CallToolResult,
     CancelledNotification,
     CancelledNotificationParams,
+    ClientCapabilities,
+    Implementation,
+    InitializeRequestParams,
+    JSONRPCNotification,
+    JSONRPCRequest,
     ListToolsResult,
     PaginatedRequestParams,
     TextContent,
@@ -90,3 +97,76 @@ async def first_request():
         assert isinstance(content, TextContent)
         assert content.text == "Call number: 2"
         assert call_count == 2
+
+
+@pytest.mark.anyio
+async def test_server_cancels_in_flight_handlers_on_transport_close():
+    """When the transport closes mid-request, server.run() must cancel in-flight
+    handlers rather than join on them.
+
+    Without the cancel, the task group waits for the handler, which then tries
+    to respond through a write stream that _receive_loop already closed,
+    raising ClosedResourceError and crashing server.run() with exit code 1.
+
+    This drives server.run() with raw memory streams because InMemoryTransport
+    wraps it in its own finally-cancel (_memory.py) which masks the bug.
+    """
+    handler_started = anyio.Event()
+    handler_cancelled = anyio.Event()
+    server_run_returned = anyio.Event()
+
+    async def handle_call_tool(ctx: ServerRequestContext, params: CallToolRequestParams) -> CallToolResult:
+        handler_started.set()
+        try:
+            await anyio.sleep_forever()
+        finally:
+            handler_cancelled.set()
+        # unreachable: sleep_forever only exits via cancellation
+        raise AssertionError  # pragma: no cover
+
+    server = Server("test", on_call_tool=handle_call_tool)
+
+    to_server, server_read = anyio.create_memory_object_stream[SessionMessage | Exception](10)
+    server_write, from_server = anyio.create_memory_object_stream[SessionMessage](10)
+
+    async def run_server():
+        await server.run(server_read, server_write, server.create_initialization_options())
+        server_run_returned.set()
+
+    init_req = JSONRPCRequest(
+        jsonrpc="2.0",
+        id=1,
+        method="initialize",
+        params=InitializeRequestParams(
+            protocol_version=LATEST_PROTOCOL_VERSION,
+            capabilities=ClientCapabilities(),
+            client_info=Implementation(name="test", version="1.0"),
+        ).model_dump(by_alias=True, mode="json", exclude_none=True),
+    )
+    initialized = JSONRPCNotification(jsonrpc="2.0", method="notifications/initialized")
+    call_req = JSONRPCRequest(
+        jsonrpc="2.0",
+        id=2,
+        method="tools/call",
+        params=CallToolRequestParams(name="slow", arguments={}).model_dump(by_alias=True, mode="json"),
+    )
+
+    with anyio.fail_after(5):
+        async with anyio.create_task_group() as tg, to_server, server_read, server_write, from_server:
+            tg.start_soon(run_server)
+
+            await to_server.send(SessionMessage(init_req))
+            await from_server.receive()  # init response
+            await to_server.send(SessionMessage(initialized))
+            await to_server.send(SessionMessage(call_req))
+
+            await handler_started.wait()
+
+            # Close the server's input stream — this is what stdin EOF does.
+            # server.run()'s incoming_messages loop ends, finally-cancel fires,
+            # handler gets CancelledError, server.run() returns.
+            await to_server.aclose()
+
+            await server_run_returned.wait()
+
+    assert handler_cancelled.is_set()