diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 10a17b3..d2b4c0b 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -28,7 +28,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - uv sync --extra dev --extra docs --extra llm + uv sync --extra dev --extra docs --extra llm --extra mcp uv run python -m ensurepip - name: Check types run: | diff --git a/app/api/utils.py b/app/api/utils.py index e869164..017cb12 100644 --- a/app/api/utils.py +++ b/app/api/utils.py @@ -347,10 +347,10 @@ async def init_vllm_engine(app: FastAPI, ) tokenizer = await engine.get_tokenizer() - vllm_config = await engine.get_vllm_config() - model_config = await engine.get_model_config() + vllm_config = await engine.get_vllm_config() # type: ignore + model_config = await engine.get_model_config() # type: ignore - await init_app_state(engine, vllm_config, app.state, args) + await init_app_state(engine, vllm_config, app.state, args) # type: ignore async def generate_text( request: Request, diff --git a/app/cli/README.md b/app/cli/README.md index ad2fbf2..a87ceff 100644 --- a/app/cli/README.md +++ b/app/cli/README.md @@ -10,6 +10,9 @@ $ cms [OPTIONS] COMMAND [ARGS]... **Options**: +* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]` +* `--host TEXT` +* `--port TEXT` * `--install-completion`: Install completion for the current shell. * `--show-completion`: Show completion for the current shell, to copy it or customize the installation. * `--help`: Show this message and exit. @@ -24,6 +27,7 @@ $ cms [OPTIONS] COMMAND [ARGS]... * `export-openapi-spec`: This generates an API document for all... * `stream`: This groups various stream operations * `package`: This groups various package operations +* `mcp`: Run the MCP server for accessing CMS... ## `cms serve` @@ -37,14 +41,17 @@ $ cms serve [OPTIONS] **Options**: -* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner]`: The type of the model to serve [required] -* `--model-path TEXT`: The file path to the model package +* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]`: The type of the model to serve [required] +* `--model-path TEXT`: Either the file path to the local model package or the URL to the remote one * `--mlflow-model-uri models:/MODEL_NAME/ENV`: The URI of the MLflow model to serve * `--host TEXT`: The hostname of the server [default: 127.0.0.1] * `--port TEXT`: The port of the server [default: 8000] * `--model-name TEXT`: The string representation of the model name * `--streamable / --no-streamable`: Serve the streamable endpoints only [default: no-streamable] * `--device [default|cpu|cuda|mps]`: The device to serve the model on [default: default] +* `--llm-engine [CMS|vLLM]`: The engine to use for text generation [default: CMS] +* `--load-in-4bit / --no-load-in-4bit`: Load the model in 4-bit precision, used by 'huggingface_llm' models [default: no-load-in-4bit] +* `--load-in-8bit / --no-load-in-8bit`: Load the model in 8-bit precision, used by 'huggingface_llm' models [default: no-load-in-8bit] * `--debug / --no-debug`: Run in the debug mode * `--help`: Show this message and exit. @@ -60,7 +67,7 @@ $ cms train [OPTIONS] **Options**: -* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner]`: The type of the model to train [required] +* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]`: The type of the model to train [required] * `--base-model-path TEXT`: The file path to the base model package to be trained on * `--mlflow-model-uri models:/MODEL_NAME/ENV`: The URI of the MLflow model to train * `--training-type [supervised|unsupervised|meta_supervised]`: The type of training [required] @@ -71,6 +78,8 @@ $ cms train [OPTIONS] * `--description TEXT`: The description of the training or change logs * `--model-name TEXT`: The string representation of the model name * `--device [default|cpu|cuda|mps]`: The device to train the model on [default: default] +* `--load-in-4bit / --no-load-in-4bit`: Load the model in 4-bit precision, used by 'huggingface_llm' models [default: no-load-in-4bit] +* `--load-in-8bit / --no-load-in-8bit`: Load the model in 8-bit precision, used by 'huggingface_llm' models [default: no-load-in-8bit] * `--debug / --no-debug`: Run in the debug mode * `--help`: Show this message and exit. @@ -86,7 +95,7 @@ $ cms register [OPTIONS] **Options**: -* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner]`: The type of the model to register [required] +* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]`: The type of the model to register [required] * `--model-path TEXT`: The file path to the model package [required] * `--model-name TEXT`: The string representation of the registered model [required] * `--training-type [supervised|unsupervised|meta_supervised]`: The type of training the model went through @@ -108,7 +117,7 @@ $ cms export-model-apis [OPTIONS] **Options**: -* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner]`: The type of the model to serve [required] +* `--model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]`: The type of the model to serve [required] * `--add-training-apis / --no-add-training-apis`: Add training APIs to the doc [default: no-add-training-apis] * `--add-evaluation-apis / --no-add-evaluation-apis`: Add evaluation APIs to the doc [default: no-add-evaluation-apis] * `--add-previews-apis / --no-add-previews-apis`: Add preview APIs to the doc [default: no-add-previews-apis] @@ -269,3 +278,47 @@ $ cms package hf-dataset [OPTIONS] * `--remove-cached / --no-remove-cached`: Whether to remove the downloaded cache after the dataset package is saved [default: no-remove-cached] * `--trust-remote-code / --no-trust-remote-code`: Whether to trust and use the remote script of the dataset [default: no-trust-remote-code] * `--help`: Show this message and exit. + +## `cms mcp` + +Run the MCP server for accessing CMS capabilities + +**Usage**: + +```console +$ cms mcp [OPTIONS] COMMAND [ARGS]... +``` + +**Options**: + +* `--help`: Show this message and exit. + +**Commands**: + +* `run`: Run the MCP server for accessing CMS... + +### `cms mcp run` + +Run the MCP server for accessing CMS capabilities + +**Usage**: + +```console +$ cms mcp run [OPTIONS] +``` + +**Options**: + +* `--host TEXT`: The hostname of the MCP server [default: 127.0.0.1] +* `--port INTEGER`: The port of the MCP server [default: 8080] +* `--transport TEXT`: The transport type (either 'stdio', 'sse' or 'http') [default: http] +* `--cms-base-url TEXT`: The base URL of the CMS API [default: http://localhost:8000] +* `--cms-api-key TEXT`: The API key for authenticating with the CMS API +* `--mcp-api-keys TEXT`: Comma-separated API keys for authenticating MCP clients +* `--cms-mcp-oauth-enabled / --no-cms-mcp-oauth-enabled`: Whether to enable OAuth2 authentication for MCP clients +* `--github-client-id TEXT`: The GitHub OAuth2 client ID +* `--github-client-secret TEXT`: The GitHub OAuth2 client secret +* `--google-client-id TEXT`: The Google OAuth2 client ID +* `--google-client-secret TEXT`: The Google OAuth2 client secret +* `--debug / --no-debug`: Run in debug mode +* `--help`: Show this message and exit. diff --git a/app/cli/cli.py b/app/cli/cli.py index 1fb9a48..f354f50 100644 --- a/app/cli/cli.py +++ b/app/cli/cli.py @@ -7,6 +7,7 @@ import uuid import inspect import warnings +import multiprocessing import subprocess current_frame = inspect.currentframe() @@ -52,9 +53,11 @@ cmd_app = typer.Typer(name="cms", help="CLI for various CogStack ModelServe operations", add_completion=True) stream_app = typer.Typer(name="stream", help="This groups various stream operations", add_completion=True) -cmd_app.add_typer(stream_app, name="stream") +mcp_app = typer.Typer(name="mcp", help="Run the MCP server for accessing CMS capabilities", add_completion=True) package_app = typer.Typer(name="package", help="This groups various package operations", add_completion=True) +cmd_app.add_typer(stream_app, name="stream") cmd_app.add_typer(package_app, name="package") +cmd_app.add_typer(mcp_app, name="mcp") logging.config.fileConfig(os.path.join(parent_dir, "logging.ini"), disable_existing_loggers=False) @cmd_app.command("serve", help="This serves various CogStack NLP models") @@ -69,6 +72,7 @@ def serve_model( device: Device = typer.Option(Device.DEFAULT.value, help="The device to serve the model on"), llm_engine: Optional[LlmEngine] = typer.Option(LlmEngine.CMS.value, help="The engine to use for text generation"), load_in_4bit: Optional[bool] = typer.Option(False, help="Load the model in 4-bit precision, used by 'huggingface_llm' models"), + load_in_8bit: Optional[bool] = typer.Option(False, help="Load the model in 8-bit precision, used by 'huggingface_llm' models"), debug: Optional[bool] = typer.Option(None, help="Run in the debug mode"), ) -> None: """ @@ -87,6 +91,7 @@ def serve_model( device (Device): The device to serve the model on. Defaults to Device.DEFAULT. llm_engine (LlmEngine): The inference engine to use. Defaults to LlmEngine.CMS. load_in_4bit (bool): Load the model in 4-bit precision, used by 'huggingface_llm' models. Defaults to False. + load_in_8bit (bool): Load the model in 8-bit precision, used by 'huggingface_llm' models. Defaults to False. debug (Optional[bool]): Run in debug mode if set to True. """ @@ -138,7 +143,7 @@ def serve_model( if model_path: model_service = model_service_dep() model_service.model_name = model_name - model_service.init_model(load_in_4bit=load_in_4bit) + model_service.init_model(load_in_4bit=load_in_4bit, load_in_8bit=load_in_8bit) cms_globals.model_manager_dep = ModelManagerDep(model_service) elif mlflow_model_uri: model_service = ModelManager.retrieve_model_service_from_uri(mlflow_model_uri, config, dst_model_path) @@ -191,6 +196,7 @@ def train_model( model_name: Optional[str] = typer.Option(None, help="The string representation of the model name"), device: Device = typer.Option(Device.DEFAULT.value, help="The device to train the model on"), load_in_4bit: Optional[bool] = typer.Option(False, help="Load the model in 4-bit precision, used by 'huggingface_llm' models"), + load_in_8bit: Optional[bool] = typer.Option(False, help="Load the model in 8-bit precision, used by 'huggingface_llm' models"), debug: Optional[bool] = typer.Option(None, help="Run in the debug mode"), ) -> None: """ @@ -211,6 +217,7 @@ def train_model( model_name (Optional[str]): The optional string representation of the model name. device (Device): The device to train the model on. Defaults to Device.DEFAULT. load_in_4bit (bool): Load the model in 4-bit precision, used by 'huggingface_llm' models. Defaults to False. + load_in_8bit (bool): Load the model in 8-bit precision, used by 'huggingface_llm' models. Defaults to False. debug (Optional[bool]): Run in debug mode if set to True. """ @@ -232,7 +239,7 @@ def train_model( pass model_service = model_service_dep() model_service.model_name = model_name if model_name is not None else "CMS model" - model_service.init_model(load_in_4bit=load_in_4bit) + model_service.init_model(load_in_4bit=load_in_4bit, load_in_8bit=load_in_8bit) elif mlflow_model_uri: model_service = ModelManager.retrieve_model_service_from_uri(mlflow_model_uri, config, dst_model_path) model_service.model_name = model_name if model_name is not None else "CMS model" @@ -495,6 +502,7 @@ def package_model( model_package_archive = os.path.abspath(os.path.expanduser(output_model_package)) if hf_repo_id: + download_path = None try: with tempfile.TemporaryDirectory() as tmp_dir: if not hf_repo_revision: @@ -510,15 +518,14 @@ def package_model( local_dir=tmp_dir, local_dir_use_symlinks=False, ) - - shutil.make_archive(model_package_archive, archive_format.value, download_path) + _make_archive_file(model_package_archive, archive_format.value, download_path) finally: - if remove_cached: + if remove_cached and download_path: cached_model_path = os.path.abspath(os.path.join(download_path, "..", "..")) shutil.rmtree(cached_model_path) elif cached_model_dir: cached_model_path = os.path.abspath(os.path.expanduser(cached_model_dir)) - shutil.make_archive(model_package_archive, archive_format.value, cached_model_path) + _make_archive_file(model_package_archive, archive_format.value, cached_model_path) typer.echo(f"Model package saved to {model_package_archive}.{'zip' if archive_format == ArchiveFormat.ZIP else 'tar.gz'}") @@ -585,6 +592,73 @@ def package_dataset( typer.echo(f"Dataset package saved to {dataset_package_archive}.{'zip' if archive_format == ArchiveFormat.ZIP else 'tar.gz'}") +@mcp_app.command("run", help="Run the MCP server for accessing CMS capabilities") +def run_mcp_server( + host: str = typer.Option("127.0.0.1", help="The hostname of the MCP server"), + port: int = typer.Option(8080, help="The port of the MCP server"), + transport: str = typer.Option("http", help="The transport type (either 'stdio', 'sse' or 'http')"), + cms_base_url: str = typer.Option("http://127.0.0.1:8000", help="The base URL of the CMS API"), + cms_api_key: str = typer.Option("Bearer", help="The API key for authenticating with the CMS API"), + mcp_api_keys: str = typer.Option("", help="Comma-separated API keys for authenticating MCP clients"), + cms_mcp_oauth_enabled: Optional[bool] = typer.Option(None, help="Whether to enable OAuth2 authentication for MCP clients"), + github_client_id: str = typer.Option("", help="The GitHub OAuth2 client ID"), + github_client_secret: str = typer.Option("", help="The GitHub OAuth2 client secret"), + google_client_id: str = typer.Option("", help="The Google OAuth2 client ID"), + google_client_secret: str = typer.Option("", help="The Google OAuth2 client secret"), + debug: Optional[bool] = typer.Option(None, help="Run in debug mode"), +) -> None: + """ + Runs the CogStack ModelServe MCP server. + + This function starts an MCP server that provides AI assistants with tools to interact + with deployed CMS models through the Model Context Protocol interface. + + Args: + host (str): The hostname of the MCP server. Defaults to "127.0.0.1". + port (int): The port of the MCP server. Defaults to 8080. + transport (str): The transport type for the MCP server. Can be "stdio" or "http". Defaults to "stdio". + cms_base_url (str): The base URL of the CMS API endpoint. Defaults to "http://localhost:8000". + debug (Optional[bool]): Run in debug mode if set to True. + """ + + logger = _get_logger(debug) + logger.info("Starting CMS MCP server...") + + os.environ["CMS_BASE_URL"] = cms_base_url + os.environ["CMS_MCP_SERVER_HOST"] = host + os.environ["CMS_MCP_SERVER_PORT"] = str(port) + os.environ["CMS_MCP_TRANSPORT"] = transport.lower() + os.environ["CMS_API_KEY"] = cms_api_key + os.environ["MCP_API_KEYS"] = mcp_api_keys + os.environ["CMS_MCP_OAUTH_ENABLED"] = "true" if cms_mcp_oauth_enabled else "false" + os.environ["GITHUB_CLIENT_ID"] = github_client_id + os.environ["GITHUB_CLIENT_SECRET"] = github_client_secret + os.environ["GOOGLE_CLIENT_ID"] = google_client_id + os.environ["GOOGLE_CLIENT_SECRET"] = google_client_secret + + if debug: + os.environ["CMS_MCP_DEV"] = "1" + + try: + from app.mcp.server import main + logger.info(f"MCP server starting with transport: {transport}") + logger.info(f"Connected to CMS API at {cms_base_url}") + main() + except ImportError as e: + logger.error(f"Cannot import MCP. Please install it with `pip install cms[mcp]`: {e}") + typer.echo(f"ERROR: Cannot import MCP: {e}") + typer.echo("Please install it with `pip install cms[mcp]`.") + raise typer.Exit(code=1) + except KeyboardInterrupt: + logger.info("MCP server stopped by the user") + typer.echo("MCP server stopped.") + raise typer.Exit(code=0) + except Exception as e: + logger.error(f"Failed to start MCP server: {e}") + typer.echo(f"ERROR: Failed to start MCP server: {e}") + raise typer.Exit(code=1) + + @cmd_app.command("build", help="This builds an OCI-compliant image to containerise CMS") def build_image( dockerfile_path: str = typer.Option(..., help="The path to the Dockerfile"), @@ -798,6 +872,24 @@ def _ensure_dst_model_path(model_path: str, parent_dir: str, config: Settings) - return dst_model_path +def _make_archive_file(base_name: str, format: str, root_dir: str) -> None: + if format == ArchiveFormat.TAR_GZ.value: + try: + result = subprocess.run(["which", "pigz"], capture_output=True, text=True, check=True) + if result.returncode == 0: + num_cores = max(1, multiprocessing.cpu_count() - 1) + compress_program = f"pigz -p {num_cores}" + subprocess.run( + ["tar", f"--use-compress-program={compress_program}", "-cf", f"{base_name}.tar.gz", "-C", root_dir, "."], + check=True + ) + return + except subprocess.CalledProcessError: + typer.echo("Use non-parallel compression...") + + shutil.make_archive(base_name, format, root_dir) + + def _get_logger( debug: Optional[bool] = None, model_type: Optional[ModelType] = None, diff --git a/app/mcp/README.md b/app/mcp/README.md new file mode 100644 index 0000000..a61fde4 --- /dev/null +++ b/app/mcp/README.md @@ -0,0 +1,86 @@ +# CogStack ModelServe MCP Server + +Model Context Protocol (MCP) server for CogStack ModelServe, providing AI assistants with tools to interact with deployed NLP models and their training metrics. + +## Quick Start + +### 1. Install Dependencies +```bash +pip install '.[mcp]' +``` + +### 2. Set Environment Variables +```bash +export CMS_BASE_URL="http://127.0.0.1:8000" # CogStack ModelServe API base URL +export MCP_API_KEYS="key1,key2,...keyN" # Optional: The API key(s) for authentication +``` + +### 3. Run the Server +```bash +# STDIO transport (default) +cms mcp run +``` + +```bash +# HTTP transport +export CMS_MCP_TRANSPORT=http +cms mcp run --transport http +``` +Once the above succeeds, the MCP server will be running on http://127.0.0.1:8080/mcp + +## Available Tools + +| Tool | Description | Arguments | +|------|-------------|-----------| +| `get_model_info` | Get running model information | None | +| `get_annotations` | Extract entities from text | `text: str` | +| `redact_text` | Redact sensitive information | `text: str` | +| `get_train_eval_info` | Get training/evaluation status | `train_eval_id: str` | +| `get_train_eval_metrics` | Get training/evaluation metrics | `train_eval_id: str` | + +## Configuration + +| Environment Variable | Default | Description | +|---------------------|---------|-------------| +| `CMS_BASE_URL` | `http://127.0.0.1:8000` | ModelServe API base URL | +| `CMS_MCP_SERVER_HOST` | `127.0.0.1` | MCP server host | +| `CMS_MCP_SERVER_PORT` | `8080` | MCP server port | +| `CMS_MCP_TRANSPORT` | `stdio` | Transport type (`stdio`, `http` or `sse`) | +| `CMS_ACCESS_TOKEN` | Empty | Bearer token for ModelServe API | +| `CMS_API_KEY` | `Bearer` | API key for ModelServe API | +| `MCP_API_KEYS` | None | Comma-separated API keys for authentication | +| `CMS_MCP_OAUTH_ENABLED` | `true` | Enable OAuth authentication | +| `CMS_MCP_BASE_URL` | `http://:` | Base URL for OAuth callback | +| `CMS_MCP_DEV` | `0` | Run in development mode (creates server instance) | + + +## Authentication + +The server supports two authentication methods: + +### 1. API Key Authentication +When `MCP_API_KEYS` is set, clients must authenticate using: +- **Header**: `x-api-key: your-key` + +### 2. OAuth Authentication (SSE Transport) +When `CMS_MCP_OAUTH_ENABLED=true`, the server provides a built-in OAuth 2.0 login flow for SSE transport. + +**OAuth Endpoints:** +- `/oauth/login` - Login page with Google and GitHub options +- `/oauth/authorize/{provider}` - Initiates OAuth flow for the specified provider +- `/oauth/callback/{provider}` - OAuth callback handler +- `/oauth/status` - Check current session status +- `/oauth/logout` - Logout and clear session + +**Environment Variables for OAuth:** +| Variable | Description | +|----------|-------------| +| `GITHUB_CLIENT_ID` | GitHub OAuth client ID | +| `GITHUB_CLIENT_SECRET` | GitHub OAuth client secret | +| `GOOGLE_CLIENT_ID` | Google OAuth client ID | +| `GOOGLE_CLIENT_SECRET` | Google OAuth client secret | + +**Note:** OAuth credentials can also be set via environment variables or `.env` file. If not configured, the server will log a warning but continue running. + +**Session Authentication:** +After OAuth login, a session cookie (`cms_mcp_session`) is set. Subsequent MCP requests should include this cookie for authentication. diff --git a/app/mcp/__init__.py b/app/mcp/__init__.py new file mode 100644 index 0000000..3f61d78 --- /dev/null +++ b/app/mcp/__init__.py @@ -0,0 +1,4 @@ +""" +CMS MCP Server Tools Package +""" +__version__ = "0.1.0" diff --git a/app/mcp/domain.py b/app/mcp/domain.py new file mode 100644 index 0000000..44c5241 --- /dev/null +++ b/app/mcp/domain.py @@ -0,0 +1,22 @@ +from dataclasses import dataclass +from enum import Enum +from cms_client import ( + MetadataApi, + AnnotationsApi, + RedactionApi, + TrainingApi, +) + + +@dataclass +class AppContext: + metadata_api: MetadataApi + annotation_api: AnnotationsApi + redaction_api: RedactionApi + training_api: TrainingApi + + +class TransportType(str, Enum): + STREAMABLE_HTTP = "http" + STDIO = "stdio" + SSE = "sse" diff --git a/app/mcp/logger.py b/app/mcp/logger.py new file mode 100644 index 0000000..1df5997 --- /dev/null +++ b/app/mcp/logger.py @@ -0,0 +1,17 @@ +import os +import sys +from loguru import logger +from loguru._logger import Logger + +LOG_FORMAT = "{time:YYYY-MM-DD HH:mm:ss.SSS} | {level: <8} | {name} - {message}" +LOG_LEVEL = os.getenv("CMS_MCP_LOG_LEVEL", "INFO").upper() +logger.remove() +logger.add( + sys.stderr, + format=LOG_FORMAT, + level=LOG_LEVEL, + colorize=True, +) + +def get_logger(name: str) -> Logger: + return logger.bind(name=name) # type: ignore diff --git a/app/mcp/oauth/__init__.py b/app/mcp/oauth/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/app/mcp/oauth/middleware.py b/app/mcp/oauth/middleware.py new file mode 100644 index 0000000..c13d7ba --- /dev/null +++ b/app/mcp/oauth/middleware.py @@ -0,0 +1,93 @@ +from typing import Optional, Callable, Any +from fastapi import Request, HTTPException +from fastapi.responses import JSONResponse +from starlette.middleware.base import BaseHTTPMiddleware +from starlette.responses import Response +from app.mcp.oauth.oauth import OAuthManager +from app.mcp.logger import get_logger + +logger = get_logger(__name__) + + +class OAuthMiddleware(BaseHTTPMiddleware): + + def __init__(self, app: Any, oauth_manager: OAuthManager, public_paths: Optional[list[str]] = None): + super().__init__(app) + self.oauth_manager = oauth_manager + self.public_paths = public_paths or [] + + def _is_public_path(self, path: str) -> bool: + return any(path.startswith(public_path) for public_path in self.public_paths) + + async def dispatch(self, request: Request, call_next: Callable) -> Response: + try: + if request.url.path.startswith("/sse"): + return await call_next(request) + + if self._is_public_path(request.url.path): + return await call_next(request) + + session_id = request.cookies.get("cms_mcp_session") + + if not session_id: + auth_header = request.headers.get("Authorization") + if auth_header and auth_header.startswith("Bearer "): + session_id = auth_header[7:] + + if not session_id: + session_id = request.query_params.get("session_id") + + if not session_id: + logger.warning(f"No session provided for path: {request.url.path}") + return JSONResponse( + status_code=401, + content={ + "error": "Unauthorized", + "message": "No session token provided. Please authenticate at /oauth/login" + } + ) + + logger.debug(f"Validating session: {session_id[:16]}...") + token = await self.oauth_manager.get_valid_token(session_id) + + if not token: + logger.warning(f"Invalid or expired session: {session_id[:16]}...") + return JSONResponse( + status_code=401, + content={ + "error": "Unauthorized", + "message": "Invalid or expired session. Please re-authenticate at /oauth/login" + } + ) + + request.state.oauth_token = token + request.state.session_id = session_id + + response = await call_next(request) + + return response + except Exception as e: + logger.error(f"Unhandled exception in OAuth middleware: {str(e)}", exc_info=True) + return JSONResponse( + status_code=500, + content={ + "error": "Internal Server Error", + "message": f"An unexpected error occurred: {str(e)}" + } + ) + + +def get_oauth_token_from_request(request: Request) -> Optional[str]: + if hasattr(request.state, "oauth_token"): + return request.state.oauth_token.access_token + return None + + +def require_auth(request: Request) -> str: + token = get_oauth_token_from_request(request) + if not token: + raise HTTPException( + status_code=401, + detail="Authentication required" + ) + return token diff --git a/app/mcp/oauth/oauth.py b/app/mcp/oauth/oauth.py new file mode 100644 index 0000000..bc37fc8 --- /dev/null +++ b/app/mcp/oauth/oauth.py @@ -0,0 +1,593 @@ +import os +import secrets +import httpx +from typing import Optional, Dict +from dataclasses import dataclass +from datetime import datetime, timedelta +from starlette.responses import HTMLResponse, RedirectResponse +from starlette.requests import Request +from starlette.routing import Route +from starlette.responses import Response +from app.mcp.logger import get_logger + + +logger = get_logger(__name__) + + +@dataclass +class OAuthConfig: + client_id: str + client_secret: str + authorization_url: str + token_url: str + userinfo_url: str + redirect_uri: str + scope: str + + +@dataclass +class OAuthToken: + access_token: str + token_type: str + expires_in: int + refresh_token: Optional[str] = None + scope: Optional[str] = None + created_at: Optional[datetime] = None + + def __post_init__(self) -> None: + if self.created_at is None: + self.created_at = datetime.utcnow() + + def is_expired(self) -> bool: + if not self.expires_in: + return False + created = self.created_at + assert created is not None + expiry_time = created + timedelta(seconds=self.expires_in) + return datetime.utcnow() >= expiry_time + + +class OAuthProvider: + + def __init__(self, config: OAuthConfig): + self.config = config + self._state_store: Dict[str, datetime] = {} # Use Redis or database for production + self._token_store: Dict[str, OAuthToken] = {} # Use secure storage for production + + def generate_authorization_url(self, state: Optional[str] = None) -> tuple[str, str]: + if state is None: + state = secrets.token_urlsafe(32) + + self._state_store[state] = datetime.utcnow() + + params = { + "client_id": self.config.client_id, + "redirect_uri": self.config.redirect_uri, + "response_type": "code", + "scope": self.config.scope, + "state": state, + } + + query_string = "&".join(f"{k}={v}" for k, v in params.items()) + auth_url = f"{self.config.authorization_url}?{query_string}" + + return auth_url, state + + def verify_state(self, state: str) -> bool: + if state not in self._state_store: + return False + + created_at = self._state_store[state] + if datetime.utcnow() - created_at > timedelta(minutes=5): + del self._state_store[state] + return False + + del self._state_store[state] + return True + + async def exchange_code_for_token(self, code: str) -> OAuthToken: + async with httpx.AsyncClient() as client: + data = { + "client_id": self.config.client_id, + "client_secret": self.config.client_secret, + "code": code, + "redirect_uri": self.config.redirect_uri, + "grant_type": "authorization_code", + } + + response = await client.post( + self.config.token_url, + data=data, + headers={"Accept": "application/json"} + ) + response.raise_for_status() + token_data = response.json() + + token = OAuthToken( + access_token=token_data["access_token"], + token_type=token_data.get("token_type", "Bearer"), + expires_in=token_data.get("expires_in", 3600), + refresh_token=token_data.get("refresh_token"), + scope=token_data.get("scope"), + ) + + logger.info("Successfully exchanged code for access token") + return token + + async def refresh_access_token(self, refresh_token: str) -> OAuthToken: + async with httpx.AsyncClient() as client: + data = { + "client_id": self.config.client_id, + "client_secret": self.config.client_secret, + "refresh_token": refresh_token, + "grant_type": "refresh_token", + } + + response = await client.post( + self.config.token_url, + data=data, + headers={"Accept": "application/json"} + ) + response.raise_for_status() + token_data = response.json() + + token = OAuthToken( + access_token=token_data["access_token"], + token_type=token_data.get("token_type", "Bearer"), + expires_in=token_data.get("expires_in", 3600), + refresh_token=token_data.get("refresh_token", refresh_token), + scope=token_data.get("scope"), + ) + + logger.info("Successfully refreshed access token") + return token + + async def get_user_info(self, access_token: str) -> dict: + async with httpx.AsyncClient() as client: + headers = { + "Authorization": f"Bearer {access_token}", + "Accept": "application/json" + } + + response = await client.get( + self.config.userinfo_url, + headers=headers + ) + response.raise_for_status() + return response.json() + + +class GoogleOAuthProvider(OAuthProvider): + + def __init__(self, redirect_uri: str): + config = OAuthConfig( + client_id=os.getenv("GOOGLE_CLIENT_ID", ""), + client_secret=os.getenv("GOOGLE_CLIENT_SECRET", ""), + authorization_url="https://accounts.google.com/o/oauth2/v2/auth", + token_url="https://oauth2.googleapis.com/token", + userinfo_url="https://www.googleapis.com/oauth2/v2/userinfo", + redirect_uri=redirect_uri, + scope="openid email profile", + ) + super().__init__(config) + + if not config.client_id or not config.client_secret: + logger.warning("Google OAuth credentials not configured") + + +class GitHubOAuthProvider(OAuthProvider): + + def __init__(self, redirect_uri: str): + config = OAuthConfig( + client_id=os.getenv("GITHUB_CLIENT_ID", ""), + client_secret=os.getenv("GITHUB_CLIENT_SECRET", ""), + authorization_url="https://github.com/login/oauth/authorize", + token_url="https://github.com/login/oauth/access_token", + userinfo_url="https://api.github.com/user", + redirect_uri=redirect_uri, + scope="read:user user:email", + ) + super().__init__(config) + + if not config.client_id or not config.client_secret: + logger.warning("GitHub OAuth credentials not configured") + + async def get_user_info(self, access_token: str) -> dict: + async with httpx.AsyncClient() as client: + headers = { + "Authorization": f"Bearer {access_token}", + "Accept": "application/json" + } + + user_response = await client.get(self.config.userinfo_url, headers=headers) + user_response.raise_for_status() + user_data = user_response.json() + + if not user_data.get("email"): + logger.debug("User email not in primary user info, fetching from /user/emails") + emails_response = await client.get("https://api.github.com/user/emails", headers=headers) + if emails_response.status_code == 200: + emails_data = emails_response.json() + for email_info in emails_data: + if email_info.get("primary"): + user_data["email"] = email_info.get("email") + break + if not user_data.get("email"): + for email_info in emails_data: + if email_info.get("verified"): + user_data["email"] = email_info.get("email") + break + else: + logger.warning(f"Failed to fetch user emails: {emails_response.status_code}") + + return user_data + + +class OAuthManager: + + def __init__(self, base_url: str): + self.base_url = base_url + self.providers = { + "google": GoogleOAuthProvider(f"{base_url}/oauth/callback/google"), + "github": GitHubOAuthProvider(f"{base_url}/oauth/callback/github"), + } + self._sessions: Dict[str, OAuthToken] = {} + + def get_provider(self, provider_name: str) -> Optional[OAuthProvider]: + return self.providers.get(provider_name.lower()) + + def store_token(self, session_id: str, token: OAuthToken) -> None: + self._sessions[session_id] = token + logger.info(f"Stored token for session: {session_id}") + + def get_token(self, session_id: str) -> Optional[OAuthToken]: + return self._sessions.get(session_id) + + def remove_token(self, session_id: str) -> None: + if session_id in self._sessions: + del self._sessions[session_id] + logger.info(f"Removed token for session: {session_id}") + + async def get_valid_token(self, session_id: str) -> Optional[OAuthToken]: + token = self.get_token(session_id) + if not token: + return None + + if token.is_expired() and token.refresh_token: + for provider in self.providers.values(): + try: + new_token = await provider.refresh_access_token(token.refresh_token) + self.store_token(session_id, new_token) + return new_token + except Exception as e: + logger.debug(f"Failed to refresh token with provider: {e}") + continue + + self.remove_token(session_id) + return None + + return token if not token.is_expired() else None + + def create_oauth_routes(self) -> list: + async def oauth_login(request: Request) -> Response: + html_content = """ + + + + CMS MCP Server - Login + + + + + + + """ + return HTMLResponse(content=html_content) + + async def oauth_authorize(request: Request) -> Response: + provider = request.path_params['provider'] + oauth_provider = self.get_provider(provider) + + if not oauth_provider: + return HTMLResponse(content=f"

Unknown provider: {provider}

", status_code=400) + + auth_url, state = oauth_provider.generate_authorization_url() + + response = RedirectResponse(url=auth_url) + response.set_cookie( + key=f"oauth_state_{provider}", + value=state, + max_age=300, + httponly=True, + samesite="lax", + secure=os.getenv("CMS_MCP_SECURE_COOKIES", "false").lower() == "true" + ) + + logger.info(f"Initiating OAuth flow for provider: {provider}") + return response + + async def oauth_callback(request: Request) -> Response: + provider = request.path_params['provider'] + code = request.query_params.get('code') + state = request.query_params.get('state') + error = request.query_params.get('error') + + if error: + logger.error(f"OAuth error for {provider}: {error}") + return HTMLResponse( + content=f"

❌ Authentication Failed

Error: {error}

", + status_code=400 + ) + + if not code or not state: + return HTMLResponse(content="

Missing code or state

", status_code=400) + + oauth_provider = self.get_provider(provider) + if not oauth_provider: + return HTMLResponse(content=f"

Unknown provider: {provider}

", status_code=400) + + stored_state = request.cookies.get(f"oauth_state_{provider}") + if not stored_state or stored_state != state: + logger.error(f"State mismatch for {provider}") + return HTMLResponse(content="

Invalid state parameter

", status_code=400) + + if not oauth_provider.verify_state(state): + logger.error(f"State verification failed for {provider}") + return HTMLResponse(content="

State verification failed

", status_code=400) + + try: + token = await oauth_provider.exchange_code_for_token(code) + user_info = await oauth_provider.get_user_info(token.access_token) + session_id = secrets.token_urlsafe(32) + + self.store_token(session_id, token) + + user_email = user_info.get("email", "N/A") + user_name = user_info.get("name") or user_info.get("login", "User") + + html_content = f""" + + + + Authentication Successful + + + +
+
✅
+

Authentication Successful!

+ +
+

Session ID:

+

{session_id}

+
+

+ You can now use the MCP server with your authenticated session. +

+ Check Session Status +
+ + + """ + + response = HTMLResponse(content=html_content) + response.set_cookie( + key="cms_mcp_session", + value=session_id, + max_age=86400, + httponly=True, + samesite="lax", + secure=os.getenv("CMS_MCP_SECURE_COOKIES", "false").lower() == "true" + ) + response.delete_cookie(f"oauth_state_{provider}") + + logger.info(f"Successfully authenticated user via {provider}: {user_email}") + return response + + except Exception as e: + logger.error(f"OAuth callback error for {provider}: {str(e)}") + return HTMLResponse( + content=f"

Authentication failed

{str(e)}

", + status_code=500 + ) + + async def oauth_status(request: Request) -> Response: + session_id = request.cookies.get("cms_mcp_session") + + if not session_id: + return HTMLResponse(content="

🔒 No Active Session

You are not authenticated.

") + + token = await self.get_valid_token(session_id) + + if not token: + return HTMLResponse(content="

⏰ Session Expired

Please login again.

") + + html_content = f""" + + + + Session Status + + + +
+

✅ Active Session

+
+ Session ID: + {session_id[:16]}... +
+
+ Token Valid: + Yes +
+
+ Expires In: + {token.expires_in} seconds +
+
+ + + """ + + return HTMLResponse(content=html_content) + + async def oauth_logout(request: Request) -> Response: + session_id = request.cookies.get("cms_mcp_session") + if session_id: + self.remove_token(session_id) + + response = RedirectResponse(url="/oauth/login") + response.delete_cookie("cms_mcp_session") + + logger.info("User logged out") + return response + + return [ + Route("/oauth/login", oauth_login), + Route("/oauth/authorize/{provider}", oauth_authorize), + Route("/oauth/callback/{provider}", oauth_callback), + Route("/oauth/status", oauth_status), + Route("/oauth/logout", oauth_logout), + ] diff --git a/app/mcp/oauth/routes.py b/app/mcp/oauth/routes.py new file mode 100644 index 0000000..b43127c --- /dev/null +++ b/app/mcp/oauth/routes.py @@ -0,0 +1,406 @@ +import os +import secrets +from typing import Optional +from fastapi import Request, Response, HTTPException, Cookie +from fastapi.responses import HTMLResponse, RedirectResponse +from fastapi import FastAPI +from app.mcp.oauth.oauth import OAuthManager +from app.mcp.logger import get_logger + +logger = get_logger(__name__) + + +def register_oauth_routes(app: FastAPI, oauth_manager: OAuthManager) -> None: + + @app.get("/oauth/login", response_class=HTMLResponse) + async def oauth_login() -> HTMLResponse: + html_content = """ + + + + CMS MCP Server - Login + + + + + + + """ + return HTMLResponse(content=html_content) + + @app.get("/oauth/authorize/{provider}") + async def oauth_authorize(provider: str, response: Response) -> RedirectResponse: + oauth_provider = oauth_manager.get_provider(provider) + if not oauth_provider: + raise HTTPException(status_code=400, detail=f"Unknown provider: {provider}") + + auth_url, state = oauth_provider.generate_authorization_url() + + response = RedirectResponse(url=auth_url) + response.set_cookie( + key=f"oauth_state_{provider}", + value=state, + max_age=300, + httponly=True, + samesite="lax", + secure=os.getenv("CMS_MCP_SECURE_COOKIES", "false").lower() == "true" + ) + + logger.info(f"Initiating OAuth flow for provider: {provider}") + return response + + @app.get("/oauth/callback/{provider}") + async def oauth_callback( + request: Request, + provider: str, + code: Optional[str] = None, + state: Optional[str] = None, + error: Optional[str] = None, + ) -> HTMLResponse: + if error: + logger.error(f"OAuth error for {provider}: {error}") + return HTMLResponse( + content=f""" + + + Authentication Error + +

❌ Authentication Failed

+

Error: {error}

+ Try again + + + """, + status_code=400 + ) + + if not code or not state: + raise HTTPException(status_code=400, detail="Missing code or state") + + if request is None: + raise HTTPException(status_code=400, detail="Request object is required") + + oauth_provider = oauth_manager.get_provider(provider) + if not oauth_provider: + raise HTTPException(status_code=400, detail=f"Unknown provider: {provider}") + + stored_state = request.cookies.get(f"oauth_state_{provider}") + if not stored_state or stored_state != state: + logger.error(f"State mismatch for {provider}") + raise HTTPException(status_code=400, detail="Invalid state parameter") + + if not oauth_provider.verify_state(state): + logger.error(f"State verification failed for {provider}") + raise HTTPException(status_code=400, detail="State verification failed") + + try: + token = await oauth_provider.exchange_code_for_token(code) + user_info = await oauth_provider.get_user_info(token.access_token) + session_id = secrets.token_urlsafe(32) + oauth_manager.store_token(session_id, token) + user_email = user_info.get("email", "N/A") + user_name = user_info.get("name") or user_info.get("login", "User") + + html_content = f""" + + + + Authentication Successful + + + +
+
✅
+

Authentication Successful!

+ +
+

Session ID:

+

{session_id}

+

+ Use this session ID in your MCP client configuration or include the session cookie. +

+
+

+ You can now use the MCP server with your authenticated session. +

+ Check Session Status +
+ + + """ + + response = HTMLResponse(content=html_content) + response.set_cookie( + key="cms_mcp_session", + value=session_id, + max_age=86400, + httponly=True, + samesite="lax", + secure=os.getenv("CMS_MCP_SECURE_COOKIES", "false").lower() == "true" + ) + + response.delete_cookie(f"oauth_state_{provider}") + + logger.info(f"Successfully authenticated user via {provider}: {user_email}") + return response + + except Exception as e: + logger.error(f"OAuth callback error for {provider}: {str(e)}") + raise HTTPException(status_code=500, detail=f"Authentication failed: {str(e)}") + + @app.get("/oauth/status") + async def oauth_status( + request: Request, + cms_mcp_session: Optional[str] = Cookie(None) + ) -> HTMLResponse: + if not cms_mcp_session: + return HTMLResponse( + content=""" + + + No Session + +

🔒 No Active Session

+

You are not currently authenticated.

+ Login + + + """ + ) + + token = await oauth_manager.get_valid_token(cms_mcp_session) + + if not token: + return HTMLResponse( + content=""" + + + Session Expired + +

⏰ Session Expired

+

Your session has expired. Please login again.

+ Login + + + """ + ) + + is_expired = "Yes" if token.is_expired() else "No" + + html_content = f""" + + + + Session Status + + + +
+

✅ Active Session

+
+ Session ID: + {cms_mcp_session[:16]}... +
+
+ Token Type: + {token.token_type} +
+
+ Expires In: + {token.expires_in} seconds +
+
+ Is Expired: + {is_expired} +
+
+ Has Refresh Token: + {"Yes" if token.refresh_token else "No"} +
+ Logout +
+ + + """ + + return HTMLResponse(content=html_content) + + @app.get("/oauth/logout") + async def oauth_logout(cms_mcp_session: Optional[str] = Cookie(None)) -> RedirectResponse: + if cms_mcp_session: + oauth_manager.remove_token(cms_mcp_session) + + response = RedirectResponse(url="/oauth/login") + response.delete_cookie("cms_mcp_session") + + logger.info("User logged out") + return response diff --git a/app/mcp/server.py b/app/mcp/server.py new file mode 100644 index 0000000..fa1b752 --- /dev/null +++ b/app/mcp/server.py @@ -0,0 +1,202 @@ +"""cms-mcp-server""" + +import os +import uvicorn +from collections.abc import AsyncIterator +from contextlib import asynccontextmanager +from typing import Optional +from starlette.applications import Starlette +from starlette.routing import Mount +from starlette.middleware import Middleware +from mcp.server.fastmcp import FastMCP +from cms_client import ( + ApiClient, + Configuration, + MetadataApi, + AnnotationsApi, + RedactionApi, + TrainingApi, +) +from app.mcp.domain import AppContext, TransportType +from app.mcp.tools import metadata, annotation, train_eval +from app.mcp.oauth.oauth import OAuthManager +from app.mcp.oauth.middleware import OAuthMiddleware +from app.mcp.logger import get_logger + +logger = get_logger(__name__) + +COGSTACK_MODELSERVE_INSTRUCTIONS = """ +You are the CogStack ModelServe assistant. You expose MCP tools to interact with deployed models via the MCP server interface. Your job is to interpret the user's natural language requests and map them to the correct MCP tool calls with appropriate arguments. Use the following guidelines: + +1. Interpret intent + - If the user asks about model information, status, or metadata (e.g. "what model is running?", "model details"), use the `get_model_info` tool. + - If the user wants to annotate text or extract entities (e.g. "annotate this text", "find entities in this document"), use the `get_annotations` tool. + - If the user wants to redact sensitive information (e.g. "redact this text", "remove personal information"), use the `redact_text` tool. + - If the user asks about training or evaluation status (e.g. "what's the status of training job X?", "evaluation info for job Y"), use the `get_train_eval_info` tool. + - If the user wants training or evaluation metrics (e.g. "get metrics for training job X", "evaluation metrics for job Y"), use the `get_train_eval_metrics` tool. + +2. Validate arguments + - For `get_model_info`: No arguments required. + - For `get_annotations`: Requires text input (string). + - For `redact_text`: Requires text input (string). + - For `get_train_eval_info`: Requires train_eval_id (string). + - For `get_train_eval_metrics`: Requires train_eval_id (string). + - Ensure inputs are provided and are valid strings. + - If required arguments are missing, ask the user to provide them. + +3. Form an MCP tool call + - Use the proper tool name and arguments according to the available tools. + - Example calls: + - get_model_info() - no arguments + - get_annotations(text="Patient has fever and chest pain") + - redact_text(text="Patient John Doe has fever") + - get_train_eval_info(train_eval_id="job123") + - get_train_eval_metrics(train_eval_id="job123") + +4. Handle responses + - Return the tool output (model info, annotations, redacted text, training/evaluation status, metrics) to the user in human-friendly form. + - If the tool returns an error, capture it and present a clear error message (e.g., "Failed to get model info: "). + +5. Fallback / clarification + - If the user's request is ambiguous (e.g. "process this text" without specifying annotation or redaction), ask for clarification: "Do you want to annotate the text or redact sensitive information?" + - If no matching tool exists for the request, respond: "I'm sorry, I don't have that capability in the CogStack ModelServe interface." + +6. Security / permissions check + - Only use the available tools: get_model_info, get_annotations, redact_text, get_train_eval_info, get_train_eval_metrics. + - Don't allow arbitrary operations outside these tools. + +Available tools: + - get_model_info(): Gets information about the running model (no arguments) + - get_annotations(text: str): Gets annotations for the provided text using the running model + - redact_text(text: str): Redacts extracted entities from the provided text using the running model + - get_train_eval_info(train_eval_id: str): Gets training or evaluation status for the specified job ID + - get_train_eval_metrics(train_eval_id: str): Gets training or evaluation metrics for the specified job ID +""" + +# Global OAuth manager +oauth_manager: Optional[OAuthManager] = None + + +@asynccontextmanager +async def app_lifespan(app: FastMCP) -> AsyncIterator[AppContext]: + """Application lifespan context manager""" + configuration = Configuration( + host=os.environ.get("CMS_BASE_URL", "http://127.0.0.1:8000") + ) + configuration.access_token = os.environ.get("CMS_ACCESS_TOKEN", "") + configuration.api_key["APIKeyCookie"] = os.environ.get("CMS_API_KEY", "Bearer") + + api_client = ApiClient(configuration) + try: + yield AppContext( + metadata_api=MetadataApi(api_client), + annotation_api=AnnotationsApi(api_client), + redaction_api=RedactionApi(api_client), + training_api=TrainingApi(api_client), + ) + finally: + pass # api_client.close() is only required when using httpx.AsyncClient + +def create_server() -> Starlette: + """Create the main Starlette application with MCP and optional OAuth""" + global oauth_manager + + host = os.environ.get("CMS_MCP_SERVER_HOST", "127.0.0.1") + port = int(os.environ.get("CMS_MCP_SERVER_PORT", "8080")) + + mcp_server = FastMCP( + "cms_mcp_server", + COGSTACK_MODELSERVE_INSTRUCTIONS, + lifespan=app_lifespan, + host=host, + port=port, + ) + + metadata.register_module(mcp_server) + annotation.register_module(mcp_server) + train_eval.register_module(mcp_server) + + routes = [] + middleware = [] + oauth_enabled = os.environ.get("CMS_MCP_OAUTH_ENABLED", "false").lower() == "true" + + if oauth_enabled: + try: + base_url = f"http://{host}:{port}" + oauth_manager = OAuthManager(base_url) + oauth_routes = oauth_manager.create_oauth_routes() + routes.extend(oauth_routes) + + middleware.append( + Middleware( + OAuthMiddleware, + oauth_manager=oauth_manager, + public_paths=[ + "/oauth/", + "/docs", + "/openapi.json", + "/redoc", + "/health", + "/.well-known/", + ] + ) + ) + + logger.info("OAuth authentication enabled") + except Exception as e: + logger.error(f"Failed to setup OAuth: {e}") + logger.warning("Server will run without OAuth authentication") + + if os.environ.get("CMS_MCP_TRANSPORT") == TransportType.SSE.value: + routes.append(Mount("/", app=mcp_server.sse_app(""))) + logger.info(f"MCP SSE endpoint mounted at http://{host}:{port}/sse") + elif os.environ.get("CMS_MCP_TRANSPORT") == TransportType.STREAMABLE_HTTP.value: + # OAuth is not supported yet for HTTP transport + logger.warning("OAuth disabled for HTTP transport due to FastMCP limitations") + logger.info(f"MCP HTTP endpoint mounted at http://{host}:{port}/mcp") + return mcp_server.streamable_http_app() + elif os.environ.get("CMS_MCP_TRANSPORT") == TransportType.STDIO.value: + logger.info("MCP running in STDIO mode") + mcp_server.run(transport=TransportType.STDIO.value) + else: + raise ValueError(f"Unsupported transport type: {os.environ.get('CMS_MCP_TRANSPORT')}") + + app = Starlette( + routes=routes, + middleware=middleware, + ) + + return app + +def main() -> None: + host = os.environ.get("CMS_MCP_SERVER_HOST", "127.0.0.1") + port = int(os.environ.get("CMS_MCP_SERVER_PORT", "8080")) + + app = create_server() + + if os.environ.get("CMS_MCP_OAUTH_ENABLED", "false").lower() == "true" and os.environ.get("CMS_MCP_TRANSPORT") != TransportType.STREAMABLE_HTTP.value: + logger.info(f"OAuth login: http://{host}:{port}/oauth/login") + + uvicorn.run( + app, + host=host, + port=port, + log_level=os.environ.get("FASTMCP_LOG_LEVEL", "info").lower(), + ) + +server: FastMCP | None = None + +if os.environ.get("CMS_MCP_DEV", "0") == "1": + server = FastMCP( + "cms_mcp_server", + COGSTACK_MODELSERVE_INSTRUCTIONS, + lifespan=app_lifespan, + host=os.environ.get("CMS_MCP_SERVER_HOST", "127.0.0.1"), + port=int(os.environ.get("CMS_MCP_SERVER_PORT", "8080")), + ) + metadata.register_module(server) + annotation.register_module(server) + train_eval.register_module(server) + +if __name__ == "__main__": + main() diff --git a/app/mcp/tools/__init__.py b/app/mcp/tools/__init__.py new file mode 100644 index 0000000..f7f9d2e --- /dev/null +++ b/app/mcp/tools/__init__.py @@ -0,0 +1 @@ +"""This package contains all the tool modules for the CMS MCP Server.""" diff --git a/app/mcp/tools/annotation/__init__.py b/app/mcp/tools/annotation/__init__.py new file mode 100644 index 0000000..6260a32 --- /dev/null +++ b/app/mcp/tools/annotation/__init__.py @@ -0,0 +1,48 @@ + +from mcp.server.fastmcp import FastMCP, Context +from mcp.server.session import ServerSession +from .get_annotations import annotate +from .get_redaction import redact +from ...domain import AppContext +from ...utils import require_api_key + + +def register_module(mcp: FastMCP) -> None: + + @mcp.tool( + name="get_annotations", + description="Gets annotations for the provided text using the running model.", + ) + @require_api_key + def get_annotations_tool(text: str, ctx: Context[ServerSession, AppContext]) -> dict: + """ + Gets annotations for the provided text using the running model. + + Args: + text (str): The input text to be annotated. + ctx (Context[ServerSession, AppContext]): The application context. + + Returns: + dict: A dictionary containing the annotations. + """ + annotation_api = ctx.request_context.lifespan_context.annotation_api + return annotate(text, annotation_api) + + @mcp.tool( + name="redact_text", + description="Redacts extracted entities from the provided text using the running model.", + ) + @require_api_key + def get_redaction_tool(text: str, ctx: Context[ServerSession, AppContext]) -> dict: + """ + Redacts extracted entities from the provided text using the running model. + + Args: + text (str): The input text to be redacted. + ctx (Context[ServerSession, AppContext]): The application context. + + Returns: + dict: A dictionary containing the redacted text. + """ + redaction_api = ctx.request_context.lifespan_context.redaction_api + return redact(text, redaction_api) diff --git a/app/mcp/tools/annotation/get_annotations.py b/app/mcp/tools/annotation/get_annotations.py new file mode 100644 index 0000000..32ddf74 --- /dev/null +++ b/app/mcp/tools/annotation/get_annotations.py @@ -0,0 +1,40 @@ +from urllib3.exceptions import TimeoutError +from cms_client import AnnotationsApi +from cms_client.exceptions import ApiException +from ...logger import get_logger + + +logger = get_logger(__name__) + +def annotate(text: str, annotation_api: AnnotationsApi) -> dict: + """ + Gets annotations for the provided text. + + Args: + text (str): The input text to be annotated. + annotation_api (AnnotationsApi): The Annotations API instance. + + Returns: + Dict: A dictionary containing the annotations. + """ + try: + api_response = annotation_api.get_entities_from_text(text) + return api_response.to_dict() + except ApiException as e: + logger.error(f"API Exception when calling get_entities_from_text: {e}") + return { + "status": "error", + "reason": e.reason, + } + except TimeoutError: + logger.error("Request timed out when calling get_entities_from_text") + return { + "status": "error", + "reason": "Request timed out. Retrying or aborting gracefully.", + } + except Exception as e: + logger.error(f"Unexpected error: {e}") + return { + "status": "error", + "reason": f"Unexpected error: {e}", + } diff --git a/app/mcp/tools/annotation/get_redaction.py b/app/mcp/tools/annotation/get_redaction.py new file mode 100644 index 0000000..421a159 --- /dev/null +++ b/app/mcp/tools/annotation/get_redaction.py @@ -0,0 +1,40 @@ +from urllib3.exceptions import TimeoutError +from cms_client import RedactionApi +from cms_client.exceptions import ApiException +from ...logger import get_logger + + +logger = get_logger(__name__) + +def redact(text: str, redaction_api: RedactionApi) -> dict: + """ + Redacts sensitive information from the provided text. + + Args: + text (str): The input text to be redacted. + redaction_api (RedactionApi): The Redaction API instance. + + Returns: + str: The redacted text. + """ + try: + api_response = redaction_api.get_redacted_text(text) + return { "redact_text": str(api_response) } + except ApiException as e: + logger.error(f"API Exception when calling get_redacted_text: {e}") + return { + "status": "error", + "reason": e.reason, + } + except TimeoutError: + logger.error("Request timed out when calling get_redacted_text") + return { + "status": "error", + "reason": "Request timed out. Retrying or aborting gracefully.", + } + except Exception as e: + logger.error(f"Unexpected error: {e}") + return { + "status": "error", + "reason": f"Unexpected error: {e}", + } diff --git a/app/mcp/tools/metadata/__init__.py b/app/mcp/tools/metadata/__init__.py new file mode 100644 index 0000000..6cba8ee --- /dev/null +++ b/app/mcp/tools/metadata/__init__.py @@ -0,0 +1,26 @@ +from mcp.server.fastmcp import FastMCP, Context +from mcp.server.session import ServerSession +from .get_model_info import model_info +from ...domain import AppContext +from ...utils import require_api_key + + +def register_module(mcp: FastMCP) -> None: + + @mcp.tool( + name="get_model_info", + description="Gets information about the running model.", + ) + @require_api_key + def get_model_info_tool(ctx: Context[ServerSession, AppContext]) -> dict: + """ + Gets information about the running model. + + Args: + ctx (Context[ServerSession, AppContext]): The application context. + + Returns: + dict: A dictionary containing the model metadata information. + """ + metadata_api = ctx.request_context.lifespan_context.metadata_api + return model_info(metadata_api) diff --git a/app/mcp/tools/metadata/get_model_info.py b/app/mcp/tools/metadata/get_model_info.py new file mode 100644 index 0000000..3a2d54f --- /dev/null +++ b/app/mcp/tools/metadata/get_model_info.py @@ -0,0 +1,39 @@ +from urllib3.exceptions import TimeoutError +from cms_client import MetadataApi +from cms_client.exceptions import ApiException +from ...logger import get_logger + + +logger = get_logger(__name__) + +def model_info(metadata_api: MetadataApi) -> dict: + """ + Gets model metadata information. + + Args: + metadata_api (MetadataApi): The Metadata API instance. + + Returns: + Dict: A dictionary containing the model metadata information. + """ + try: + api_response = metadata_api.get_model_card() + return api_response.to_dict() + except ApiException as e: + logger.error(f"API Exception when calling get_model_card: {e}") + return { + "status": "error", + "reason": e.reason, + } + except TimeoutError: + logger.error("Request timed out when calling get_model_card") + return { + "status": "error", + "reason": "Request timed out. Retrying or aborting gracefully.", + } + except Exception as e: + logger.error(f"Unexpected error: {e}") + return { + "status": "error", + "reason": f"Unexpected error: {e}", + } diff --git a/app/mcp/tools/train_eval/__init__.py b/app/mcp/tools/train_eval/__init__.py new file mode 100644 index 0000000..793aa4d --- /dev/null +++ b/app/mcp/tools/train_eval/__init__.py @@ -0,0 +1,47 @@ +from mcp.server.fastmcp import FastMCP, Context +from mcp.server.session import ServerSession +from .get_train_eval_info import get_train_eval_info +from .get_train_eval_metrics import get_train_eval_metrics +from ...domain import AppContext +from ...utils import require_api_key + + +def register_module(mcp: FastMCP) -> None: + + @mcp.tool( + name="get_train_eval_info", + description="Gets training or evaluation status of the running model.", + ) + @require_api_key + def get_train_eval_info_tool(train_eval_id: str, ctx: Context[ServerSession, AppContext]) -> dict: + """ + Gets training or evaluation status of the running model. + + Args: + train_eval_id (str): The ID of the training or evaluation job. + ctx (Context[ServerSession, AppContext]): The application context. + + Returns: + dict: A dictionary containing the training or evaluation status. + """ + training_api = ctx.request_context.lifespan_context.training_api + return get_train_eval_info(train_eval_id, training_api) + + @mcp.tool( + name="get_train_eval_metrics", + description="Gets training or evaluation metrics.", + ) + @require_api_key + def get_train_eval_metrics_tool(train_eval_id: str, ctx: Context[ServerSession, AppContext]) -> dict: + """ + Gets training or evaluation metrics. + + Args: + train_eval_id (str): The ID of the training or evaluation job. + ctx (Context[ServerSession, AppContext]): The application context. + + Returns: + dict: A dictionary containing the training or evaluation metrics. + """ + training_api = ctx.request_context.lifespan_context.training_api + return get_train_eval_metrics(train_eval_id, training_api) diff --git a/app/mcp/tools/train_eval/get_train_eval_info.py b/app/mcp/tools/train_eval/get_train_eval_info.py new file mode 100644 index 0000000..c278fa5 --- /dev/null +++ b/app/mcp/tools/train_eval/get_train_eval_info.py @@ -0,0 +1,40 @@ +from urllib3.exceptions import TimeoutError +from cms_client import TrainingApi +from cms_client.exceptions import ApiException +from ...logger import get_logger + + +logger = get_logger(__name__) + +def get_train_eval_info(train_eval_id: str, training_api: TrainingApi) -> dict: + """ + Gets training or evaluation status of the running model. + + Args: + train_eval_id (str): The ID of the training or evaluation job. + training_api (TrainingApi): The Training API instance. + + Returns: + Dict: A dictionary containing the training or evaluation status. + """ + try: + api_response = training_api.train_eval_info(train_eval_id) + return api_response[0] # type: ignore + except ApiException as e: + logger.error(f"API Exception when calling train_eval_info: {e}") + return { + "status": "error", + "reason": e.reason, + } + except TimeoutError: + logger.error("Request timed out when calling train_eval_info") + return { + "status": "error", + "reason": "Request timed out. Retrying or aborting gracefully.", + } + except Exception as e: + logger.error(f"Unexpected error: {e}") + return { + "status": "error", + "reason": f"Unexpected error: {e}", + } diff --git a/app/mcp/tools/train_eval/get_train_eval_metrics.py b/app/mcp/tools/train_eval/get_train_eval_metrics.py new file mode 100644 index 0000000..f1bb4c0 --- /dev/null +++ b/app/mcp/tools/train_eval/get_train_eval_metrics.py @@ -0,0 +1,40 @@ +from urllib3.exceptions import TimeoutError +from cms_client import TrainingApi +from cms_client.exceptions import ApiException +from ...logger import get_logger + + +logger = get_logger(__name__) + +def get_train_eval_metrics(train_eval_id: str, training_api: TrainingApi) -> dict: + """ + Gets training or evaluation metrics. + + Args: + train_eval_id (str): The ID of the training or evaluation job. + training_api (TrainingApi): The Training API instance. + + Returns: + Dict: A dictionary containing the training or evaluation metrics. + """ + try: + api_response = training_api.train_eval_metrics(train_eval_id) + return api_response[0] # type: ignore + except ApiException as e: + logger.error(f"API Exception when calling train_eval_metrics: {e}") + return { + "status": "error", + "reason": e.reason, + } + except TimeoutError: + logger.error("Request timed out when calling train_eval_metrics") + return { + "status": "error", + "reason": "Request timed out. Retrying or aborting gracefully.", + } + except Exception as e: + logger.error(f"Unexpected error: {e}") + return { + "status": "error", + "reason": f"Unexpected error: {e}", + } diff --git a/app/mcp/utils.py b/app/mcp/utils.py new file mode 100644 index 0000000..10d5050 --- /dev/null +++ b/app/mcp/utils.py @@ -0,0 +1,29 @@ +import os +from typing import Callable, Any, Awaitable, Union +from functools import wraps + + +def require_api_key(tool_fn: Callable[..., Union[Any, Awaitable[Any]]]) -> Callable[..., Union[Any, Awaitable[Any]]]: + @wraps(tool_fn) + def wrapper(*args: Any, **kwargs: Any) -> Union[Any, Awaitable[Any]]: + ctx = kwargs["ctx"] if kwargs and "ctx" in kwargs else None + if ctx and hasattr(ctx, "request_context"): + api_key = ( + ctx.request_context.request.headers.get("x-api-key", None) or + ctx.request_context.request.headers.get("X-API-Key", None) or + ctx.request_context.request.headers.get("X-Api-Key", None) + ) + else: + api_key = None + api_keys_env = os.environ.get("MCP_API_KEYS") + + if not api_keys_env: # No API-key-based authentication required + return tool_fn(*args, **kwargs) + + allowed_keys = [key.strip() for key in api_keys_env.split(",")] + + if not api_key or api_key not in allowed_keys: + raise PermissionError("The API key is either invalid or missing") + + return tool_fn(*args, **kwargs) + return wrapper diff --git a/pyproject.toml b/pyproject.toml index ffb26c7..dc6c874 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,23 +9,23 @@ description = "A model serving and governance system for CogStack NLP solutions" requires-python = ">3.10,<3.13" dynamic = ["version"] dependencies = [ - "medcat[spacy,meta-cat,deid,rel-cat]~=2.2.0; python_version>='3.10'", + "medcat[spacy,meta-cat,deid,rel-cat]~=2.3.0", "datasets>=2.21.0", "fastapi~=0.115.0", - "uvicorn~=0.29.0", + "uvicorn~=0.31.1", "python-multipart~=0.0.7", "ijson~=3.1.4", - "python-dotenv~=0.20.0", + "python-dotenv~=1.0.0", "mlflow~=2.16.2", "psycopg2-binary~=2.9.4", - "boto3~=1.28.84", + "boto3~=1.41.1", "click<8.2.0", - "typer~=0.15.1", + "typer~=0.16.0", "prometheus-fastapi-instrumentator~=7.0.0", "sentencepiece~=0.2.0", - "slowapi~=0.1.7", + "slowapi~=0.1.9", "graypy~=2.1.0", - "fastapi-users~=13.0.0", + "fastapi-users~=15.0.3", "fastapi-users-db-sqlalchemy~=5.0.0", "asyncpg~=0.29.0", "aiosqlite~=0.19.0", @@ -34,9 +34,10 @@ dependencies = [ "pynvml~=11.5.3", "toml~=0.10.2", "peft<0.14.0", - "huggingface-hub~=0.33.0", + "huggingface-hub~=0.34.0", "spacy>3.8", "seqeval>=1.2.2", + "transformers~=4.56.2", ] readme = "README.md" keywords = ["natural-language-processing", "electronic-health-records", "clinical-data"] @@ -63,11 +64,11 @@ dev = [ "pytest-asyncio~=0.23.7", "pytest-cov~=4.1.0", "pytest-bdd~=7.2.0", - "httpx~=0.24.1", + "httpx~=0.27.1", "mypy~=1.18.0", "ruff==0.6.9", "locust<2.32.0", - "typer-cli~=0.15.1", + "typer-cli~=0.16.0", "types-toml==0.10.8.20240310", "types-requests>=2.31.0.6", "openai>=1.84.0", @@ -79,9 +80,16 @@ docs = [ "sphinx-rtd-theme~=3.0.2", ] llm = [ - "vllm~=0.8.5", + "vllm>=0.9.0", "trl~=0.15.0", "bitsandbytes==0.49.0", + "triton~=3.5.0", + "kernels~=0.11.7", +] +mcp = [ + "mcp[cli]==1.26.0", + "cms-client==0.0.1", + "loguru~=0.7.3" ] # For pip versions not supporting PEP 735 @@ -94,11 +102,11 @@ dev = [ "pytest-asyncio~=0.23.7", "pytest-cov~=4.1.0", "pytest-bdd~=7.2.0", - "httpx~=0.24.1", + "httpx~=0.27.1", "mypy~=1.18.0", "ruff==0.6.9", "locust<2.32.0", - "typer-cli~=0.15.1", + "typer-cli~=0.16.0", "types-requests>=2.31.0.6", "types-toml==0.10.8.20240310", "openai>=1.84.0", @@ -111,9 +119,16 @@ docs = [ ] llm = [ - "vllm~=0.8.5", + "vllm>=0.9.0", "trl>=0.11.4", "bitsandbytes>=0.45.5", + "triton~=3.5.0", + "kernels~=0.11.7", +] +mcp = [ + "mcp[cli]==1.26.0", + "cms-client==0.0.1", + "loguru~=0.7.3", ] [tool.setuptools] @@ -175,6 +190,7 @@ check_untyped_defs = true no_implicit_reexport = true disallow_untyped_defs = true disable_error_code = "method-assign" +exclude = "app/model/" plugins = [ "pydantic.mypy" ] diff --git a/tests/app/cli/test_cli.py b/tests/app/cli/test_cli.py index 4512fc7..e760590 100644 --- a/tests/app/cli/test_cli.py +++ b/tests/app/cli/test_cli.py @@ -106,3 +106,15 @@ def test_generate_api_doc(): result = runner.invoke(cmd_app, ["export-openapi-spec", "--api-title", "TestAPIs"]) assert result.exit_code == 0 assert "OpenAPI doc exported to testapis.json" in result.output + + +def test_mcp_help(): + result = runner.invoke(cmd_app, ["mcp", "--help"]) + assert result.exit_code == 0 + assert "Run the MCP server for accessing CMS capabilities" in result.output + + +def test_mcp_run_help(): + result = runner.invoke(cmd_app, ["mcp", "run", "--help"]) + assert result.exit_code == 0 + assert "Run the MCP server for accessing CMS capabilities" in result.output diff --git a/tests/app/mcp/oauth/test_middleware.py b/tests/app/mcp/oauth/test_middleware.py new file mode 100644 index 0000000..dde5860 --- /dev/null +++ b/tests/app/mcp/oauth/test_middleware.py @@ -0,0 +1,275 @@ +import pytest +from unittest.mock import Mock, AsyncMock +from fastapi import Request, HTTPException +from fastapi.responses import JSONResponse +from app.mcp.oauth.middleware import OAuthMiddleware, get_oauth_token_from_request, require_auth +from app.mcp.oauth.oauth import OAuthManager, OAuthToken + +@pytest.fixture +def mock_oauth_manager(): + manager = Mock(spec=OAuthManager) + return manager + +@pytest.fixture +def oauth_token(): + return OAuthToken( + access_token="test_access_token", + token_type="Bearer", + expires_in=3600, + refresh_token="test_refresh_token", + ) +@pytest.fixture +def mock_app(): + async def mock_scope(scope, receive, send): + pass + return mock_scope + +class TestOAuthMiddleware: + def test_init_with_public_paths(self, mock_app, mock_oauth_manager): + public_paths = ["/oauth/", "/docs", "/health"] + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=public_paths + ) + + assert middleware.oauth_manager == mock_oauth_manager + assert middleware.public_paths == public_paths + + def test_init_without_public_paths(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager + ) + + assert middleware.oauth_manager == mock_oauth_manager + assert middleware.public_paths == [] + + def test_is_public_path_with_match(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/", "/docs", "/health"] + ) + + assert middleware._is_public_path("/oauth/login") is True + assert middleware._is_public_path("/docs") is True + assert middleware._is_public_path("/health") is True + + def test_is_public_path_without_match(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/", "/docs", "/health"] + ) + + assert middleware._is_public_path("/api/endpoint") is False + assert middleware._is_public_path("/protected/path") is False + assert middleware._is_public_path("/users/profile") is False + + @pytest.mark.asyncio + async def test_dispatch_sse_bypasses_auth(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/sse" + request.cookies = {} + request.headers = {} + call_next = AsyncMock(return_value=Mock()) + + await middleware.dispatch(request, call_next) + + call_next.assert_called_once_with(request) + + @pytest.mark.asyncio + async def test_dispatch_public_path_bypasses_auth(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/", "/docs", "/health"] + ) + request = Mock(spec=Request) + request.url.path = "/oauth/login" + request.cookies = {} + request.headers = {} + call_next = AsyncMock(return_value=Mock()) + + await middleware.dispatch(request, call_next) + + call_next.assert_called_once_with(request) + + @pytest.mark.asyncio + async def test_dispatch_no_session_returns_401(self, mock_app, mock_oauth_manager): + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {} + request.headers = {} + request.query_params = {} + call_next = AsyncMock(return_value=Mock()) + + response = await middleware.dispatch(request, call_next) + + assert isinstance(response, JSONResponse) + assert response.status_code == 401 + call_next.assert_not_called() + + @pytest.mark.asyncio + async def test_dispatch_session_cookie_authenticated(self, mock_app, mock_oauth_manager, oauth_token): + mock_oauth_manager.get_valid_token = AsyncMock(return_value=oauth_token) + + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {"cms_mcp_session": "valid_session_id"} + request.headers = {} + request.query_params = {} + request.state = Mock() + call_next = AsyncMock(return_value=Mock()) + + await middleware.dispatch(request, call_next) + + mock_oauth_manager.get_valid_token.assert_called_once_with("valid_session_id") + call_next.assert_called_once_with(request) + assert request.state.oauth_token == oauth_token + assert request.state.session_id == "valid_session_id" + + @pytest.mark.asyncio + async def test_dispatch_bearer_token_authenticated(self, mock_app, mock_oauth_manager, oauth_token): + mock_oauth_manager.get_valid_token = AsyncMock(return_value=oauth_token) + + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {} + request.headers = {"Authorization": "Bearer valid_token"} + request.query_params = {} + request.state = Mock() + call_next = AsyncMock(return_value=Mock()) + + await middleware.dispatch(request, call_next) + + mock_oauth_manager.get_valid_token.assert_called_once_with("valid_token") + call_next.assert_called_once_with(request) + + @pytest.mark.asyncio + async def test_dispatch_query_param_session_authenticated(self, mock_app, mock_oauth_manager, oauth_token): + mock_oauth_manager.get_valid_token = AsyncMock(return_value=oauth_token) + + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {} + request.headers = {} + request.query_params = {"session_id": "valid_session_id"} + request.state = Mock() + call_next = AsyncMock(return_value=Mock()) + + await middleware.dispatch(request, call_next) + + mock_oauth_manager.get_valid_token.assert_called_once_with("valid_session_id") + call_next.assert_called_once_with(request) + + @pytest.mark.asyncio + async def test_dispatch_invalid_session_returns_401(self, mock_app, mock_oauth_manager): + """Test that invalid/expired session returns 401""" + mock_oauth_manager.get_valid_token = AsyncMock(return_value=None) + + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {"cms_mcp_session": "invalid_session_id"} + request.headers = {} + request.query_params = {} + request.state = Mock() + call_next = AsyncMock(return_value=Mock()) + + response = await middleware.dispatch(request, call_next) + + assert isinstance(response, JSONResponse) + assert response.status_code == 401 + call_next.assert_not_called() + + @pytest.mark.asyncio + async def test_dispatch_exception_returns_500(self, mock_app, mock_oauth_manager): + mock_oauth_manager.get_valid_token = AsyncMock(side_effect=Exception("Database error")) + + middleware = OAuthMiddleware( + app=mock_app, + oauth_manager=mock_oauth_manager, + public_paths=["/oauth/"] + ) + request = Mock(spec=Request) + request.url.path = "/api/protected" + request.cookies = {"cms_mcp_session": "valid_session_id"} + request.headers = {} + request.query_params = {} + request.state = Mock() + call_next = AsyncMock(return_value=Mock()) + + response = await middleware.dispatch(request, call_next) + + assert isinstance(response, JSONResponse) + assert response.status_code == 500 + +class TestGetOAuthTokenFromRequest: + + def test_with_oauth_token(self, oauth_token): + request = Mock(spec=Request) + request.state.oauth_token = oauth_token + + token = get_oauth_token_from_request(request) + + assert token == "test_access_token" + + def test_without_oauth_token(self): + request = Mock(spec=Request) + del request.state.oauth_token + + token = get_oauth_token_from_request(request) + + assert token is None + +class TestRequireAuth: + + def test_with_valid_token(self, oauth_token): + request = Mock(spec=Request) + request.state.oauth_token = oauth_token + + token = require_auth(request) + + assert token == "test_access_token" + + def test_without_token_raises_401(self): + + request = Mock(spec=Request) + del request.state.oauth_token + + with pytest.raises(HTTPException) as exc_info: + require_auth(request) + + assert exc_info.value.status_code == 401 + assert exc_info.value.detail == "Authentication required" diff --git a/tests/app/mcp/oauth/test_oauth.py b/tests/app/mcp/oauth/test_oauth.py new file mode 100644 index 0000000..c1e9ec4 --- /dev/null +++ b/tests/app/mcp/oauth/test_oauth.py @@ -0,0 +1,320 @@ +import pytest +from unittest.mock import AsyncMock, Mock, patch +from datetime import datetime, timedelta +from app.mcp.oauth.oauth import ( + OAuthConfig, + OAuthProvider, + GitHubOAuthProvider, + GoogleOAuthProvider, + OAuthManager, + OAuthToken, +) + + +@pytest.fixture +def oauth_token(): + return OAuthToken( + access_token="test_access_token", + token_type="Bearer", + expires_in=3600, + refresh_token="test_refresh_token" + ) + + +@pytest.fixture +def oauth_config(): + return OAuthConfig( + client_id="test_client_id", + client_secret="test_client_secret", + authorization_url="https://example.com/auth", + token_url="https://example.com/token", + userinfo_url="https://example.com/userinfo", + redirect_uri="http://localhost:8080/oauth/callback", + scope="openid email profile" + ) + + +@pytest.fixture +def oauth_provider(oauth_config): + return OAuthProvider(config=oauth_config) + + +@pytest.fixture +def oauth_manager(): + return OAuthManager(base_url="http://localhost:8080") + + +class TestOAuthProvider: + + def test_generate_authorization_url_without_state(self, oauth_provider): + auth_url, state = oauth_provider.generate_authorization_url() + + assert auth_url.startswith("https://example.com/auth?") + assert "client_id=test_client_id" in auth_url + assert "redirect_uri=http://localhost:8080/oauth/callback" in auth_url + assert "response_type=code" in auth_url + assert "scope=openid email profile" in auth_url + assert "state=" in auth_url + assert len(state) == 43 + assert state in oauth_provider._state_store + + def test_generate_authorization_url_with_state(self, oauth_provider): + custom_state = "custom_state_123" + _, state = oauth_provider.generate_authorization_url(state=custom_state) + + assert state == custom_state + assert custom_state in oauth_provider._state_store + + def test_verify_state_valid(self, oauth_provider): + _, state = oauth_provider.generate_authorization_url() + + result = oauth_provider.verify_state(state) + + assert result is True + assert state not in oauth_provider._state_store + + def test_verify_state_invalid_not_found(self, oauth_provider): + result = oauth_provider.verify_state("nonexistent_state") + + assert result is False + + def test_verify_state_expired(self, oauth_provider): + _, state = oauth_provider.generate_authorization_url() + + oauth_provider._state_store[state] = datetime.utcnow() - timedelta(minutes=10) + + result = oauth_provider.verify_state(state) + + assert result is False + assert state not in oauth_provider._state_store + + @pytest.mark.asyncio + async def test_exchange_code_for_token(self, oauth_provider): + with patch("app.mcp.oauth.oauth.httpx.AsyncClient") as mock_client: + mock_response = Mock() + mock_response.json.return_value = { + "access_token": "new_access_token", + "token_type": "Bearer", + "expires_in": 3600, + "refresh_token": "new_refresh_token", + "scope": "openid email" + } + + mock_client_instance = AsyncMock() + mock_client_instance.post.return_value = mock_response + mock_client.return_value.__aenter__.return_value = mock_client_instance + + token = await oauth_provider.exchange_code_for_token("authorization_code") + + assert token.access_token == "new_access_token" + assert token.token_type == "Bearer" + assert token.expires_in == 3600 + assert token.refresh_token == "new_refresh_token" + assert token.scope == "openid email" + + @pytest.mark.asyncio + async def test_refresh_access_token(self, oauth_provider): + with patch("app.mcp.oauth.oauth.httpx.AsyncClient") as mock_client: + mock_response = Mock() + mock_response.json.return_value = { + "access_token": "refreshed_access_token", + "token_type": "Bearer", + "expires_in": 7200, + "refresh_token": "new_refresh_token", + } + + mock_client_instance = AsyncMock() + mock_client_instance.post.return_value = mock_response + mock_client.return_value.__aenter__.return_value = mock_client_instance + + token = await oauth_provider.refresh_access_token("old_refresh_token") + + assert token.access_token == "refreshed_access_token" + assert token.expires_in == 7200 + + @pytest.mark.asyncio + async def test_get_user_info(self, oauth_provider): + with patch("app.mcp.oauth.oauth.httpx.AsyncClient") as mock_client: + mock_response = Mock() + mock_response.json.return_value = { + "sub": "1234567890", + "name": "Test User", + "email": "test@example.com" + } + + mock_client_instance = AsyncMock() + mock_client_instance.get.return_value = mock_response + mock_client.return_value.__aenter__.return_value = mock_client_instance + + user_info = await oauth_provider.get_user_info("test_access_token") + + assert user_info["sub"] == "1234567890" + assert user_info["name"] == "Test User" + assert user_info["email"] == "test@example.com" + + +class TestGitHubOAuthProvider: + + def test_github_oauth_provider_initialization(self): + with patch.dict("os.environ", { + "GITHUB_CLIENT_ID": "test_github_client_id", + "GITHUB_CLIENT_SECRET": "test_github_client_secret" + }): + provider = GitHubOAuthProvider(redirect_uri="http://localhost:8080/oauth/callback") + + assert provider.config.client_id == "test_github_client_id" + assert provider.config.client_secret == "test_github_client_secret" + assert provider.config.authorization_url == "https://github.com/login/oauth/authorize" + assert provider.config.token_url == "https://github.com/login/oauth/access_token" + assert provider.config.userinfo_url == "https://api.github.com/user" + + @pytest.mark.asyncio + async def test_get_user_info_with_email(self, oauth_token): + with patch("app.mcp.oauth.oauth.httpx.AsyncClient") as mock_client: + mock_user_response = Mock() + mock_user_response.json.return_value = { + "login": "testuser", + "name": "Test User", + "email": "test@example.com" + } + + mock_client_instance = AsyncMock() + mock_client_instance.get.return_value = mock_user_response + mock_client.return_value.__aenter__.return_value = mock_client_instance + + provider = GitHubOAuthProvider(redirect_uri="http://localhost:8080/oauth/callback") + user_info = await provider.get_user_info("test_access_token") + + assert user_info["email"] == "test@example.com" + + +class TestGoogleOAuthProvider: + + def test_google_oauth_provider_initialization(self): + """Test creating a GoogleOAuthProvider""" + with patch.dict("os.environ", { + "GOOGLE_CLIENT_ID": "test_google_client_id", + "GOOGLE_CLIENT_SECRET": "test_google_client_secret" + }): + provider = GoogleOAuthProvider(redirect_uri="http://localhost:8080/oauth/callback") + + assert provider.config.client_id == "test_google_client_id" + assert provider.config.client_secret == "test_google_client_secret" + assert provider.config.authorization_url == "https://accounts.google.com/o/oauth2/v2/auth" + assert provider.config.token_url == "https://oauth2.googleapis.com/token" + assert provider.config.userinfo_url == "https://www.googleapis.com/oauth2/v2/userinfo" + + def test_google_oauth_provider_missing_credentials(self): + with patch.dict("os.environ", {}, clear=True): + import os + # Ensure env vars are not set + os.environ.pop("GOOGLE_CLIENT_ID", None) + os.environ.pop("GOOGLE_CLIENT_SECRET", None) + + provider = GoogleOAuthProvider(redirect_uri="http://localhost:8080/oauth/callback") + + assert provider.config.client_id == "" + assert provider.config.client_secret == "" + + +class TestOAuthManager: + + def test_get_provider_github(self, oauth_manager): + provider = oauth_manager.get_provider("github") + + assert provider is not None + assert isinstance(provider, GitHubOAuthProvider) + + def test_get_provider_google(self, oauth_manager): + provider = oauth_manager.get_provider("google") + + assert provider is not None + assert isinstance(provider, GoogleOAuthProvider) + + def test_get_provider_unknown(self, oauth_manager): + provider = oauth_manager.get_provider("unknown") + + assert provider is None + + def test_store_and_get_token(self, oauth_manager, oauth_token): + session_id = "test_session_123" + + oauth_manager.store_token(session_id, oauth_token) + + retrieved_token = oauth_manager.get_token(session_id) + assert retrieved_token is not None + assert retrieved_token.access_token == "test_access_token" + + def test_get_token_nonexistent(self, oauth_manager): + token = oauth_manager.get_token("nonexistent_session") + + assert token is None + + def test_remove_token(self, oauth_manager, oauth_token): + session_id = "test_session_123" + + oauth_manager.store_token(session_id, oauth_token) + oauth_manager.remove_token(session_id) + + token = oauth_manager.get_token(session_id) + assert token is None + + @pytest.mark.asyncio + async def test_get_valid_token(self, oauth_manager, oauth_token): + session_id = "test_session_123" + oauth_manager.store_token(session_id, oauth_token) + + token = await oauth_manager.get_valid_token(session_id) + + assert token is not None + assert token.access_token == "test_access_token" + + @pytest.mark.asyncio + async def test_get_valid_token_expired_no_refresh(self, oauth_manager): + expired_token = OAuthToken( + access_token="expired_token", + token_type="Bearer", + expires_in=1, + refresh_token=None + ) + + object.__setattr__(expired_token, "created_at", datetime.utcnow() - timedelta(hours=2)) + + session_id = "test_session_123" + oauth_manager.store_token(session_id, expired_token) + + token = await oauth_manager.get_valid_token(session_id) + + assert token is None + + @pytest.mark.asyncio + async def test_get_valid_token_expired_with_refresh(self, oauth_manager, oauth_token): + expired_token = OAuthToken( + access_token="expired_token", + token_type="Bearer", + expires_in=1, + refresh_token="refresh_token" + ) + object.__setattr__(expired_token, "created_at", datetime.utcnow() - timedelta(hours=2)) + + session_id = "test_session_123" + oauth_manager.store_token(session_id, expired_token) + + for provider in oauth_manager.providers.values(): + provider.refresh_access_token = AsyncMock(return_value=oauth_token) + + token = await oauth_manager.get_valid_token(session_id) + + assert token is not None + assert token.access_token == "test_access_token" + + def test_create_oauth_routes(self, oauth_manager): + routes = oauth_manager.create_oauth_routes() + + assert len(routes) == 5 + route_paths = [route.path for route in routes] + assert "/oauth/login" in route_paths + assert "/oauth/authorize/{provider}" in route_paths + assert "/oauth/callback/{provider}" in route_paths + assert "/oauth/status" in route_paths + assert "/oauth/logout" in route_paths diff --git a/tests/app/mcp/oauth/test_routes.py b/tests/app/mcp/oauth/test_routes.py new file mode 100644 index 0000000..9845b15 --- /dev/null +++ b/tests/app/mcp/oauth/test_routes.py @@ -0,0 +1,176 @@ +"""Tests for OAuth routes""" +import pytest +from unittest.mock import Mock, patch, AsyncMock +from fastapi import FastAPI +from fastapi.testclient import TestClient +from app.mcp.oauth.routes import register_oauth_routes +from app.mcp.oauth.oauth import OAuthManager, OAuthToken + + +@pytest.fixture +def app(): + """Create a test FastAPI app""" + return FastAPI() + + +@pytest.fixture +def oauth_manager(): + """Create an OAuthManager instance""" + return OAuthManager(base_url="http://localhost:8080") + + +@pytest.fixture +def test_client(app, oauth_manager): + """Create a test client with OAuth routes registered""" + register_oauth_routes(app, oauth_manager) + return TestClient(app) + + +class TestOAuthRoutes: + """Tests for OAuth route handlers""" + + def test_oauth_login_returns_html(self, test_client): + """Test that /oauth/login returns HTML content""" + response = test_client.get("/oauth/login") + + assert response.status_code == 200 + assert "text/html" in response.headers["content-type"] + assert "CMS MCP Server" in response.text + assert "Continue with Google" in response.text + assert "Continue with GitHub" in response.text + + def test_oauth_authorize_unknown_provider(self, test_client): + """Test that unknown provider returns 400""" + response = test_client.get("/oauth/authorize/unknown_provider") + + assert response.status_code == 400 + assert "Unknown provider" in response.text + + def test_oauth_authorize_google_redirects(self, test_client): + """Test that Google authorization redirects""" + response = test_client.get("/oauth/authorize/google", follow_redirects=False) + + assert response.status_code == 307 # Temporary redirect + assert response.headers["location"].startswith("https://accounts.google.com") + + def test_oauth_authorize_github_redirects(self, test_client): + """Test that GitHub authorization redirects""" + response = test_client.get("/oauth/authorize/github", follow_redirects=False) + + assert response.status_code == 307 + assert response.headers["location"].startswith("https://github.com/login/oauth/authorize") + + def test_oauth_callback_missing_code_or_state(self, test_client): + """Test that missing code or state returns 400""" + response = test_client.get("/oauth/callback/google") + + assert response.status_code == 400 + assert "Missing code or state" in response.text + + def test_oauth_callback_unknown_provider(self, test_client): + """Test that unknown provider returns 400""" + response = test_client.get( + "/oauth/callback/unknown_provider", + params={"code": "test_code", "state": "test_state"} + ) + + assert response.status_code == 400 + assert "Unknown provider" in response.text + + def test_oauth_status_no_session(self, test_client): + """Test that /oauth/status returns login page when no session""" + response = test_client.get("/oauth/status") + + assert response.status_code == 200 + assert "No Active Session" in response.text or "not authenticated" in response.text.lower() + + def test_oauth_logout_redirects(self, test_client): + """Test that /oauth/login redirects to login page""" + response = test_client.get("/oauth/logout", follow_redirects=False) + + assert response.status_code == 307 + assert response.headers["location"] == "/oauth/login" + + +class TestRegisterOAuthRoutes: + """Tests for register_oauth_routes function""" + + def test_register_routes_adds_all_endpoints(self, app, oauth_manager): + """Test that all OAuth routes are registered""" + register_oauth_routes(app, oauth_manager) + + # Check that routes are added + route_paths = [route.path for route in app.routes] + assert "/oauth/login" in route_paths + assert "/oauth/authorize/{provider}" in route_paths + assert "/oauth/callback/{provider}" in route_paths + assert "/oauth/status" in route_paths + assert "/oauth/logout" in route_paths + + def test_register_routes_with_different_oauth_manager(self, app): + """Test registering routes with a custom OAuth manager""" + custom_manager = OAuthManager(base_url="http://custom:9000") + register_oauth_routes(app, custom_manager) + + # Verify the routes were added + route_paths = [route.path for route in app.routes] + assert "/oauth/login" in route_paths + assert "/oauth/authorize/{provider}" in route_paths + + +class TestOAuthCallbackWithMockedProvider: + """Tests for OAuth callback with mocked provider""" + + @pytest.fixture + def mock_oauth_manager(self): + """Create a mock OAuth manager""" + manager = Mock(spec=OAuthManager) + return manager + + @pytest.fixture + def client_with_mock(self, app, mock_oauth_manager): + """Create a test client with mocked OAuth manager""" + register_oauth_routes(app, mock_oauth_manager) + return TestClient(app) + + def test_oauth_callback_with_error(self, client_with_mock): + """Test OAuth callback handles errors""" + response = client_with_mock.get( + "/oauth/callback/google", + params={"error": "access_denied", "code": None, "state": None} + ) + + assert response.status_code == 400 + assert "Authentication Error" in response.text or "Authentication Failed" in response.text + + def test_oauth_callback_state_mismatch(self, app, mock_oauth_manager, client_with_mock): + """Test OAuth callback rejects state mismatch""" + # Setup mock to return a provider + mock_provider = Mock() + mock_provider.generate_authorization_url.return_value = ("https://auth.url", "correct_state") + mock_provider.verify_state.return_value = True + mock_oauth_manager.get_provider.return_value = mock_provider + + response = client_with_mock.get( + "/oauth/callback/google", + params={"code": "test_code", "state": "wrong_state"}, + cookies={"oauth_state_google": "correct_state"} + ) + + assert response.status_code == 400 + assert "Invalid state" in response.text + + def test_oauth_callback_verification_failure(self, app, mock_oauth_manager, client_with_mock): + """Test OAuth callback fails when state verification fails""" + mock_provider = Mock() + mock_provider.verify_state.return_value = False + mock_oauth_manager.get_provider.return_value = mock_provider + + response = client_with_mock.get( + "/oauth/callback/google", + params={"code": "test_code", "state": "test_state"}, + cookies={"oauth_state_google": "test_state"} + ) + + assert response.status_code == 400 + assert "State verification failed" in response.text diff --git a/tests/app/mcp/test_server.py b/tests/app/mcp/test_server.py new file mode 100644 index 0000000..421a3f6 --- /dev/null +++ b/tests/app/mcp/test_server.py @@ -0,0 +1,34 @@ +import os +import app.mcp +from unittest.mock import patch +from starlette.applications import Starlette +from app.mcp.server import create_server, COGSTACK_MODELSERVE_INSTRUCTIONS + + +class TestMpcServer: + + @patch.dict(os.environ, {"CMS_MCP_TRANSPORT": "http"}, clear=True) + def test_create_server(self): + app = create_server() + assert app is not None + assert isinstance(app, Starlette) + + def test_server_version(self): + assert hasattr(app.mcp, "__version__") + assert isinstance(app.mcp.__version__, str) + + @patch.dict( + os.environ, + {"MCP_API_KEYS": "key1,key2,key3", "CMS_MCP_TRANSPORT": "http"}, + clear=True + ) + def test_create_server_with_api_keys(self): + app = create_server() + assert app is not None + assert os.environ.get("MCP_API_KEYS") == "key1,key2,key3" + + @patch.dict(os.environ, {"CMS_MCP_TRANSPORT": "http"}, clear=True) + def test_create_server_without_api_keys(self): + app = create_server() + assert app is not None + assert os.environ.get("MCP_API_KEYS") is None diff --git a/tests/app/mcp/test_tools.py b/tests/app/mcp/test_tools.py new file mode 100644 index 0000000..a7b0627 --- /dev/null +++ b/tests/app/mcp/test_tools.py @@ -0,0 +1,208 @@ +import urllib3 +import cms_client +from unittest.mock import MagicMock +from cms_client.models.model_card import ModelCard +from cms_client.models.model_type import ModelType +from cms_client.models.text_with_annotations import TextWithAnnotations +from cms_client.models.annotation import Annotation +from app.mcp.tools.annotation.get_annotations import annotate +from app.mcp.tools.annotation.get_redaction import redact +from app.mcp.tools.metadata.get_model_info import model_info +from app.mcp.tools.train_eval.get_train_eval_info import get_train_eval_info +from app.mcp.tools.train_eval.get_train_eval_metrics import get_train_eval_metrics + + +class TestModelInfoTool: + def test_model_info_success(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_response = ModelCard( + api_version="api_version", + model_type=ModelType.MEDCAT_SNOMED, + model_description="model_description", + model_card={}, + ) + mock_api_instance.get_model_card.return_value = mock_response + + output = model_info(mock_api_instance) + assert output == mock_response.to_dict() + + def test_model_info_api_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_model_card.side_effect = cms_client.exceptions.ApiException(reason="API error") + + output = model_info(mock_api_instance) + assert output == {"status": "error", "reason": "API error"} + + def test_model_info_timeout_error(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_model_card.side_effect = urllib3.exceptions.TimeoutError() + + output = model_info(mock_api_instance) + assert output == {"status": "error", "reason": "Request timed out. Retrying or aborting gracefully."} + + def test_model_info_general_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_model_card.side_effect = Exception("Unexpected error") + + output = model_info(mock_api_instance) + assert output == {"status": "error", "reason": "Unexpected error: Unexpected error"} + + +class TestAnnotateTool: + def test_annotate_success(self, mocker): + cms_client.TextWithAnnotations = MagicMock() + mock_api_instance = mocker.MagicMock() + mock_response = TextWithAnnotations( + text="Spinal stenosis", + annotations=[ + Annotation.from_dict({ + "label_name": "Spinal stenosis", + "label_id": "76107001", + "start": 0, + "end": 15, + "accuracy": 1.0, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999833106994629, + "name": "Status" + } + }, + }) + ] + ) + mock_api_instance.get_entities_from_text.return_value = mock_response + + output = annotate("Spinal stenosis", mock_api_instance) + assert output == mock_response.to_dict() + + def test_annotate_api_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_entities_from_text.side_effect = cms_client.exceptions.ApiException(reason="API error") + + output = annotate("Spinal stenosis", mock_api_instance) + assert output == {"status": "error", "reason": "API error"} + + def test_annotate_timeout_error(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_entities_from_text.side_effect = urllib3.exceptions.TimeoutError() + + output = annotate("test text", mock_api_instance) + assert output == {"status": "error", "reason": "Request timed out. Retrying or aborting gracefully."} + + def test_annotate_general_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_entities_from_text.side_effect = Exception("Unexpected error") + + output = annotate("test text", mock_api_instance) + assert output == {"status": "error", "reason": "Unexpected error: Unexpected error"} + + +class TestRedactTool: + def test_redact_success(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_redacted_text.return_value = "[Spinal stenosis]" + + output = redact("Spinal stenosis", mock_api_instance) + assert output == {"redact_text": "[Spinal stenosis]"} + + def test_redact_api_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_redacted_text.side_effect = cms_client.exceptions.ApiException(reason="API error") + + output = redact("test text", mock_api_instance) + assert output == {"status": "error", "reason": "API error"} + + def test_redact_timeout_error(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_redacted_text.side_effect = urllib3.exceptions.TimeoutError() + + output = redact("test text", mock_api_instance) + assert output == {"status": "error", "reason": "Request timed out. Retrying or aborting gracefully."} + + def test_redact_general_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.get_redacted_text.side_effect = Exception("Unexpected error") + + output = redact("test text", mock_api_instance) + assert output == {"status": "error", "reason": "Unexpected error: Unexpected error"} + + +class TestGetTrainEvalInfoTool: + def test_get_train_eval_info_success(self, mocker): + train_eval_info = { + "artifact_uri": "s3://my-bucket/path/to/artifact", + "experiment_id": "experiment_id", + "run_id": "run_id", + "run_name": "run_name", + "status": "RUNNING", + "tags": {}, + } + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_info.return_value = [train_eval_info] + + output = get_train_eval_info("train_eval_id", mock_api_instance) + assert output == train_eval_info + + def test_get_train_eval_info_api_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_info.side_effect = cms_client.exceptions.ApiException(reason="API error") + + output = get_train_eval_info("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "API error"} + + def test_get_train_eval_info_timeout_error(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_info.side_effect = urllib3.exceptions.TimeoutError() + + output = get_train_eval_info("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "Request timed out. Retrying or aborting gracefully."} + + def test_get_train_eval_info_general_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_info.side_effect = Exception("Unexpected error") + + output = get_train_eval_info("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "Unexpected error: Unexpected error"} + + +class TestGetTrainEvalMetricsTool: + def test_get_train_eval_metrics_success(self, mocker): + train_eval_metrics = { + "per_concept_counts": 1, + "per_concept_count_train": 1, + "per_concept_acc_fn": 0, + "per_concept_acc_fp": 1, + "per_concept_acc_tp": 1, + "per_concept_acc_cc": 1.0, + "per_concept_precision": 1.0, + "per_concept_recall": 1.0, + "per_concept_f1": 1.0, + } + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_metrics.return_value = [train_eval_metrics] + + output = get_train_eval_metrics("train_eval_id", mock_api_instance) + assert output == train_eval_metrics + + def test_get_train_eval_metrics_api_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_metrics.side_effect = cms_client.exceptions.ApiException(reason="API error") + + output = get_train_eval_metrics("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "API error"} + + def test_get_train_eval_metrics_timeout_error(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_metrics.side_effect = urllib3.exceptions.TimeoutError() + + output = get_train_eval_metrics("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "Request timed out. Retrying or aborting gracefully."} + + def test_get_train_eval_metrics_general_exception(self, mocker): + mock_api_instance = mocker.MagicMock() + mock_api_instance.train_eval_metrics.side_effect = Exception("Unexpected error") + + output = get_train_eval_metrics("train_eval_id", mock_api_instance) + assert output == {"status": "error", "reason": "Unexpected error: Unexpected error"} + \ No newline at end of file diff --git a/tests/app/mcp/test_utils.py b/tests/app/mcp/test_utils.py new file mode 100644 index 0000000..50ed358 --- /dev/null +++ b/tests/app/mcp/test_utils.py @@ -0,0 +1,29 @@ +import os +import pytest +from unittest.mock import Mock, patch +from app.mcp.utils import require_api_key + + +@pytest.mark.asyncio +async def test_require_api_key(): + + @require_api_key + async def mock_tool(anystr, ctx): + return "success" + + with patch.dict(os.environ, {"MCP_API_KEYS": "key1,key2"}, clear=True): + ctx = Mock() + ctx.request_context.request.headers.get.return_value = "key1" + result = await mock_tool("test", ctx=ctx) + assert result == "success" + + with patch.dict(os.environ, {"MCP_API_KEYS": "key1,key2"}, clear=True): + ctx = Mock() + ctx.request_context.request.headers.get.return_value = "invalid" + with pytest.raises(PermissionError): + await mock_tool("test", ctx=ctx) + + with patch.dict(os.environ, {}, clear=True): + ctx = Mock() + result = await mock_tool("test", ctx=ctx) + assert result == "success" diff --git a/uv.lock b/uv.lock index 6414061..7295a63 100644 --- a/uv.lock +++ b/uv.lock @@ -130,15 +130,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/ef/4f/22d2edd4cd2a84e179f8c43806cb29cf03a344d2f27a7c6d5afef43bbe7e/aiosqlite-0.19.0-py3-none-any.whl", hash = "sha256:edba222e03453e094a3ce605db1b970c4b3376264e56f32e2a4959f948d66a96", size = 15942, upload-time = "2023-04-17T06:28:47.856Z" }, ] -[[package]] -name = "airportsdata" -version = "20250909" -source = { registry = "https://pypi.org/simple" } -sdist = { url = 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