Support using MCP tools in research mode

- Server admin can add MCP servers via the admin panel
- Enabled MCP server tools are exposed to the research agent for use
- Use MCP library to standardize interactions with mcp servers
  - Support SSE or Stdio as transport to interact with mcp servers
  - Reuse session established to MCP servers across research iterations

pyproject.toml

@@ -93,6 +93,7 @@ dependencies = [
     "resend == 1.0.1",
     "email-validator == 2.2.0",
     "e2b-code-interpreter ~= 1.0.0",
+    "mcp >= 1.12.4",
 ]
 dynamic = ["version"]
 

src/khoj/database/adapters/__init__.py

@@ -49,6 +49,7 @@ from khoj.database.models import (
     GoogleUser,
     KhojApiUser,
     KhojUser,
+    McpServer,
     NotionConfig,
     PriceTier,
     ProcessLock,
@@ -2127,3 +2128,15 @@ class AutomationAdapters:
 
         automation.remove()
         return automation_metadata
+
+
+class McpServerAdapters:
+    @staticmethod
+    async def aget_all_mcp_servers() -> List[McpServer]:
+        """Asynchronously retrieve all McpServer objects from the database."""
+        servers: List[McpServer] = []
+        try:
+            servers = [server async for server in McpServer.objects.all()]
+        except Exception as e:
+            logger.error(f"Error retrieving MCP servers: {e}", exc_info=True)
+        return servers

src/khoj/database/admin.py

@@ -23,6 +23,7 @@ from khoj.database.models import (
     Entry,
     GithubConfig,
     KhojUser,
+    McpServer,
     NotionConfig,
     ProcessLock,
     RateLimitRecord,
@@ -183,6 +184,16 @@ admin.site.register(UserRequests, unfold_admin.ModelAdmin)
 admin.site.register(RateLimitRecord, unfold_admin.ModelAdmin)
 
 
+@admin.register(McpServer)
+class McpServerAdmin(unfold_admin.ModelAdmin):
+    list_display = (
+        "id",
+        "name",
+        "path",
+    )
+    search_fields = ("id", "name", "path")
+
+
 @admin.register(Agent)
 class AgentAdmin(unfold_admin.ModelAdmin):
     list_display = (

src/khoj/database/migrations/0096_mcpserver.py

@@ -0,0 +1,26 @@
+# Generated by Django 5.1.14 on 2025-11-13 20:58
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("database", "0095_alter_webscraper_type"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="McpServer",
+            fields=[
+                ("id", models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
+                ("created_at", models.DateTimeField(auto_now_add=True)),
+                ("updated_at", models.DateTimeField(auto_now=True)),
+                ("name", models.CharField(max_length=50, unique=True)),
+                ("path", models.CharField(max_length=200, unique=True)),
+                ("api_key", models.CharField(blank=True, max_length=4000, null=True)),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

src/khoj/database/models/__init__.py

@@ -806,3 +806,12 @@ class DataStore(DbBaseModel):
     value = models.JSONField(default=dict)
     private = models.BooleanField(default=False)
     owner = models.ForeignKey(KhojUser, on_delete=models.CASCADE, default=None, null=True, blank=True)
+
+
+class McpServer(DbBaseModel):
+    name = models.CharField(max_length=50, unique=True)
+    path = models.CharField(max_length=200, unique=True)
+    api_key = models.CharField(max_length=4000, blank=True, null=True)
+
+    def __str__(self):
+        return self.name

src/khoj/processor/tools/mcp.py

@@ -0,0 +1,124 @@
+import logging
+from contextlib import AsyncExitStack
+from typing import Optional
+
+from mcp import ClientSession, StdioServerParameters
+from mcp.client.sse import sse_client
+from mcp.client.stdio import stdio_client
+from mcp.types import AudioContent, ImageContent, TextContent
+
+logger = logging.getLogger(__name__)
+
+
+class MCPClient:
+    """
+    A client for interacting with MCP servers.
+    Establishes a session with the server and provides methods to get and run tools.
+    Supports both stdio and sse communication methods.
+    """
+
+    def __init__(self, name: str, path: str, api_key: Optional[str] = None):
+        self.name = name
+        self.path = path
+        self.api_key = api_key
+        self.session: Optional[ClientSession] = None
+        self.exit_stack = AsyncExitStack()
+
+    async def connect(self):
+        """
+        Connect to the MCP server based on the specified path.
+        Uses stdio for local scripts and SSE for remote servers.
+        """
+        if self.path.startswith("http://") or self.path.startswith("https://"):
+            # Path is a URL, so use SSE to connect to the server
+            await self._connect_to_sse_server()
+        else:
+            # Path is a script, so use stdio to connect to the server
+            await self._connect_to_stdio_server()
+
+    async def get_tools(self):
+        """
+        Retrieve the list of tools available on the MCP server.
+        """
+        # Ensure connection is established
+        if not self.session:
+            await self.connect()
+
+        tools_response = await self.session.list_tools()
+        return tools_response.tools
+
+    async def run_tool(self, tool_name: str, input_data: dict):
+        """
+        Run a specified tool on the MCP server with the given input data.
+        """
+        # Ensure connection is established
+        if not self.session:
+            await self.connect()
+
+        result = await self.session.call_tool(tool_name, input_data)
+
+        # Process result content based on its type
+        if len(result.content) > 0 and isinstance(result.content[0], TextContent):
+            return [item.text for item in result.content]
+        elif len(result.content) > 0 and isinstance(result.content[0], AudioContent):
+            return [{"data": item.data, "format": item.mimeType} for item in result.content]
+        elif len(result.content) > 0 and isinstance(result.content[0], ImageContent):
+            return [{"data": item.data, "format": item.mimeType} for item in result.content]
+        return result.content
+
+    async def _connect_to_sse_server(self):
+        """
+        Connect to the MCP server using Server-Sent Events (SSE).
+        """
+        self._streams_context = sse_client(url=self.path)
+        streams = await self._streams_context.__aenter__()
+
+        self._session_context = ClientSession(*streams)
+        self.session = await self._session_context.__aenter__()
+
+        # Initialize
+        await self.session.initialize()
+
+    async def _connect_to_stdio_server(self):
+        """
+        Connect to the MCP server using stdio communication.
+        """
+        is_python = False
+        is_javascript = False
+        command = None
+        args = [self.path]
+
+        # Determine if the server is a file path or npm package
+        if self.path.startswith("@") or "/" not in self.path:
+            # Assume it's an npm package
+            is_javascript = True
+            command = "npx"
+        else:
+            # It's a file path
+            is_python = self.path.endswith(".py")
+            is_javascript = self.path.endswith(".js")
+            if not (is_python or is_javascript):
+                raise ValueError("Server script must be a .py, .js file or npm package.")
+
+            command = "python" if is_python else "node"
+
+        server_params = StdioServerParameters(command=command, args=args, env=None)
+
+        logger.debug(f"Connecting to stdio MCP server with command: {command} and args: {args}")
+
+        # Start the server
+        stdio_transport = await self.exit_stack.enter_async_context(stdio_client(server_params))
+        self.stdio, self.writer = stdio_transport
+        self.session = await self.exit_stack.enter_async_context(ClientSession(self.stdio, self.writer))
+
+        await self.session.initialize()
+
+    async def close(self):
+        """
+        Close the MCP client session and clean up resources.
+        """
+        await self.exit_stack.aclose()
+        if hasattr(self, "_session_context") and self._session_context:
+            await self._session_context.__aexit__(None, None, None)
+        if hasattr(self, "_streams_context") and self._streams_context:
+            await self._streams_context.__aexit__(None, None, None)

src/khoj/routers/research.py

@@ -7,7 +7,7 @@ from typing import Callable, Dict, List, Optional
 
 import yaml
 
-from khoj.database.adapters import AgentAdapters, EntryAdapters
+from khoj.database.adapters import AgentAdapters, EntryAdapters, McpServerAdapters
 from khoj.database.models import Agent, ChatMessageModel, KhojUser
 from khoj.processor.conversation import prompts
 from khoj.processor.conversation.utils import (
@@ -19,6 +19,7 @@ from khoj.processor.conversation.utils import (
     load_complex_json,
 )
 from khoj.processor.operator import operate_environment
+from khoj.processor.tools.mcp import MCPClient
 from khoj.processor.tools.online_search import read_webpages_content, search_online
 from khoj.processor.tools.run_code import run_code
 from khoj.routers.helpers import (
@@ -61,6 +62,7 @@ async def apick_next_tool(
     max_document_searches: int = 7,
     max_online_searches: int = 3,
     max_webpages_to_read: int = 3,
+    mcp_clients: List[MCPClient] = [],
     send_status_func: Optional[Callable] = None,
     tracer: dict = {},
 ):
@@ -144,6 +146,23 @@ async def apick_next_tool(
                 )
             )
 
+    # Get MCP tools
+    for mcp_client in mcp_clients:
+        try:
+            mcp_tools = await mcp_client.get_tools()
+            for mcp_tool in mcp_tools:
+                qualified_tool_name = f"{mcp_client.name}/{mcp_tool.name}"
+                tool_options_str += f'- "{qualified_tool_name}": "{mcp_tool.description}"\n'
+                tools.append(
+                    ToolDefinition(
+                        name=qualified_tool_name,
+                        description=mcp_tool.description,
+                        schema=mcp_tool.inputSchema,
+                    )
+                )
+        except Exception as e:
+            logger.warning(f'Failed to get tools from MCP server "{mcp_client.name}", so skipping: {e}.')
+
     today = datetime.today()
     location_data = f"{location}" if location else "Unknown"
     agent_chat_model = AgentAdapters.get_agent_chat_model(agent, user) if agent else None
@@ -240,6 +259,10 @@ async def research(
     current_iteration = 0
     MAX_ITERATIONS = int(os.getenv("KHOJ_RESEARCH_ITERATIONS", 5))
 
+    # Construct MCP clients
+    mcp_servers = await McpServerAdapters.aget_all_mcp_servers()
+    mcp_clients = [MCPClient(server.name, server.path, server.api_key) for server in mcp_servers]
+
     # Incorporate previous partial research into current research chat history
     research_conversation_history = [chat for chat in deepcopy(conversation_history) if chat.message]
     if current_iteration := len(previous_iterations) > 0:
@@ -277,6 +300,7 @@ async def research(
         code_results: Dict = dict()
         document_results: List[Dict[str, str]] = []
         operator_results: OperatorRun = None
+        mcp_results: List = []
         this_iteration = ResearchIteration(query=query)
 
         async for result in apick_next_tool(
@@ -293,6 +317,7 @@ async def research(
             max_document_searches=max_document_searches,
             max_online_searches=max_online_searches,
             max_webpages_to_read=max_webpages_to_read,
+            mcp_clients=mcp_clients,
             send_status_func=send_status_func,
             tracer=tracer,
         ):
@@ -540,13 +565,41 @@ async def research(
                 this_iteration.warning = f"Error searching with regex: {e}"
                 logger.error(this_iteration.warning, exc_info=True)
 
+        elif "/" in this_iteration.query.name:
+            try:
+                # Identify MCP client to use
+                server_name, tool_name = this_iteration.query.name.split("/", 1)
+                mcp_client = next((client for client in mcp_clients if client.name == server_name), None)
+                if not mcp_client:
+                    raise ValueError(f"Could not find MCP server with name {server_name}")
+
+                # Invoke tool on the identified MCP server
+                mcp_results = await mcp_client.run_tool(tool_name, this_iteration.query.args)
+
+                # Record tool result in context
+                if this_iteration.context is None:
+                    this_iteration.context = []
+                this_iteration.context += mcp_results
+                async for result in send_status_func(f"**Used MCP Tool**: {tool_name} on {mcp_client.name}"):
+                    yield result
+            except Exception as e:
+                this_iteration.warning = f"Error using MCP tool: {e}"
+                logger.error(this_iteration.warning, exc_info=True)
+
         else:
             # No valid tools. This is our exit condition.
             current_iteration = MAX_ITERATIONS
 
         current_iteration += 1
 
-        if document_results or online_results or code_results or operator_results or this_iteration.warning:
+        if (
+            document_results
+            or online_results
+            or code_results
+            or operator_results
+            or mcp_results
+            or this_iteration.warning
+        ):
             results_data = f"\n<iteration_{current_iteration}_results>"
             if document_results:
                 results_data += f"\n<document_references>\n{yaml.dump(document_results, allow_unicode=True, sort_keys=False, default_flow_style=False)}\n</document_references>"
@@ -558,6 +611,8 @@ async def research(
                 results_data += (
                     f"\n<browser_operator_results>\n{operator_results.response}\n</browser_operator_results>"
                 )
+            if mcp_results:
+                results_data += f"\n<mcp_tool_results>\n{yaml.dump(mcp_results, allow_unicode=True, sort_keys=False, default_flow_style=False)}\n</mcp_tool_results>"
             if this_iteration.warning:
                 results_data += f"\n<warning>\n{this_iteration.warning}\n</warning>"
             results_data += f"\n</iteration_{current_iteration}_results>"
@@ -568,3 +623,7 @@ async def research(
         this_iteration.summarizedResult = this_iteration.summarizedResult or "Failed to get results."
         previous_iterations.append(this_iteration)
         yield this_iteration
+
+    # Close MCP client connections
+    for mcp_client in mcp_clients:
+        await mcp_client.close()

uv.lock

@@ -1162,6 +1162,33 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/71/92/5e77f98553e9e75130c78900d000368476aed74276eb8ae8796f65f00918/jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942", size = 7595, upload-time = "2024-06-10T19:24:40.698Z" },
 ]
 
+[[package]]
+name = "jsonschema"
+version = "4.25.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "attrs" },
+    { name = "jsonschema-specifications" },
+    { name = "referencing" },
+    { name = "rpds-py" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/74/69/f7185de793a29082a9f3c7728268ffb31cb5095131a9c139a74078e27336/jsonschema-4.25.1.tar.gz", hash = "sha256:e4a9655ce0da0c0b67a085847e00a3a51449e1157f4f75e9fb5aa545e122eb85", size = 357342, upload-time = "2025-08-18T17:03:50.038Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/bf/9c/8c95d856233c1f82500c2450b8c68576b4cf1c871db3afac5c34ff84e6fd/jsonschema-4.25.1-py3-none-any.whl", hash = "sha256:3fba0169e345c7175110351d456342c364814cfcf3b964ba4587f22915230a63", size = 90040, upload-time = "2025-08-18T17:03:48.373Z" },
+]
+
+[[package]]
+name = "jsonschema-specifications"
+version = "2025.9.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "referencing" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/19/74/a633ee74eb36c44aa6d1095e7cc5569bebf04342ee146178e2d36600708b/jsonschema_specifications-2025.9.1.tar.gz", hash = "sha256:b540987f239e745613c7a9176f3edb72b832a4ac465cf02712288397832b5e8d", size = 32855, upload-time = "2025-09-08T01:34:59.186Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/41/45/1a4ed80516f02155c51f51e8cedb3c1902296743db0bbc66608a0db2814f/jsonschema_specifications-2025.9.1-py3-none-any.whl", hash = "sha256:98802fee3a11ee76ecaca44429fda8a41bff98b00a0f2838151b113f210cc6fe", size = 18437, upload-time = "2025-09-08T01:34:57.871Z" },
+]
+
 [[package]]
 name = "khoj"
 source = { editable = "." }
@@ -1197,6 +1224,7 @@ dependencies = [
     { name = "magika" },
     { name = "markdown-it-py" },
     { name = "markdownify" },
+    { name = "mcp" },
     { name = "openai" },
     { name = "openai-whisper" },
     { name = "pgvector" },
@@ -1296,6 +1324,7 @@ requires-dist = [
     { name = "magika", specifier = "~=0.5.1" },
     { name = "markdown-it-py", specifier = "~=3.0.0" },
     { name = "markdownify", specifier = "~=0.11.6" },
+    { name = "mcp", specifier = ">=1.12.4" },
     { name = "mypy", marker = "extra == 'dev'", specifier = ">=1.0.1" },
     { name = "openai", specifier = ">=2.0.0,<3.0.0" },
     { name = "openai-whisper", specifier = ">=20231117" },
@@ -1577,6 +1606,28 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/34/75/51952c7b2d3873b44a0028b1bd26a25078c18f92f256608e8d1dc61b39fd/marshmallow-3.26.1-py3-none-any.whl", hash = "sha256:3350409f20a70a7e4e11a27661187b77cdcaeb20abca41c1454fe33636bea09c", size = 50878, upload-time = "2025-02-03T15:32:22.295Z" },
 ]
 
+[[package]]
+name = "mcp"
+version = "1.12.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "anyio" },
+    { name = "httpx" },
+    { name = "httpx-sse" },
+    { name = "jsonschema" },
+    { name = "pydantic" },
+    { name = "pydantic-settings" },
+    { name = "python-multipart" },
+    { name = "pywin32", marker = "sys_platform == 'win32'" },
+    { name = "sse-starlette" },
+    { name = "starlette" },
+    { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/31/88/f6cb7e7c260cd4b4ce375f2b1614b33ce401f63af0f49f7141a2e9bf0a45/mcp-1.12.4.tar.gz", hash = "sha256:0765585e9a3a5916a3c3ab8659330e493adc7bd8b2ca6120c2d7a0c43e034ca5", size = 431148, upload-time = "2025-08-07T20:31:18.082Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ad/68/316cbc54b7163fa22571dcf42c9cc46562aae0a021b974e0a8141e897200/mcp-1.12.4-py3-none-any.whl", hash = "sha256:7aa884648969fab8e78b89399d59a683202972e12e6bc9a1c88ce7eda7743789", size = 160145, upload-time = "2025-08-07T20:31:15.69Z" },
+]
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -2780,6 +2831,22 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/11/c3/005fcca25ce078d2cc29fd559379817424e94885510568bc1bc53d7d5846/pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725", size = 508002, upload-time = "2024-09-11T02:24:45.8Z" },
 ]
 
+[[package]]
+name = "pywin32"
+version = "311"
+source = { registry = "https://pypi.org/simple" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/7b/40/44efbb0dfbd33aca6a6483191dae0716070ed99e2ecb0c53683f400a0b4f/pywin32-311-cp310-cp310-win32.whl", hash = "sha256:d03ff496d2a0cd4a5893504789d4a15399133fe82517455e78bad62efbb7f0a3", size = 8760432, upload-time = "2025-07-14T20:13:05.9Z" },
+    { url = "https://files.pythonhosted.org/packages/5e/bf/360243b1e953bd254a82f12653974be395ba880e7ec23e3731d9f73921cc/pywin32-311-cp310-cp310-win_amd64.whl", hash = "sha256:797c2772017851984b97180b0bebe4b620bb86328e8a884bb626156295a63b3b", size = 9590103, upload-time = "2025-07-14T20:13:07.698Z" },
+    { url = "https://files.pythonhosted.org/packages/57/38/d290720e6f138086fb3d5ffe0b6caa019a791dd57866940c82e4eeaf2012/pywin32-311-cp310-cp310-win_arm64.whl", hash = "sha256:0502d1facf1fed4839a9a51ccbcc63d952cf318f78ffc00a7e78528ac27d7a2b", size = 8778557, upload-time = "2025-07-14T20:13:11.11Z" },
+    { url = "https://files.pythonhosted.org/packages/7c/af/449a6a91e5d6db51420875c54f6aff7c97a86a3b13a0b4f1a5c13b988de3/pywin32-311-cp311-cp311-win32.whl", hash = "sha256:184eb5e436dea364dcd3d2316d577d625c0351bf237c4e9a5fabbcfa5a58b151", size = 8697031, upload-time = "2025-07-14T20:13:13.266Z" },
+    { url = "https://files.pythonhosted.org/packages/51/8f/9bb81dd5bb77d22243d33c8397f09377056d5c687aa6d4042bea7fbf8364/pywin32-311-cp311-cp311-win_amd64.whl", hash = "sha256:3ce80b34b22b17ccbd937a6e78e7225d80c52f5ab9940fe0506a1a16f3dab503", size = 9508308, upload-time = "2025-07-14T20:13:15.147Z" },
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