ClickHouse

ClickHouse MCP Server

An MCP server for ClickHouse.

The server implements MCP 2026-07-28 and supports legacy initialize handshakes from 2024-11-05 through 2025-11-25. Modern clients use sessionless requests and server/discover. Existing clients can continue to negotiate the legacy protocol.

[!NOTE] HTTP requests without MCP-Protocol-Version are routed through legacy handling so clients from before 2025-06-18 can continue to connect. MCP 2026-07-28 permits this behavior on servers that support those clients. Modern clients should send the header on every POST request.

Features

ClickHouse Tools

ClickHouse tool responses are JSON-encoded strings. Integers outside [-9007199254740991, 9007199254740991] are returned as decimal strings to preserve exact values in JavaScript clients. This applies to query rows and integer table metadata. Safe-range integers and booleans keep their JSON types.

• run_query

  • Execute SQL queries on your ClickHouse cluster.
  • Input: query (string): The SQL query to execute.
  • Optional input: params (object): Named values for ClickHouse {name:Type} placeholders. See Query parameters.
  • Queries run in read-only mode by default (CLICKHOUSE_ALLOW_WRITE_ACCESS=false), but writes can be enabled explicitly if needed.
  • DESCRIBE (<query>) and EXPLAIN ESTIMATE <query> run here too and are optional ways to inspect a query's result schema or its estimated reads. See Checking a query before running it.

• list_databases

  • List all databases on your ClickHouse cluster.

• list_tables

  • List tables in a database with pagination.
  • Required input: database (string).
  • Optional inputs:
    • like / not_like (string): Apply LIKE or NOT LIKE filters to table names.
    • page_token (string): Single-use token returned by a previous call. It is retained for up to one hour.
    • page_size (int, default 50): Number of tables returned per page; must be greater than 0.
    • include_detailed_columns (bool, default true): When false, omits column metadata for lighter responses while keeping the full create_table_query.
  • Response shape:
    • tables: Array of table objects for the current page.
    • next_page_token: Pass this single-use value back before it expires to fetch the next page, or null when there are no more tables.
    • total_tables: Total count of tables that match the supplied filters.

Agents Schema discovery

The server instructions suggest reading Agents Schema's canonical AGENTS.ROOT through run_query when list_databases reveals an AGENTS database, before writing analytical SQL. This is guidance for the agent: no metadata is fetched automatically, tool results are unchanged, and existing ClickHouse permissions still apply. If AGENTS.ROOT is missing or inaccessible, normal discovery and queries remain available.

Query parameters

Pass values separately from SQL through the optional params object:

{
  "query": "SELECT {id:UInt32} AS id, {name:String} AS name",
  "params": {"id": 13, "name": "O'Reilly"}
}

Use ClickHouse's {name:Type} placeholders without quoting them. Keep the opening brace, name, and colon adjacent, as in {id:UInt32}. Spaces after the colon and within the type are supported, as in {id: UInt32} and {amount:Decimal(18, 4)}. For compatibility across supported driver versions, start names with a letter or underscore and use only letters, digits, and underscores. Python-style %s or %(name)s formatting and the driver's $name$ raw binary parameters are not supported. Calls with only query still work. Omitting params, passing null, or passing an empty object leaves the query unbound.

Parameter values can be JSON strings, numbers, booleans, null, or arrays, provided they match the declared ClickHouse type:

• Use null with a Nullable(...) type.
• Pass exact integers outside JavaScript's safe range as decimal strings, for example "18446744073709551615" with {id:UInt64}. Dates, timestamps, and exact decimals can also be passed as strings with the corresponding ClickHouse type.
• Bind vectors as one array, for example {vector:Array(Float32)} with "params": {"vector": [0.25, 0.5, 0.75]}.
• Nulls inside arrays depend on the installed driver. They work with clickhouse-connect 1.8.0 but fail with the supported minimum 1.0.0.
• JSON lists and objects cannot bind to ClickHouse Tuple and Map types.

Missing values and incompatible types return query errors. With non-empty params, a query carrying many unterminated {name: placeholder starts is rejected, including placeholder-like text in comments or string literals. Parameterized queries use the same write protection, timeouts, cancellation, and JSON result encoding as other queries.

Parameter values stay out of the MCP server's normal SQL log messages, but remain in MCP tool arguments and may appear in backend errors. ClickHouse 26.3.20.7 substitutes values into the query text in system.query_log, system.processes, and system.text_log. Parameter binding is not a privacy feature and does not reduce the number of vector values sent in a tool call.

Checking a query before running it

run_query also runs DESCRIBE and EXPLAIN ESTIMATE. Both are optional checks: reach for DESCRIBE when you need a query's output columns and types, and for EXPLAIN ESTIMATE before a SELECT that could be expensive.

DESCRIBE (<query>) inspects the result schema and returns the same output-column metadata as DESCRIBE TABLE:

DESCRIBE (SELECT user, sum(amt) FROM events WHERE ts > now() - INTERVAL 30 DAY GROUP BY user)

user      String
sum(amt)  Decimal(38, 2)

ClickHouse has to analyze the query to answer, so analysis errors surface here, with ClickHouse's own message, instead of part way through execution:

DESCRIBE (SELECT usr FROM events)  -> Code: 47. Unknown expression identifier `usr` ... Maybe you meant: ['user']
DESCRIBE (SELECT * FROM nosuch)    -> Code: 60. Unknown table expression identifier 'nosuch'

A query that describes cleanly can still fail when it runs, on a memory limit or a remote server error, and it says nothing about cost.

EXPLAIN ESTIMATE <query> returns the parts, rows and marks the query would read, one row per table, which is what separates a primary key lookup from a full scan:

EXPLAIN ESTIMATE SELECT count() FROM events WHERE id = 42

database  table   parts  rows   marks
default   events  1      8192   1

Those are estimated reads from MergeTree family tables, after primary key and partition pruning. They are not run time and not result size, and other table engines are not covered.

Neither statement runs the query body, but analysis is not always free: DESCRIBE (SELECT (SELECT sleep(1))) executes the scalar subquery while analyzing. Both are read-only and work under the default CLICKHOUSE_ALLOW_WRITE_ACCESS=false. See the ClickHouse documentation for EXPLAIN ESTIMATE and DESCRIBE.

chDB Tools

• run_chdb_select_query
  • Execute SQL queries using chDB's embedded ClickHouse engine.
  • Input: query (string): The SQL query to execute.
  • Integers outside [-9007199254740991, 9007199254740991] are returned as decimal strings.
  • Query data directly from various sources (files, URLs, databases) without ETL processes.
  • Requires the optional chdb extra: pip install 'mcp-clickhouse[chdb]'

Health Check Endpoint

When running with HTTP or SSE transport, a health check endpoint is available at /health. This endpoint:

• Returns 200 OK (body: OK) if the server is healthy and can connect to ClickHouse
• Returns 503 Service Unavailable with a generic error message if the server cannot connect to ClickHouse
• Returns 503 if a ClickHouse probe does not finish within two seconds. Concurrent requests share one in-flight probe
• Reuses a completed probe result for one second, so probes that arrive in quick succession do not each connect to ClickHouse. A failure or a recovery can therefore be reported up to a second late

GET and HEAD requests to the endpoint are intentionally unauthenticated and exempt from Host and Origin validation so orchestrator probes (e.g. Kubernetes liveness/readiness, load balancers) can use runtime-assigned pod or target IPs without extra configuration. /health is reserved and cannot be used as the MCP transport path. The response body is deliberately minimal to avoid leaking backend version strings or error details; debug failures via the server logs.

Example:

curl http://localhost:8000/health
# Response: OK

Security

Authentication for HTTP/SSE Transports

When using HTTP or SSE transport, authentication is required by default. The stdio transport (default) does not require authentication as it only communicates via standard input/output.

Three authentication modes are supported. Pick one:

Startup fails if none of these are configured for HTTP/SSE transports.

Setting Up Authentication

1. Generate a secure token (can be any random string):

   # Using uuidgen (macOS/Linux)
   uuidgen
   
   # Using openssl
   openssl rand -hex 32
   

2. Configure the server with the token:

   export CLICKHOUSE_MCP_AUTH_TOKEN="your-generated-token"
   

3. Configure your MCP client to include the token in requests:

   For Claude Desktop with HTTP/SSE transport:

   {
     "mcpServers": {
       "mcp-clickhouse": {
         "url": "http://127.0.0.1:8000",
         "headers": {
           "Authorization": "Bearer your-generated-token"
         }
       }
     }
   }
   

   Note: the /health endpoint is intentionally unauthenticated (see Health Check Endpoint above). To verify that bearer-token auth is actually rejecting unauthenticated requests, hit the MCP endpoint itself e.g. with the MCP Inspector, or by POSTing a JSON-RPC request to /mcp with and without the Authorization header and confirming the unauthenticated call returns 401.

OAuth / OIDC via FastMCP

For production deployments with identity providers (Azure Entra, Google, GitHub, WorkOS, etc.), delegate authentication to FastMCP's built-in auth providers instead of using a static token. Set FASTMCP_SERVER_AUTH to the full class path of a FastMCP auth provider, along with the provider-specific FASTMCP_SERVER_AUTH_* variables, and leave CLICKHOUSE_MCP_AUTH_TOKEN unset.

Example (Azure Entra):

export FASTMCP_SERVER_AUTH=fastmcp.server.auth.providers.azure.AzureProvider
export FASTMCP_SERVER_AUTH_AZURE_TENANT_ID="<tenant-id>"
export FASTMCP_SERVER_AUTH_AZURE_CLIENT_ID="<client-id>"
export FASTMCP_SERVER_AUTH_AZURE_CLIENT_SECRET="<client-secret>"
export FASTMCP_SERVER_AUTH_AZURE_BASE_URL="https://mcp.example.com"
export FASTMCP_SERVER_AUTH_AZURE_REQUIRED_SCOPES="read access_as_user"

mcp-clickhouse retains these FastMCP 2.14.7 environment prefixes for the FastMCP 4.0.0 built-in providers:

Append the uppercase provider field name to the prefix. See the FastMCP docs for each provider's configuration requirements.

Auth values set directly in the process environment take precedence case-insensitively. The default .env load starts at the installed mcp_clickhouse package directory, resolves symlinks first, and walks upward to the filesystem root. It loads the first .env it finds and loads nothing if there is none. It never reads the working directory, regardless of how the server is launched. A source checkout normally finds the repository root .env. That file may also provide FASTMCP_SERVER_AUTH and its provider fields. Its values take precedence over the explicit or compatibility auth file. For FastMCP 2 compatibility, mcp-clickhouse reads missing provider fields from .env in the working directory, but that compatibility fallback cannot select FASTMCP_SERVER_AUTH. A process-set FASTMCP_ENV_FILE replaces that compatibility fallback and may provide both the selector and provider fields. Set it before startup. The mcp-clickhouse compatibility loader reads only FASTMCP_SERVER_AUTH and FASTMCP_SERVER_AUTH_* from that file, so it cannot inject CLICKHOUSE_* settings. FastMCP 4 may use the same file for its own broader settings. A custom provider receives no environment-derived constructor arguments and must support no-argument construction.

Treat both discovered and working-directory .env files as trusted authentication configuration. Anyone who can create or write a .env in any directory from the package directory up to the filesystem root can control which file is discovered, select the provider, and set its fields. Anyone who can write the working-directory file controls every provider field absent from the process and discovered configuration, including signing keys, issuers and endpoints, and client secrets. A process-set FASTMCP_ENV_FILE that points to an operator-owned file disables the working-directory fallback.

FastMCP 4 changed the default OAuth proxy client store. Deployments that relied on FastMCP 2's default OAuth proxy storage must have clients register and authorize again. Compatible custom storage, static bearer tokens, and JWT verification are unaffected.

Development Mode (Disabling Authentication)

For local development and testing only, you can disable authentication by setting:

export CLICKHOUSE_MCP_AUTH_DISABLED=true
export CLICKHOUSE_MCP_ALLOWED_HOSTS=127.0.0.1:8000,localhost:8000

WARNING: Only use this for local development. Do not disable authentication when the server is exposed to any network.

Configuration

This MCP server supports both ClickHouse and chDB. You can enable either or both depending on your needs. Python 3.10 through 3.14 are supported. Python 3.12 is recommended for local launches.

1. Open the Claude Desktop configuration file located at:

   • On macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • On Windows: %APPDATA%/Claude/claude_desktop_config.json

2. Add the following:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp-clickhouse",
        "--python",
        "3.12",
        "mcp-clickhouse"
      ],
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_PORT": "<clickhouse-port>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "CLICKHOUSE_ROLE": "<clickhouse-role>",
        "CLICKHOUSE_SECURE": "true",
        "CLICKHOUSE_VERIFY": "true",
        "CLICKHOUSE_CONNECT_TIMEOUT": "30"
      }
    }
  }
}

Update the environment variables to point to your own ClickHouse service.

Or, if you'd like to try it out with the ClickHouse SQL Playground, you can use the following config:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp-clickhouse",
        "--python",
        "3.12",
        "mcp-clickhouse"
      ],
      "env": {
        "CLICKHOUSE_HOST": "sql-clickhouse.clickhouse.com",
        "CLICKHOUSE_PORT": "8443",
        "CLICKHOUSE_USER": "demo",
        "CLICKHOUSE_PASSWORD": "",
        "CLICKHOUSE_SECURE": "true",
        "CLICKHOUSE_VERIFY": "true",
        "CLICKHOUSE_CONNECT_TIMEOUT": "30"
      }
    }
  }
}

For chDB (embedded ClickHouse engine), add the following configuration:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp-clickhouse[chdb]",
        "--python",
        "3.12",
        "mcp-clickhouse"
      ],
      "env": {
        "CHDB_ENABLED": "true",
        "CLICKHOUSE_ENABLED": "false",
        "CHDB_DATA_PATH": "/path/to/chdb/data"
      }
    }
  }
}

You can also enable both ClickHouse and chDB simultaneously:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp-clickhouse[chdb]",
        "--python",
        "3.12",
        "mcp-clickhouse"
      ],
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_PORT": "<clickhouse-port>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "CLICKHOUSE_SECURE": "true",
        "CLICKHOUSE_VERIFY": "true",
        "CLICKHOUSE_CONNECT_TIMEOUT": "30",
        "CHDB_ENABLED": "true",
        "CHDB_DATA_PATH": "/path/to/chdb/data"
      }
    }
  }
}

3. Locate the command entry for uv and replace it with the absolute path to the uv executable. This ensures that the correct version of uv is used when starting the server. On a mac, you can find this path using which uv.

4. Restart Claude Desktop to apply the changes.

Optional Write Access

By default, this MCP enforces read-only queries so that accidental mutations cannot happen during exploration. To allow DDL or INSERT statements, set the CLICKHOUSE_ALLOW_WRITE_ACCESS environment variable to true. The server keeps enforcing read-only mode if the ClickHouse instance itself disallows writes.

Read-only mode still permits the ClickHouse user to cancel its own queries, including queries from other connections using the same user. Use a dedicated ClickHouse user even in read-only mode. Use separate ClickHouse users for workloads that must not cancel each other's queries.

Destructive Operation Protection

Even when write access is enabled (CLICKHOUSE_ALLOW_WRITE_ACCESS=true), destructive operations require an additional opt-in flag for safety. The check covers any DROP statement (including the ALTER TABLE ... DROP PARTITION / DROP PART / DROP COLUMN clauses), any TRUNCATE, DELETE and UPDATE (both the lightweight statements and the ALTER TABLE ... DELETE / ALTER TABLE ... UPDATE mutations), REPLACE TABLE, CREATE OR REPLACE, ALTER TABLE ... REPLACE PARTITION, ALTER TABLE ... CLEAR COLUMN / CLEAR INDEX / CLEAR PROJECTION, and DETACH ... PERMANENTLY. Keywords inside string literals, quoted identifiers, SQL comments, and {name:Type} parameter names are ignored, so they neither trigger the check nor hide a statement from it.

This check runs in the MCP server and is a best-effort guard against accidents. It is not a security boundary. The security boundary is the ClickHouse user's grants. Read-only mode (the default) is enforced server-side via readonly=1. The destructive-operation gate is not server-enforced.

For write mode, give the MCP server a dedicated ClickHouse user with only the privileges it needs:

CREATE USER mcp_agent IDENTIFIED BY '...';
GRANT SELECT, INSERT, CREATE TABLE, ALTER ADD COLUMN ON mydb.* TO mcp_agent;

Data-changing operations that require privileges outside these grants fail server-side with ACCESS_DENIED, regardless of MCP flags. The server settings max_table_size_to_drop and max_partition_size_to_drop can also cap blast radius if pinned with settings constraints.

To enable destructive operations, set both flags:

"env": {
  "CLICKHOUSE_ALLOW_WRITE_ACCESS": "true",
  "CLICKHOUSE_ALLOW_DROP": "true"
}

This two-tier approach makes accidental deletion difficult:

• Write operations (INSERT, CREATE, ALTER ADD COLUMN) require CLICKHOUSE_ALLOW_WRITE_ACCESS=true
• Destructive operations (DROP, TRUNCATE, DELETE, UPDATE, and the rest of the list above) additionally require CLICKHOUSE_ALLOW_DROP=true

Running Without uv (Using System Python)

If you prefer to use the system Python installation instead of uv, you can install the package from PyPI and run it directly:

1. Install the package using pip:

   python3 -m pip install mcp-clickhouse
   

   To install chDB support as well:

   python3 -m pip install 'mcp-clickhouse[chdb]'
   

   To upgrade to the latest version:

   python3 -m pip install --upgrade mcp-clickhouse
   

2. Update your Claude Desktop configuration to use Python directly:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "python3",
      "args": [
        "-m",
        "mcp_clickhouse.main"
      ],
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_PORT": "<clickhouse-port>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "CLICKHOUSE_SECURE": "true",
        "CLICKHOUSE_VERIFY": "true",
        "CLICKHOUSE_CONNECT_TIMEOUT": "30"
      }
    }
  }
}

Alternatively, you can use the installed script directly:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "mcp-clickhouse",
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_PORT": "<clickhouse-port>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "CLICKHOUSE_SECURE": "true",
        "CLICKHOUSE_VERIFY": "true",
        "CLICKHOUSE_CONNECT_TIMEOUT": "30"
      }
    }
  }
}

Note: Make sure to use the full path to the Python executable or the mcp-clickhouse script if they are not in your system PATH. You can find the paths using:

• which python3 for the Python executable
• which mcp-clickhouse for the installed script

Custom Middleware

You can add custom middleware to the MCP server without modifying the source code. FastMCP provides a middleware system that allows you to intercept and process MCP protocol messages (tool calls, resource reads, prompts, etc.).

How to Use

1. Create a Python module with middleware classes extending Middleware and a setup_middleware(mcp) function:

# my_middleware.py
import logging
from fastmcp.server.middleware import Middleware, MiddlewareContext, CallNext

logger = logging.getLogger("my-middleware")

class LoggingMiddleware(Middleware):
    """Log all tool calls."""
    
    async def on_call_tool(self, context: MiddlewareContext, call_next: CallNext):
        tool_name = context.message.name if hasattr(context.message, 'name') else 'unknown'
        logger.info(f"Calling tool: {tool_name}")
        result = await call_next(context)
        logger.info(f"Tool {tool_name} completed")
        return result

def setup_middleware(mcp):
    """Register middleware with the MCP server."""
    mcp.add_middleware(LoggingMiddleware())

2. Set the MCP_MIDDLEWARE_MODULE environment variable to the module name (without .py extension):

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": ["run", "--with", "mcp-clickhouse", "--python", "3.12", "mcp-clickhouse"],
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "MCP_MIDDLEWARE_MODULE": "my_middleware"
      }
    }
  }
}

3. Ensure your middleware module is in Python's import path (e.g., in the same directory where the MCP server runs, or installed as a package).

Example Middleware

An example middleware module is provided in example_middleware.py showing common patterns:

• Logging all MCP requests
• Logging tool calls specifically
• Measuring request processing time

To use the example:

"env": {
  "MCP_MIDDLEWARE_MODULE": "example_middleware"
}

Middleware Capabilities

The Middleware base class provides hooks for different MCP operations:

• on_message(context, call_next) - Called for all messages
• on_request(context, call_next) - Called for all requests
• on_notification(context, call_next) - Called for all notifications
• on_call_tool(context, call_next) - Called when a tool is executed
• on_read_resource(context, call_next) - Called when a resource is read
• on_get_prompt(context, call_next) - Called when a prompt is retrieved
• on_list_tools(context, call_next) - Called when listing tools
• on_list_resources(context, call_next) - Called when listing resources
• on_list_resource_templates(context, call_next) - Called when listing resource templates
• on_list_prompts(context, call_next) - Called when listing prompts

Each hook receives a MiddlewareContext object containing the message and metadata, and a call_next function to continue the pipeline.

Dynamic Client Configuration via Context State

Middleware can override ClickHouse client configuration on a per-request basis using the CLIENT_CONFIG_OVERRIDES_KEY context state key. The server merges these overrides with the base configuration from environment variables.

from fastmcp.server.dependencies import get_context
from fastmcp.server.middleware import CallNext, Middleware, MiddlewareContext
from mcp_clickhouse.mcp_server import CLIENT_CONFIG_OVERRIDES_KEY

class ClientConfigMiddleware(Middleware):
    async def on_call_tool(self, context: MiddlewareContext, call_next: CallNext):
        ctx = get_context()
        await ctx.set_state(
            CLIENT_CONFIG_OVERRIDES_KEY,
            {
                "connect_timeout": 60,
                "send_receive_timeout": 120,
            },
            serializable=False,
        )
        return await call_next(context)

This enables advanced use cases like dynamic timeout adjustments, tenant-specific routing, or per-user connection settings.

The state value must be a dictionary. Nested settings and generic_args values must be mappings and are merged with the base configuration. Invalid values fail the tool call before a ClickHouse client is created. CLICKHOUSE_ROLE remains active unless the override explicitly supplies settings.role. Top-level role and ch_role keys, plus the same keys under generic_args, are rejected.

Set verify, ca_cert, client_cert, client_cert_key, tls_mode, server_host_name, and pool_mgr only as top-level overrides. They cannot be nested under generic_args. A custom pool_mgr cannot be combined with managed CA or client certificate settings. DSN query parameters cannot set these keys, and a DSN cannot select the chdb backend. Use explicit top-level host, port, username, password, database, and secure overrides to change the connection. A forwarded DSN does not replace populated base connection fields or select TLS. It can fill empty fields and supply supported query parameters such as query_limit. secure and verify overrides accept booleans or the strings true and false. verify also accepts proxy, which behaves as tls_mode: proxy when tls_mode is unset and therefore uses Basic authentication with the environment password. A secure override selects the matching https or http interface and does not change the port. An explicit interface override must be http or https and agree with secure. After merging overrides, default and mutual client certificate modes omit the password. proxy and strict modes use Basic authentication with the environment password unless the override supplies its own credentials.

Treat these overrides as trusted middleware input. Middleware must authenticate and authorize request-derived values before setting them. Use serializable=False so FastMCP keeps the value in request-local state. The default serializable=True stores session state and is rejected by the server. The server snapshots the value before dispatching blocking database work. Do not store tenant data in session-scoped Context state. A rejected session-scoped override remains attached to a legacy MCP session and causes later tool calls in that session to fail until the client reconnects. A per-request ClickHouse role is connection configuration, not a tenant authorization boundary. Enforce tenant isolation with ClickHouse users, roles, and grants.

Development

1. In test-services directory run docker compose up -d to start the ClickHouse cluster.

2. Add the following variables to a .env file in the root of the repository.

Note: The use of the default user in this context is intended solely for local development purposes.

CLICKHOUSE_HOST=localhost
CLICKHOUSE_PORT=8123
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=clickhouse

3. Run uv sync to install the dependencies. To install uv follow the instructions here. Then do source .venv/bin/activate.

4. For easy testing with the MCP Inspector, run uv run fastmcp dev inspector mcp_clickhouse/mcp_server.py:mcp to start the MCP server.

5. To test with HTTP transport and the health check endpoint:

   # For development, disable authentication
   CLICKHOUSE_MCP_SERVER_TRANSPORT=http CLICKHOUSE_MCP_AUTH_DISABLED=true CLICKHOUSE_MCP_ALLOWED_HOSTS=127.0.0.1:8000,localhost:8000 python -m mcp_clickhouse.main
   
   # Or with authentication (generate a token first)
   CLICKHOUSE_MCP_SERVER_TRANSPORT=http CLICKHOUSE_MCP_AUTH_TOKEN="your-token" python -m mcp_clickhouse.main
   
   # Then in another terminal:
   curl http://localhost:8000/health
   

Code layout

The package uses a flat module layout. Start with mcp_server.py for server assembly and registration, then follow the implementation into its owning module.

Each server assembly owns its worker pools, client cache, active queries, pagination cache, health state, and chDB backend. Worker and client cleanup runs at process exit. Package imports initialize the default server, including when first importing an extracted module.

In tests, patch the module or owner instance where the code reads a dependency. For example, patch mcp_clickhouse.clients.clickhouse_connect.get_client for client creation. Compatibility imports in mcp_server.py can be separate bindings from the ones an implementation uses.

Environment Variables

Configuration is split into independent groups. Mixing them up is a common cause of hard-to-debug connection failures:

[!IMPORTANT] CLICKHOUSE_SECURE, CLICKHOUSE_VERIFY, CLICKHOUSE_CA_CERT, CLICKHOUSE_CLIENT_CERT, CLICKHOUSE_CLIENT_CERT_KEY, CLICKHOUSE_TLS_MODE, and CLICKHOUSE_PORT apply to the outbound ClickHouse database connection only. They do not configure TLS, client certificates, ports, or authentication for the inbound MCP HTTP/SSE endpoint.

Example: if the MCP server runs in Kubernetes behind an ingress that terminates TLS, that is an MCP transport concern. Keep CLICKHOUSE_SECURE aligned with how the pod reaches ClickHouse itself (HTTPS → true, plain HTTP → false). Setting CLICKHOUSE_SECURE=false because the MCP server is behind an ingress will make the server dial ClickHouse over HTTP—often against an HTTPS-only port—and produce opaque HTTP/TLS errors in the server logs.

ClickHouse database connection

These variables configure the clickhouse-connect HTTP client and the behavior of ClickHouse-backed tools such as run_query, list_databases, and list_tables. mcp-clickhouse requires clickhouse-connect 1.x, starting with 1.0.0.

Required Variables

• CLICKHOUSE_HOST: The hostname of your ClickHouse server (database endpoint, not the MCP server bind address)
• CLICKHOUSE_USER: The username for ClickHouse authentication
• CLICKHOUSE_PASSWORD: The password for ClickHouse authentication
  • Required unless CLICKHOUSE_CLIENT_CERT uses the default or "mutual" TLS mode
  • In default or "mutual" mode, certificate authentication is used and the password is not sent

[!CAUTION] It is important to treat your MCP database user as you would any external client connecting to your database, granting only the minimum necessary privileges required for its operation. The use of default or administrative users should be strictly avoided at all times.

Optional Variables

• CLICKHOUSE_PORT: HTTP interface port of your ClickHouse server
  • Default: 8443 if CLICKHOUSE_SECURE=true, 8123 if CLICKHOUSE_SECURE=false
  • Usually doesn't need to be set unless using a non-standard port
  • Must be an HTTP interface port, not the native TCP protocol port used by clickhouse-client
  • Common values:
    • HTTP: 8123 (plain) / 8443 (TLS) — used by this server and ClickHouse Cloud HTTPS
    • Native TCP (not supported here): 9000 (plain) / 9440 (TLS) — used by clickhouse-client
  • If the server responds with Port 9000 is for clickhouse-client program, you are pointed at the native protocol; switch to the HTTP port (8123/8443 or your deployment's HTTP mapping)
• CLICKHOUSE_ROLE: The ClickHouse role to use for authentication
  • Default: None
  • Set this if your user requires a specific role
• CLICKHOUSE_SECURE: Enable HTTPS for the ClickHouse database connection (not for MCP clients)
  • Default: "true"
  • Set to "false" only when the MCP server reaches ClickHouse over plain HTTP (typical for local Docker Compose on port 8123)
  • Leave "true" for ClickHouse Cloud and any HTTPS database endpoint—even if the MCP server itself is exposed via HTTP, stdio, or an ingress that terminates TLS separately
  • Mismatching this flag with the database port (e.g. CLICKHOUSE_SECURE=false against port 8443) is a frequent setup mistake and usually surfaces as confusing HTTP client errors rather than a clear "wrong scheme" message
• CLICKHOUSE_VERIFY: Enable/disable SSL certificate verification for the ClickHouse HTTPS connection
  • Default: "true"
  • Set to "false" to disable certificate verification (not recommended for production)
  • TLS certificates: The package uses your operating system trust store via truststore.inject_into_ssl() at startup. Python's default SSL handling is used if injection is disabled with MCP_CLICKHOUSE_TRUSTSTORE_DISABLE=1 or fails.
• MCP_CLICKHOUSE_TRUSTSTORE_DISABLE: Disable the process-wide operating system trust store integration for TLS

ClickHouse TLS certificate files

The certificate variables contain file paths, not PEM contents. mcp-clickhouse passes these paths to clickhouse-connect. For Docker or Kubernetes, mount the certificate and private key as read-only files and use their paths inside the container. Do not bake a private key into an image, commit it to source control, or put its contents in an environment variable.

In mutual mode, the configured client certificate identifies this mcp-clickhouse process as CLICKHOUSE_USER. It does not authenticate inbound MCP clients or pass their identities to ClickHouse. Configure MCP transport authentication separately.

Restart mcp-clickhouse after replacing a certificate or key at the same path when immediate rotation or revocation is required. Cached clients can retain existing TLS connections, and the cache does not track file contents or modification times.

ClickHouse Cloud does not support X.509 client certificate authentication for database users. Use CLICKHOUSE_USER and CLICKHOUSE_PASSWORD for ClickHouse Cloud. A CA certificate can still be useful when a private proxy in front of an endpoint presents a certificate signed by a private CA.

MCP server and transport

These variables control the MCP process itself, including transport, authentication, and query-tool execution limits. They are independent of the ClickHouse database settings above. See also Authentication for HTTP/SSE Transports.

• CLICKHOUSE_MCP_SERVER_TRANSPORT: Sets the transport method for the MCP server
  • Default: "stdio"
  • Valid options: "stdio", "http", "sse". This is useful for local development with tools like MCP Inspector.
  • stdio is typical for Claude Desktop; http/sse expose a network listener (bind host/port below)
  • "sse" selects the deprecated standalone HTTP+SSE transport and logs a warning. Use "http" for Streamable HTTP in new deployments.
• CLICKHOUSE_MCP_BIND_HOST: Host to bind the MCP server to when using HTTP or SSE transport
  • Default: "127.0.0.1"
  • Set to "0.0.0.0" to bind to all network interfaces (useful for Docker or remote access)
  • Only used when transport is "http" or "sse" — not related to CLICKHOUSE_HOST
• CLICKHOUSE_MCP_BIND_PORT: Port to bind the MCP server to when using HTTP or SSE transport
  • Default: "8000"
  • Only used when transport is "http" or "sse" — not related to CLICKHOUSE_PORT
• CLICKHOUSE_MCP_QUERY_TIMEOUT: Timeout in seconds for query tool calls
  • Default: "30"
  • Increase this if you see Query timed out after ... errors for heavy queries
  • When a query times out, the server attempts to cancel it with KILL QUERY
  • Unless CLICKHOUSE_SEND_RECEIVE_TIMEOUT is explicitly set, the HTTP read timeout is capped at this value plus five seconds
• CLICKHOUSE_MCP_MAX_WORKERS: Maximum number of concurrent query worker threads
  • Default: "10"
  • Increase if your workload requires many concurrent tool calls
  • Metadata tools use a separate pool with min(4, CLICKHOUSE_MCP_MAX_WORKERS) threads so schema discovery cannot delay queries
• CLICKHOUSE_MCP_AUTH_TOKEN: Static bearer token for HTTP/SSE transports
  • Default: None
  • One of CLICKHOUSE_MCP_AUTH_TOKEN, FASTMCP_SERVER_AUTH, or CLICKHOUSE_MCP_AUTH_DISABLED=true is required for HTTP/SSE transports

Reverse proxy Host handling

Preserve Host when possible. This keeps forwarded Host trust disabled:

location / {
    proxy_pass http://mcp-clickhouse:8000;
    proxy_set_header Host $http_host;
    proxy_set_header X-Forwarded-Host "";
    proxy_set_header X-Forwarded-For $remote_addr;
    proxy_set_header X-Forwarded-Proto $scheme;
}

Sanitize X-Forwarded-For and X-Forwarded-Proto independently of X-Forwarded-Host trust. Uvicorn may trust those headers based on the proxy peer even when CLICKHOUSE_MCP_TRUSTED_PROXIES is unset.

CLICKHOUSE_MCP_ALLOWED_HOSTS=mcp.example.com

Stock nginx changes Host to the upstream name for proxied requests. It does not create or overwrite X-Forwarded-Host. If preserving Host is not possible, overwrite the forwarded header at the trusted edge:

location / {
    proxy_pass http://mcp-clickhouse:8000;
    proxy_set_header X-Forwarded-Host $http_host;
    proxy_set_header X-Forwarded-For $remote_addr;
    proxy_set_header X-Forwarded-Proto $scheme;
}

CLICKHOUSE_MCP_ALLOWED_HOSTS=mcp.example.com
CLICKHOUSE_MCP_TRUSTED_PROXIES=10.20.0.8

The second configuration is safe only when 10.20.0.8 is the proxy's immediate source address, the server port is isolated from other clients, and nginx overwrites the incoming forwarding headers as shown. For a proxy chain, each trusted hop must discard unverified incoming values before constructing the new forwarding headers.

On an IPv6 or dual-stack bind, IPv4 proxies may appear as IPv4-mapped addresses such as ::ffff:10.20.0.8; these are matched against IPv4 entries automatically. Envoy's append_x_forwarded_host appends to an existing X-Forwarded-Host rather than overwriting it, producing a comma separated list that is rejected, so configure the trusted hop to overwrite the header instead. On Kubernetes with source NAT (for example externalTrafficPolicy: Cluster) the observed peer may be a node IP rather than the proxy pod, so trust the pod or node CIDR as appropriate; ingress-nginx overwrites both Host and X-Forwarded-Host itself.

Middleware Variables

• MCP_MIDDLEWARE_MODULE: Python module name containing custom middleware to inject into the MCP server
  • Default: None (no middleware loaded)
  • Set to the module name (without .py extension) of your middleware module
  • The module must provide a setup_middleware(mcp) function
  • See Custom Middleware for details and examples

chDB Variables

• CHDB_ENABLED: Enable/disable chDB functionality
  • Default: "false"
  • Set to "true" to enable chDB tools
  • Requires installing the optional extra: mcp-clickhouse[chdb]
• CHDB_DATA_PATH: The path to the chDB data directory
  • Default: ":memory:" (in-memory database)
  • Use :memory: for in-memory database
  • Use a file path for persistent storage (e.g., /path/to/chdb/data)

Common configuration pitfalls

• CLICKHOUSE_SECURE vs MCP / ingress TLS — Turning off CLICKHOUSE_SECURE because the MCP server sits behind Kubernetes ingress, a reverse proxy, or is reached over plain HTTP does not disable database TLS; it only changes how this process connects to ClickHouse. Configure ingress TLS separately from the database client settings.
• Native protocol ports — CLICKHOUSE_PORT must target ClickHouse's HTTP interface (8123/8443 by default). Ports 9000/9440 are for the native TCP protocol (clickhouse-client) and will not work with this server.
• Host confusion — CLICKHOUSE_HOST is the database hostname. CLICKHOUSE_MCP_BIND_HOST is only the address the MCP HTTP/SSE server listens on.

Example Configurations

For local development with Docker:

# Required variables
CLICKHOUSE_HOST=localhost
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=clickhouse

# Optional: Override defaults for local development
CLICKHOUSE_SECURE=false  # Uses port 8123 automatically
CLICKHOUSE_VERIFY=false

For ClickHouse Cloud:

# Required variables
CLICKHOUSE_HOST=your-instance.clickhouse.cloud
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=your-password

# Optional: These use secure defaults
# CLICKHOUSE_SECURE=true  # Uses port 8443 automatically
# CLICKHOUSE_DATABASE=your_database

For ClickHouse SQL Playground:

CLICKHOUSE_HOST=sql-clickhouse.clickhouse.com
CLICKHOUSE_USER=demo
CLICKHOUSE_PASSWORD=
# Uses secure defaults (HTTPS on port 8443)

For a private server CA without client certificate authentication:

CLICKHOUSE_HOST=your-secure-clickhouse.example.com
CLICKHOUSE_USER=your-user
CLICKHOUSE_PASSWORD=your-password
CLICKHOUSE_SECURE=true
CLICKHOUSE_VERIFY=true
CLICKHOUSE_CA_CERT=/run/secrets/clickhouse-ca.pem

For ClickHouse X.509 client certificate authentication:

CLICKHOUSE_HOST=your-secure-clickhouse.example.com
CLICKHOUSE_USER=your-certificate-user
CLICKHOUSE_SECURE=true
CLICKHOUSE_CLIENT_CERT=/run/secrets/clickhouse-client.pem
CLICKHOUSE_CLIENT_CERT_KEY=/run/secrets/clickhouse-client-key.pem
# CLICKHOUSE_CA_CERT=/run/secrets/clickhouse-ca.pem  # Only for a private server CA
# CLICKHOUSE_TLS_MODE=mutual  # Optional. This is the default with a client certificate.

For a client certificate required by a strict TLS server while ClickHouse uses Basic authentication:

CLICKHOUSE_HOST=your-secure-clickhouse.example.com
CLICKHOUSE_USER=your-user
CLICKHOUSE_PASSWORD=your-password
CLICKHOUSE_SECURE=true
CLICKHOUSE_CLIENT_CERT=/run/secrets/clickhouse-client.pem
CLICKHOUSE_CLIENT_CERT_KEY=/run/secrets/clickhouse-client-key.pem
CLICKHOUSE_TLS_MODE=strict

Use CLICKHOUSE_TLS_MODE=proxy instead when a TLS-terminating proxy requires the client certificate and ClickHouse still uses Basic authentication.

For chDB only (in-memory):

# chDB configuration
CHDB_ENABLED=true
CLICKHOUSE_ENABLED=false
# CHDB_DATA_PATH defaults to :memory:

For chDB with persistent storage:

# chDB configuration
CHDB_ENABLED=true
CLICKHOUSE_ENABLED=false
CHDB_DATA_PATH=/path/to/chdb/data

For MCP Inspector or remote access with HTTP transport:

CLICKHOUSE_HOST=localhost
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=clickhouse
CLICKHOUSE_MCP_SERVER_TRANSPORT=http
CLICKHOUSE_MCP_BIND_HOST=0.0.0.0  # Bind to all interfaces
CLICKHOUSE_MCP_BIND_PORT=4200  # Custom port (default: 8000)
CLICKHOUSE_MCP_AUTH_TOKEN=your-generated-token  # One auth mode required for HTTP/SSE (or FASTMCP_SERVER_AUTH, or CLICKHOUSE_MCP_AUTH_DISABLED=true)
CLICKHOUSE_MCP_ALLOWED_HOSTS=127.0.0.1:4200,localhost:4200,mcp.example.com:4200  # Include every Host value clients and proxies send

For local development with HTTP transport (authentication disabled):

CLICKHOUSE_HOST=localhost
CLICKHOUSE_USER=default
CLICKHOUSE_PASSWORD=clickhouse
CLICKHOUSE_MCP_SERVER_TRANSPORT=http
CLICKHOUSE_MCP_AUTH_DISABLED=true  # Only for local development!
CLICKHOUSE_MCP_ALLOWED_HOSTS=127.0.0.1:8000,localhost:8000

When using HTTP transport, the server will run on the configured port (default 8000). For example, with the above configuration:

• MCP endpoint: http://localhost:8000/mcp
• Health check: http://localhost:8000/health

You can set these variables in your environment, in a .env file, or in the Claude Desktop configuration:

{
  "mcpServers": {
    "mcp-clickhouse": {
      "command": "uv",
      "args": [
        "run",
        "--with",
        "mcp-clickhouse",
        "--python",
        "3.12",
        "mcp-clickhouse"
      ],
      "env": {
        "CLICKHOUSE_HOST": "<clickhouse-host>",
        "CLICKHOUSE_USER": "<clickhouse-user>",
        "CLICKHOUSE_PASSWORD": "<clickhouse-password>",
        "CLICKHOUSE_DATABASE": "<optional-database>",
        "CLICKHOUSE_MCP_SERVER_TRANSPORT": "stdio",
        "CLICKHOUSE_MCP_BIND_HOST": "127.0.0.1",
        "CLICKHOUSE_MCP_BIND_PORT": "8000"
      }
    }
  }
}

Note: The bind host and port settings are only used when transport is set to "http" or "sse".

Running tests

uv sync --all-extras --dev # install dev dependencies
uv run ruff check . # run linting

docker compose up -d test_services # start ClickHouse
uv run pytest -v tests
uv run pytest -v tests/test_tool.py # ClickHouse only
CHDB_ENABLED=true uv run --extra chdb pytest -v tests/test_chdb_tool.py # chDB only

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