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Source code for galaxy.webapps.galaxy.api

"""
This module *does not* contain API routes. It exclusively contains dependencies to be used in FastAPI routes
"""
import inspect
from enum import Enum
from string import Template
from typing import (
    Any,
    AsyncGenerator,
    cast,
    NamedTuple,
    Optional,
    Tuple,
    Type,
    TypeVar,
)
from urllib.parse import urlencode

from fastapi import (
    Form,
    Header,
    Query,
    Request,
    Response,
    Security,
)
from fastapi.exceptions import RequestValidationError
from fastapi.params import Depends
from fastapi.routing import APIRoute
from fastapi.security import (
    APIKeyCookie,
    APIKeyHeader,
    APIKeyQuery,
)
from fastapi_utils.cbv import cbv
from fastapi_utils.inferring_router import InferringRouter
from pydantic import ValidationError
from pydantic.main import BaseModel
from starlette.datastructures import Headers
from starlette.routing import (
    Match,
    NoMatchFound,
)
from starlette.types import Scope

try:
    from starlette_context import context as request_context
except ImportError:
    request_context = None  # type: ignore[assignment]

from galaxy import (
    app as galaxy_app,
    model,
    web,
)
from galaxy.exceptions import (
    AdminRequiredException,
    UserCannotRunAsException,
)
from galaxy.managers.session import GalaxySessionManager
from galaxy.managers.users import UserManager
from galaxy.model import User
from galaxy.schema.fields import DecodedDatabaseIdField
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.structured_app import StructuredApp
from galaxy.web.framework.decorators import require_admin_message
from galaxy.webapps.base.controller import BaseAPIController
from galaxy.work.context import (
    GalaxyAbstractRequest,
    GalaxyAbstractResponse,
    SessionRequestContext,
)

api_key_query = APIKeyQuery(name="key", auto_error=False)
api_key_header = APIKeyHeader(name="x-api-key", auto_error=False)
api_key_cookie = APIKeyCookie(name="galaxysession", auto_error=False)


[docs]def get_app() -> StructuredApp: return cast(StructuredApp, galaxy_app.app)
[docs]async def get_app_with_request_session() -> AsyncGenerator[StructuredApp, None]: app = get_app() request_id = request_context.data["X-Request-ID"] app.model.set_request_id(request_id) try: yield app finally: app.model.unset_request_id(request_id)
DependsOnApp = cast(StructuredApp, Depends(get_app_with_request_session)) T = TypeVar("T")
[docs]class GalaxyTypeDepends(Depends): """Variant of fastapi Depends that can also work on WSGI Galaxy controllers."""
[docs] def __init__(self, callable, dep_type): super().__init__(callable) self.galaxy_type_depends = dep_type
[docs]def depends(dep_type: Type[T]) -> T: def _do_resolve(request: Request): return get_app().resolve(dep_type) return cast(T, GalaxyTypeDepends(_do_resolve, dep_type))
[docs]def get_session_manager(app: StructuredApp = DependsOnApp) -> GalaxySessionManager: # TODO: find out how to adapt dependency for Galaxy/Report/TS return GalaxySessionManager(app.model)
[docs]def get_session( session_manager=cast(GalaxySessionManager, Depends(get_session_manager)), security: IdEncodingHelper = depends(IdEncodingHelper), galaxysession: str = Security(api_key_cookie), ) -> Optional[model.GalaxySession]: if galaxysession: session_key = security.decode_guid(galaxysession) if session_key: return session_manager.get_session_from_session_key(session_key) # TODO: What should we do if there is no session? Since this is the API, maybe nothing is the right choice? return None
[docs]def get_api_user( user_manager: UserManager = depends(UserManager), key: str = Security(api_key_query), x_api_key: str = Security(api_key_header), run_as: Optional[DecodedDatabaseIdField] = Header( default=None, title="Run as User", description=( "The user ID that will be used to effectively make this API call. " "Only admins and designated users can make API calls on behalf of other users." ), ), ) -> Optional[User]: api_key = key or x_api_key if not api_key: return None user = user_manager.by_api_key(api_key=api_key) if run_as: if user_manager.user_can_do_run_as(user): return user_manager.by_id(run_as) else: raise UserCannotRunAsException return user
[docs]def get_user( galaxy_session=cast(Optional[model.GalaxySession], Depends(get_session)), api_user=cast(Optional[User], Depends(get_api_user)), ) -> Optional[User]: if galaxy_session: return galaxy_session.user return api_user
[docs]class UrlBuilder:
[docs] def __init__(self, request: Request): self.request = request
def __call__(self, name: str, **path_params): qualified = path_params.pop("qualified", False) # starlette does not support query parameters in url_path_for: https://github.com/encode/starlette/issues/560 query_params = path_params.pop("query_params", None) try: if qualified: url = self.request.url_for(name, **path_params) else: url = self.request.app.url_path_for(name, **path_params) if query_params: url = f"{url}?{urlencode(query_params)}" return url except NoMatchFound: # Fallback to legacy url_for if query_params: path_params.update(query_params) return web.url_for(name, **path_params)
[docs]class GalaxyASGIRequest(GalaxyAbstractRequest): """Wrapper around Starlette/FastAPI Request object. Implements the GalaxyAbstractRequest interface to provide access to some properties of the request commonly used."""
[docs] def __init__(self, request: Request): self.__request = request
@property def base(self) -> str: return str(self.__request.base_url) @property def host(self) -> str: client = self.__request.client assert client is not None return str(client.host)
[docs]class GalaxyASGIResponse(GalaxyAbstractResponse): """Wrapper around Starlette/FastAPI Response object. Implements the GalaxyAbstractResponse interface to provide access to some properties of the response object commonly used."""
[docs] def __init__(self, response: Response): self.__response = response
@property def headers(self): return self.__response.headers
DependsOnUser = cast(Optional[User], Depends(get_user))
[docs]def get_current_history_from_session(galaxy_session: Optional[model.GalaxySession]) -> Optional[model.History]: if galaxy_session: return galaxy_session.current_history return None
[docs]def get_trans( request: Request, response: Response, app: StructuredApp = DependsOnApp, user=cast(Optional[User], Depends(get_user)), galaxy_session=cast(Optional[model.GalaxySession], Depends(get_session)), ) -> SessionRequestContext: url_builder = UrlBuilder(request) galaxy_request = GalaxyASGIRequest(request) galaxy_response = GalaxyASGIResponse(response) return SessionRequestContext( app=app, user=user, galaxy_session=galaxy_session, url_builder=url_builder, request=galaxy_request, response=galaxy_response, history=get_current_history_from_session(galaxy_session), )
DependsOnTrans: SessionRequestContext = cast(SessionRequestContext, Depends(get_trans))
[docs]def get_admin_user(trans: SessionRequestContext = DependsOnTrans): if not trans.user_is_admin: raise AdminRequiredException(require_admin_message(trans.app.config, trans.user)) return trans.user
AdminUserRequired = Depends(get_admin_user)
[docs]class BaseGalaxyAPIController(BaseAPIController):
[docs] def __init__(self, app: StructuredApp): super().__init__(app)
[docs]class RestVerb(str, Enum): get = "GET" head = "HEAD" post = "POST" put = "PUT" patch = "PATCH" delete = "DELETE" options = "OPTIONS"
[docs]class Router(InferringRouter): """A FastAPI Inferring Router tailored to Galaxy."""
[docs] def wrap_with_alias(self, verb: RestVerb, *args, alias: Optional[str] = None, **kwd): """ Wraps FastAPI methods with additional alias keyword and require_admin handling. @router.get("/api/thing", alias="/api/deprecated_thing") will then create routes for /api/thing and /api/deprecated_thing. """ kwd = self._handle_galaxy_kwd(kwd) include_in_schema = kwd.pop("include_in_schema", True) def decorate_route(route, include_in_schema=include_in_schema): # Decorator solely exists to allow passing `route_class_override` to add_api_route def decorated_route(func): self.add_api_route( route, endpoint=func, methods=[verb], include_in_schema=include_in_schema, **kwd, ) return func return decorated_route routes = [] for path in self.construct_aliases(args[0], alias): if path != "/" and path.endswith("/"): routes.append(decorate_route(path, include_in_schema=False)) else: routes.append(decorate_route(path)) def dec(f): for route in routes: f = route(f) return f return dec
[docs] @staticmethod def construct_aliases(path: str, alias: Optional[str]): yield path if path != "/" and not path.endswith("/"): yield f"{path}/" if alias: yield alias if not alias == "/" and not alias.endswith("/"): yield f"{alias}/"
[docs] def get(self, *args, **kwd): """Extend FastAPI.get to accept a require_admin Galaxy flag.""" return self.wrap_with_alias(RestVerb.get, *args, **kwd)
[docs] def patch(self, *args, **kwd): """Extend FastAPI.patch to accept a require_admin Galaxy flag.""" return self.wrap_with_alias(RestVerb.patch, *args, **kwd)
[docs] def put(self, *args, **kwd): """Extend FastAPI.put to accept a require_admin Galaxy flag.""" return self.wrap_with_alias(RestVerb.put, *args, **kwd)
[docs] def post(self, *args, **kwd): """Extend FastAPI.post to accept a require_admin Galaxy flag.""" return self.wrap_with_alias(RestVerb.post, *args, **kwd)
[docs] def delete(self, *args, **kwd): """Extend FastAPI.delete to accept a require_admin Galaxy flag.""" return self.wrap_with_alias(RestVerb.delete, *args, **kwd)
[docs] def options(self, *args, **kwd): return self.wrap_with_alias(RestVerb.options, *args, **kwd)
[docs] def head(self, *args, **kwd): return self.wrap_with_alias(RestVerb.head, *args, **kwd)
def _handle_galaxy_kwd(self, kwd): require_admin = kwd.pop("require_admin", False) if require_admin: if "dependencies" in kwd: kwd["dependencies"].append(AdminUserRequired) else: kwd["dependencies"] = [AdminUserRequired] return kwd @property def cbv(self): """Short-hand for frequently used Galaxy-pattern of FastAPI class based views. Creates a class-based view for for this router, for more information see: https://fastapi-utils.davidmontague.xyz/user-guide/class-based-views/ """ return cbv(self)
[docs]class APIContentTypeRoute(APIRoute): """ Determines endpoint to match using content-type. """ match_content_type: str
[docs] def accept_matches(self, scope: Scope) -> Tuple[Match, Scope]: content_type_header = Headers(scope=scope).get("content-type", None) if not content_type_header: return Match.PARTIAL, scope if self.match_content_type not in content_type_header: return Match.NONE, scope return Match.FULL, scope
[docs] def matches(self, scope: Scope) -> Tuple[Match, Scope]: accept_match, accept_scope = self.accept_matches(scope) if accept_match == Match.NONE: return accept_match, accept_scope match, child_scope = super().matches(accept_scope) return ( match if match.value < accept_match.value else accept_match, child_scope, )
[docs]def as_form(cls: Type[BaseModel]): """ Adds an as_form class method to decorated models. The as_form class method can be used with FastAPI endpoints. See https://github.com/tiangolo/fastapi/issues/2387#issuecomment-731662551 """ new_params = [ inspect.Parameter( field.alias, inspect.Parameter.POSITIONAL_ONLY, default=(Form(field.default) if not field.required else Form(...)), ) for field in cls.__fields__.values() ] async def _as_form(**data): try: return cls(**data) except ValidationError as e: raise RequestValidationError(e.raw_errors) sig = inspect.signature(_as_form) sig = sig.replace(parameters=new_params) _as_form.__signature__ = sig # type: ignore[attr-defined] cls.as_form = _as_form # type: ignore[attr-defined] return cls
[docs]async def try_get_request_body_as_json(request: Request) -> Optional[Any]: """Returns the request body as a JSON object if the content type is JSON.""" if "application/json" in request.headers.get("content-type", ""): body = await request.json() return body return None
search_description_template = Template( """A mix of free text and GitHub-style tags used to filter the index operation. ## Query Structure GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name *generally* (but not exclusively) corresponds to the name of an attribute on the model being indexed (i.e. a column in the database). If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted, generally a partial match will be used to filter the query (i.e. in terms of the implementation this means the database operation `ILIKE` will typically be used). Once the tagged filters are extracted from the search query, the remaining text is just used to search various documented attributes of the object. ## GitHub-style Tags Available ${tags} ## Free Text Free text search terms will be searched against the following attributes of the ${model_name}s: ${freetext}. """ )
[docs]class IndexQueryTag(NamedTuple): tag: str description: str alias: Optional[str] = None admin_only: bool = False
[docs] def as_markdown(self): desc = self.description alias = self.alias if alias: desc += f" (The tag `{alias}` can be used a short hand alias for this tag to filter on this attribute.)" if self.admin_only: desc += " This tag is only available for requests using admin keys and/or sessions." return f"`{self.tag}`\n: {desc}"
[docs]def search_query_param(model_name: str, tags: list, free_text_fields: list) -> Optional[str]: tags_markdown_str = "\n\n".join([t.as_markdown() for t in tags]) description = search_description_template.safe_substitute( model_name=model_name, tags=tags_markdown_str, freetext=", ".join([f"`{t}`" for t in free_text_fields]) ) return Query( default=None, title="Search query.", description=description, )