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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
from galaxy import (
model,
web,
)
from galaxy.exceptions import (
AdminRequiredException,
UserCannotRunAsException,
UserInvalidRunAsException,
)
from galaxy.managers.session import GalaxySessionManager
from galaxy.managers.users import UserManager
from galaxy.model import User
from galaxy.schema.fields import EncodedDatabaseIdField
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]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 = 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: 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(
security: IdEncodingHelper = depends(IdEncodingHelper),
user_manager: UserManager = depends(UserManager),
key: str = Security(api_key_query),
x_api_key: str = Security(api_key_header),
run_as: Optional[EncodedDatabaseIdField] = 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):
try:
decoded_run_as_id = security.decode_id(run_as)
except Exception:
raise UserInvalidRunAsException
return user_manager.by_id(decoded_run_as_id)
else:
raise UserCannotRunAsException
return user
[docs]def get_user(
galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
api_user: Optional[User] = Depends(get_api_user),
) -> Optional[User]:
if galaxy_session:
return galaxy_session.user
return api_user
[docs]class UrlBuilder:
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."""
@property
def base(self) -> str:
return str(self.__request.base_url)
@property
def host(self) -> str:
return self.__request.base_url.netloc
[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."""
@property
def headers(self):
return self.__response.headers
DependsOnUser = 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: Optional[User] = Depends(get_user),
galaxy_session: 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 = 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 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)
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 remaing 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,
)