Unverified Commit dfea749b authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_24.0' into release_24.1

parents f8175ef7 c3738ad9

lib/galaxy/model/__init__.py

+0 −2
Original line number Diff line number Diff line
@@ -4377,8 +4377,6 @@ class Dataset(Base, StorableObject, Serializable): 
        # TODO: purge metadata files

        self.deleted = True

        self.purged = True

        self.file_size = 0

        self.total_size = 0



    def get_access_roles(self, security_agent):

        roles = []

lib/galaxy/web/framework/base.py

+5 −2
Original line number Diff line number Diff line
@@ -104,6 +104,7 @@ class WebApplication: 
        self.transaction_factory = DefaultWebTransaction

        # Set if trace logging is enabled

        self.trace_logger = None

        self.session_factories = []



    def add_ui_controller(self, controller_name, controller):

        """
@@ -170,10 +171,12 @@ class WebApplication: 
        path_info = environ.get("PATH_INFO", "")



        try:

            self._model.set_request_id(request_id)  # Start SQLAlchemy session scope

            for session_factory in self.session_factories:

                session_factory.set_request_id(request_id)  # Start SQLAlchemy session scope

            return self.handle_request(request_id, path_info, environ, start_response)

        finally:

            self._model.unset_request_id(request_id)  # End SQLAlchemy session scope

            for session_factory in self.session_factories:

                session_factory.unset_request_id(request_id)  # End SQLAlchemy session scope

            self.trace(message="Handle request finished")

            if self.trace_logger:

                self.trace_logger.context_remove("request_id")

lib/galaxy/webapps/base/webapp.py

+1 −1
Original line number Diff line number Diff line
@@ -119,7 +119,7 @@ class WebApplication(base.WebApplication): 


        # We need this to set the REQUEST_ID contextvar in model.base *BEFORE* a GalaxyWebTransaction is created.

        # This will ensure a SQLAlchemy session is request-scoped for legacy (non-fastapi) endpoints.

        self._model = galaxy_app.model

        self.session_factories.append(galaxy_app.model)



    def build_apispec(self):

        """

lib/galaxy/webapps/galaxy/api/__init__.py

+6 −3
Original line number Diff line number Diff line
@@ -98,10 +98,12 @@ 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)

    app.install_model.set_request_id(request_id)

    try:

        yield app

    finally:

        app.model.unset_request_id(request_id)

        app.install_model.unset_request_id(request_id)





DependsOnApp = cast(StructuredApp, Depends(get_app_with_request_session))
@@ -118,9 +120,10 @@ class GalaxyTypeDepends(Depends): 
        self.galaxy_type_depends = dep_type





def depends(dep_type: Type[T], get_app=get_app) -> T:

    def _do_resolve(request: Request):

        return get_app().resolve(dep_type)

def depends(dep_type: Type[T], app=get_app_with_request_session) -> T:

    async def _do_resolve(request: Request):

        async for _dep in app():

            yield _dep.resolve(dep_type)



    return cast(T, GalaxyTypeDepends(_do_resolve, dep_type))

lib/galaxy/webapps/galaxy/buildapp.py

+8 −0
Original line number Diff line number Diff line
@@ -7,6 +7,7 @@ import logging 
import sys

import threading

import traceback

from typing import Optional

from urllib.parse import urljoin



from paste import httpexceptions
@@ -20,6 +21,7 @@ import galaxy.web.framework 
import galaxy.webapps.base.webapp

from galaxy import util

from galaxy.security.validate_user_input import VALID_PUBLICNAME_RE

from galaxy.structured_app import MinimalApp

from galaxy.util import asbool

from galaxy.util.properties import load_app_properties

from galaxy.web.framework.middleware.error import ErrorMiddleware
@@ -34,6 +36,12 @@ log = logging.getLogger(__name__) 
class GalaxyWebApplication(galaxy.webapps.base.webapp.WebApplication):

    injection_aware = True



    def __init__(

        self, galaxy_app: MinimalApp, session_cookie: str = "galaxysession", name: Optional[str] = None

    ) -> None:

        super().__init__(galaxy_app, session_cookie, name)

        self.session_factories.append(galaxy_app.install_model)





def app_factory(*args, **kwargs):

    """