Source code for galaxy.webapps.galaxy.fast_app

from a2wsgi import WSGIMiddleware
from fastapi import (
    FastAPI,
    Request,
)
from starlette.middleware.cors import CORSMiddleware
from starlette.responses import Response

from galaxy.version import VERSION
from galaxy.webapps.base.api import (
    add_empty_response_middleware,
    add_exception_handler,
    add_request_id_middleware,
    GalaxyFileResponse,
    include_all_package_routers,
)
from galaxy.webapps.base.webapp import config_allows_origin
from galaxy.webapps.openapi.utils import get_openapi

# https://fastapi.tiangolo.com/tutorial/metadata/#metadata-for-tags
api_tags_metadata = [
    {
        "name": "configuration",
        "description": "Configuration-related endpoints.",
    },
    {"name": "datasets", "description": "Operations on datasets."},
    {"name": "dataset collections"},
    {
        "name": "datatypes",
        "description": "Operations with supported data types.",
    },
    {
        "name": "datatypes",
        "description": "Operations on dataset collections.",
    },
    {
        "name": "genomes",
        "description": "Operations with genome data.",
    },
    {
        "name": "group_roles",
        "description": "Operations with group roles.",
    },
    {
        "name": "group_users",
        "description": "Operations with group users.",
    },
    {"name": "histories"},
    {"name": "libraries"},
    {"name": "folders"},
    {"name": "job_lock"},
    {"name": "metrics"},
    {"name": "default"},
    {"name": "users"},
    {"name": "jobs"},
    {"name": "roles"},
    {"name": "quotas"},
    {"name": "visualizations"},
    {"name": "pages"},
    {
        "name": "licenses",
        "description": "Operations with [SPDX licenses](https://spdx.org/licenses/).",
    },
    {
        "name": "tags",
        "description": "Operations with tags.",
    },
    {
        "name": "tool data tables",
        "description": "Operations with tool [Data Tables](https://galaxyproject.org/admin/tools/data-tables/).",
    },
    {
        "name": "tours",
        "description": "Operations with interactive tours.",
    },
    {
        "name": "remote files",
        "description": "Operations with remote dataset sources.",
    },
    {"name": "undocumented", "description": "API routes that have not yet been ported to FastAPI."},
]


class GalaxyCORSMiddleware(CORSMiddleware):
    def __init__(self, *args, **kwds):
        self.config = kwds.pop("config")
        super().__init__(*args, **kwds)

    def is_allowed_origin(self, origin: str) -> bool:
        return config_allows_origin(origin, self.config)


[docs]def add_galaxy_middleware(app: FastAPI, gx_app): x_frame_options = gx_app.config.x_frame_options if x_frame_options: @app.middleware("http") async def add_x_frame_options(request: Request, call_next): response = await call_next(request) response.headers["X-Frame-Options"] = x_frame_options return response GalaxyFileResponse.nginx_x_accel_redirect_base = gx_app.config.nginx_x_accel_redirect_base GalaxyFileResponse.apache_xsendfile = gx_app.config.apache_xsendfile if gx_app.config.sentry_dsn: from sentry_sdk.integrations.asgi import SentryAsgiMiddleware app.add_middleware(SentryAsgiMiddleware) if gx_app.config.get("allowed_origin_hostnames", None): app.add_middleware( GalaxyCORSMiddleware, config=gx_app.config, allow_headers=["*"], allow_methods=["*"], max_age=600, ) else: # handle CORS preflight requests - synchronize with wsgi behavior. @app.options("/api/{rest_of_path:path}") async def preflight_handler(request: Request, rest_of_path: str) -> Response: response = Response() response.headers["Access-Control-Allow-Headers"] = "*" response.headers["Access-Control-Max-Age"] = "600" return response
def include_legacy_openapi(app, gx_app): if app.openapi_schema: return app.openapi_schema openapi_schema = get_openapi( title="Galaxy API", version=VERSION, routes=app.routes, tags=api_tags_metadata, ) legacy_openapi = gx_app.api_spec.to_dict() legacy_openapi["paths"].update(openapi_schema["paths"]) openapi_schema["paths"] = legacy_openapi["paths"] app.openapi_schema = openapi_schema return app.openapi_schema
[docs]def initialize_fast_app(gx_wsgi_webapp, gx_app): app = FastAPI( title="Galaxy API", docs_url="/api/docs", openapi_tags=api_tags_metadata, ) add_exception_handler(app) add_galaxy_middleware(app, gx_app) add_request_id_middleware(app) include_all_package_routers(app, "galaxy.webapps.galaxy.api") include_legacy_openapi(app, gx_app) wsgi_handler = WSGIMiddleware(gx_wsgi_webapp) gx_app.haltables.append(("WSGI Middleware threadpool", wsgi_handler.executor.shutdown)) app.mount("/", wsgi_handler) add_empty_response_middleware(app) if gx_app.config.galaxy_url_prefix != "/": parent_app = FastAPI() parent_app.mount(gx_app.config.galaxy_url_prefix, app=app) return parent_app return app
__all__ = ( "add_galaxy_middleware", "initialize_fast_app", )