fix: isolate subprocess stdin and decouple startup to prevent MCP stdio deadlocks

- Set stdin=subprocess.DEVNULL across runtime, client, and utility subprocess calls to avoid hijacking the parent process's stdin.
- Run awake service initialization asynchronously on a daemon thread in MCP server startup.
- Redirect logger header printing to stderr to ensure stdio JSON-RPC purity.
- Add unit and lifecycle tests for MCP stdio protocol handshake and stdin isolation.

artemis/clients/ui_automator_client.py

@@ -174,6 +174,7 @@ def _is_package_installed(device_id: str, pkg: str) -> bool:
     try:
         result = subprocess.run(
             ["adb", "-s", device_id, "shell", "pm", "list", "packages"],
+            stdin=subprocess.DEVNULL,
             capture_output=True,
             text=True,
             timeout=10,
@@ -208,6 +209,7 @@ def _uninstall_package(device_id: str, pkg: str) -> bool:
                 "0",
                 pkg,
             ],
+            stdin=subprocess.DEVNULL,
             capture_output=True,
             text=True,
             timeout=30,
@@ -379,6 +381,7 @@ class UIAutomatorClient:
         try:
             result = subprocess.run(
                 ["adb", "-s", self._device_id, "exec-out", "screencap", "-p"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 timeout=10,
                 check=True,

artemis/interfaces/cli/commands/mcp.py

@@ -19,6 +19,7 @@ import os
 from pathlib import Path
 import re
 import sys
+import threading
 import tomllib
 from typing import Annotated
 
@@ -724,7 +725,9 @@ def mcp_command(
         console.print(syntax)
         raise typer.Exit(0)
 
-    start_awake_service()
+    threading.Thread(
+        target=start_awake_service, daemon=True, name="artemis-awake-init"
+    ).start()
     try:
         st = server_type.lower()
         if st in ("agent", "mobile", "artemis", "default"):

artemis/runtime/awake_lease.py

@@ -153,6 +153,7 @@ class ScreenAwakeLease:
         try:
             result = subprocess.run(
                 ["adb", "-s", self.device_id, *args],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=10,

artemis/runtime/awake_service.py

@@ -48,6 +48,7 @@ def _run_awake_adb_command(
     try:
         result = subprocess.run(
             ["adb", "-s", device_id, *args],
+            stdin=subprocess.DEVNULL,
             capture_output=True,
             text=True,
             timeout=10,
@@ -185,21 +186,25 @@ class ScreenAwakeService:
         self._heartbeat_threads: dict[str, threading.Thread] = {}
         self._monitor_stop: threading.Event | None = None
         self._monitor_thread: threading.Thread | None = None
+        self._shutdown_requested = False
 
     def start(self, device_ids: Iterable[str] | None = None) -> dict[str, str | None]:
+        if self._shutdown_requested:
+            return {}
         selected = list(device_ids) if device_ids is not None else _discover_connected_device_ids()
-        results = {
-            device_id: self.ensure_device(device_id)
-            for device_id in dict.fromkeys(selected)
-            if device_id
-        }
-        if _awake_enabled() and os.environ.get("ARTEMIS_CLOUD_MODE") != "1":
+        results = {}
+        for device_id in dict.fromkeys(selected):
+            if self._shutdown_requested:
+                break
+            if device_id:
+                results[device_id] = self.ensure_device(device_id)
+        if _awake_enabled() and os.environ.get("ARTEMIS_CLOUD_MODE") != "1" and not self._shutdown_requested:
             self._start_device_monitor()
         return results
 
     def ensure_device(self, device_id: str) -> str | None:
         """Configure one device once per process; Android owns unplug behavior."""
-        if not device_id or not _awake_enabled() or os.environ.get("ARTEMIS_CLOUD_MODE") == "1":
+        if not device_id or not _awake_enabled() or os.environ.get("ARTEMIS_CLOUD_MODE") == "1" or self._shutdown_requested:
             return None
         with self._lock:
             existing = self._strategies.get(device_id)
@@ -277,6 +282,7 @@ class ScreenAwakeService:
 
     def shutdown(self) -> None:
         """Stop host work; unplug behavior remains owned by Android's USB policy."""
+        self._shutdown_requested = True
         with self._lock:
             monitor_stop = self._monitor_stop
             monitor_thread = self._monitor_thread

artemis/runtime/device_pool.py

@@ -81,6 +81,7 @@ class DevicePool:
         try:
             res = subprocess.run(
                 [adb, "devices", "-l"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=timeout,

artemis/runtime/server_lifecycle.py

@@ -135,6 +135,7 @@ def find_server_pids(port: int = 8000) -> list[int]:
         try:
             res = subprocess.run(
                 ["lsof", "-ti", f":{port}", "-sTCP:LISTEN"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=2.0,
@@ -152,6 +153,7 @@ def find_server_pids(port: int = 8000) -> list[int]:
         try:
             res = subprocess.run(
                 ["fuser", f"{port}/tcp"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=2.0,
@@ -168,6 +170,7 @@ def find_server_pids(port: int = 8000) -> list[int]:
         try:
             res = subprocess.run(
                 ["netstat", "-ano"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=3.0,

artemis/utils/logger.py

@@ -168,9 +168,9 @@ class ArtemisLogger:
         colored_separator = f"{Fore.CYAN}{separator}{Style.RESET_ALL}"
         colored_message = f"{Fore.CYAN}{message}{Style.RESET_ALL}"
 
-        print(colored_separator)
-        print(colored_message)
-        print(colored_separator)
+        print(colored_separator, file=sys.stderr)
+        print(colored_message, file=sys.stderr)
+        print(colored_separator, file=sys.stderr)
         self.logger.info(f"\n{separator}\n{message}\n{separator}")
 
 

artemis/utils/shell_utils.py

@@ -20,6 +20,7 @@ def run_shell_command_on_host(command: str) -> str:
     try:
         result = subprocess.run(
             command,
+            stdin=subprocess.DEVNULL,
             shell=True,
             check=True,
             capture_output=True,

mcp_server/server.py

@@ -59,9 +59,13 @@ import mcp_server.tools  # noqa: F401
 from artemis.runtime import shutdown_awake_service, start_awake_service
 
 
+import threading
+
 def main(transport: str = "stdio", host: str = "127.0.0.1", port: int = 8001):
     """Main entrypoint to run the Artemis Mobile Agent MCP server."""
-    start_awake_service()
+    threading.Thread(
+        target=start_awake_service, daemon=True, name="artemis-awake-init"
+    ).start()
     try:
         if transport.lower() == "sse":
             mcp.run(transport="sse", host=host, port=port)

mcp_server/utils/device_utils.py

@@ -99,6 +99,7 @@ def get_connected_devices(adb_path: str | None = None) -> list[str]:
     try:
         res = subprocess.run(
             [adb, "devices"],
+            stdin=subprocess.DEVNULL,
             capture_output=True,
             text=True,
             timeout=5,
@@ -137,7 +138,7 @@ def ensure_emulator(
     if not emu_exe or not os.path.exists(emu_exe):
         return False
 
-    popen_kwargs = {"stdout": subprocess.DEVNULL, "stderr": subprocess.DEVNULL}
+    popen_kwargs = {"stdin": subprocess.DEVNULL, "stdout": subprocess.DEVNULL, "stderr": subprocess.DEVNULL}
     if sys.platform == "win32":
         popen_kwargs["creationflags"] = (
             subprocess.CREATE_NEW_PROCESS_GROUP | subprocess.DETACHED_PROCESS  # type: ignore[attr-defined]
@@ -158,6 +159,7 @@ def ensure_emulator(
         try:
             res = subprocess.run(
                 [adb, "-s", "emulator-5554", "shell", "getprop", "sys.boot_completed"],
+                stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
                 timeout=3,

mcp_server/utils/env_utils.py

@@ -49,6 +49,7 @@ def resolve_python_executable(project_root: str | None = None) -> str:
 def get_detached_process_kwargs() -> dict[str, Any]:
     """Returns kwargs for subprocess.Popen to run a fully detached background process cross-platform."""
     kwargs: dict[str, Any] = {
+        "stdin": subprocess.DEVNULL,
         "stdout": subprocess.DEVNULL,
         "stderr": subprocess.DEVNULL,
     }

tests/unit/mcp/test_mcp_stdio_lifecycle.py

@@ -0,0 +1,199 @@
+# Copyright 2026 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Unit and integration tests verifying MCP stdio handshake reliability,
+
+subprocess stdin isolation against pipe hijacking, and stdout purity.
+"""
+
+import io
+import json
+import os
+import subprocess
+import sys
+import time
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from artemis.clients import ui_automator_client
+from artemis.runtime.awake_lease import ScreenAwakeLease
+from artemis.runtime.awake_service import _run_awake_adb_command
+from artemis.utils.logger import get_logger
+from mcp_server.utils import device_utils, env_utils
+
+
+def test_mcp_stdio_handshake_immediate_input():
+    """Verify that MCP server over stdio responds to an immediate initialize request
+
+    without hanging, even when stdin data is pushed concurrently with process startup.
+    """
+    project_root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
+    python_exe = sys.executable
+
+    p = subprocess.Popen(
+        [python_exe, "-m", "mcp_server"],
+        stdin=subprocess.PIPE,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        env={
+            "PYTHONUNBUFFERED": "1",
+            "PATH": os.environ.get("PATH", ""),
+            "PYTHONPATH": project_root,
+        },
+        cwd=project_root,
+    )
+
+    try:
+        # Immediately write the JSON-RPC initialize request into stdin
+        init_req = {
+            "jsonrpc": "2.0",
+            "id": 1,
+            "method": "initialize",
+            "params": {
+                "protocolVersion": "2024-11-05",
+                "capabilities": {},
+                "clientInfo": {"name": "test-client", "version": "1.0.0"},
+            },
+        }
+        p.stdin.write(json.dumps(init_req).encode("utf-8") + b"\n")
+        p.stdin.flush()
+
+        # Read initialize response with a strict timeout
+        start = time.time()
+        init_resp_line = None
+        while time.time() - start < 6.0:
+            import select
+
+            r, _, _ = select.select([p.stdout], [], [], 0.2)
+            if r:
+                init_resp_line = p.stdout.readline().decode("utf-8").strip()
+                break
+
+        assert init_resp_line is not None, "MCP server failed to respond to initialize request within 6 seconds (deadlock detected)!"
+        init_data = json.loads(init_resp_line)
+        assert init_data.get("id") == 1
+        assert "result" in init_data
+
+        # Follow up with initialized notification and tools/list request
+        notif = {"jsonrpc": "2.0", "method": "notifications/initialized", "params": {}}
+        tools_req = {"jsonrpc": "2.0", "id": 2, "method": "tools/list", "params": {}}
+        p.stdin.write(json.dumps(notif).encode("utf-8") + b"\n")
+        p.stdin.write(json.dumps(tools_req).encode("utf-8") + b"\n")
+        p.stdin.flush()
+
+        tools_resp_line = None
+        start = time.time()
+        while time.time() - start < 4.0:
+            import select
+
+            r, _, _ = select.select([p.stdout], [], [], 0.2)
+            if r:
+                tools_resp_line = p.stdout.readline().decode("utf-8").strip()
+                break
+
+        assert tools_resp_line is not None, "MCP server failed to respond to tools/list request!"
+        tools_data = json.loads(tools_resp_line)
+        assert tools_data.get("id") == 2
+        tools = tools_data.get("result", {}).get("tools", [])
+        tool_names = {t["name"] for t in tools}
+        assert {
+            "mobile_run_task",
+            "mobile_manage_task",
+            "mobile_get_device_state",
+            "mobile_inspect_trace",
+        }.issubset(tool_names)
+
+    finally:
+        p.terminate()
+        try:
+            p.wait(timeout=3)
+        except subprocess.TimeoutExpired:
+            p.kill()
+
+
+def test_awake_service_adb_command_isolates_stdin():
+    """Verify _run_awake_adb_command always sets stdin=subprocess.DEVNULL."""
+    with patch("artemis.runtime.awake_service.subprocess.run") as mock_run:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        _run_awake_adb_command("test-dev-1", ["shell", "date"], "test command")
+
+        assert mock_run.called
+        kwargs = mock_run.call_args.kwargs
+        assert kwargs.get("stdin") == subprocess.DEVNULL, "Expected stdin=subprocess.DEVNULL to prevent stdin hijacking!"
+
+
+def test_awake_lease_run_isolates_stdin():
+    """Verify ScreenAwakeLease._run always sets stdin=subprocess.DEVNULL."""
+    lease = ScreenAwakeLease("test-dev-1")
+    with patch("artemis.runtime.awake_lease.subprocess.run") as mock_run:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        lease._run(["shell", "date"], "test lease command")
+
+        assert mock_run.called
+        kwargs = mock_run.call_args.kwargs
+        assert kwargs.get("stdin") == subprocess.DEVNULL, "Expected stdin=subprocess.DEVNULL to prevent stdin hijacking!"
+
+
+def test_detached_process_kwargs_isolates_stdin():
+    """Verify get_detached_process_kwargs always sets stdin=subprocess.DEVNULL."""
+    kwargs = env_utils.get_detached_process_kwargs()
+    assert kwargs.get("stdin") == subprocess.DEVNULL, "Expected stdin=subprocess.DEVNULL for detached background tasks!"
+
+
+def test_device_utils_isolates_stdin():
+    """Verify device_utils subprocess calls always set stdin=subprocess.DEVNULL."""
+    with patch("mcp_server.utils.device_utils.subprocess.run") as mock_run:
+        mock_run.return_value = MagicMock(returncode=0, stdout="List of devices attached\n", stderr="")
+        device_utils.get_connected_devices()
+        assert mock_run.called
+        assert mock_run.call_args.kwargs.get("stdin") == subprocess.DEVNULL
+
+
+def test_ui_automator_client_isolates_stdin():
+    """Verify ui_automator_client helper commands isolate stdin."""
+    with patch("artemis.clients.ui_automator_client.subprocess.run") as mock_run:
+        mock_run.return_value = MagicMock(returncode=0, stdout="package:com.test\n", stderr="")
+        ui_automator_client._is_package_installed("dev-1", "com.test")
+        assert mock_run.called
+        assert mock_run.call_args.kwargs.get("stdin") == subprocess.DEVNULL
+
+    with patch("artemis.clients.ui_automator_client.subprocess.run") as mock_run:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        ui_automator_client._uninstall_package("dev-1", "com.test")
+        assert mock_run.called
+        assert mock_run.call_args.kwargs.get("stdin") == subprocess.DEVNULL
+
+
+def test_logger_header_does_not_pollute_stdout():
+    """Verify logger.header directs output to stderr and never pollutes sys.stdout."""
+    logger = get_logger("test_purity_logger")
+    captured_stdout = io.StringIO()
+    captured_stderr = io.StringIO()
+
+    orig_stdout = sys.stdout
+    orig_stderr = sys.stderr
+    try:
+        sys.stdout = captured_stdout
+        sys.stderr = captured_stderr
+        logger.header("IMPORTANT PROTOCOL BANNER")
+    finally:
+        sys.stdout = orig_stdout
+        sys.stderr = orig_stderr
+
+    assert captured_stdout.getvalue() == "", (
+        f"Detected stdout pollution from logger.header: {captured_stdout.getvalue()!r}. "
+        "In MCP stdio mode, stdout MUST be reserved exclusively for JSON-RPC messages!"
+    )
+    assert "IMPORTANT PROTOCOL BANNER" in captured_stderr.getvalue()