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Drop Python 3.8 support in 5 Pulsar-compatible packages (job_metrics, tool_util, tool_util_models, util, objectstore) and run pyupgrade --py310-plus on their source code. - Bump requires-python from >=3.8 to >=3.10 in all 5 packages - Remove Python 3.8 and 3.9 classifiers - Remove ruff per-file-ignores for UP rules on these paths - Remove backports.zoneinfo conditional dependency - Remove pydyf<0.11 pin from conditional-requirements.txt - Update Makefile pyupgrade target (remove PY38_PYUPGRADE_PATHS) - Update CI workflow to test with Python 3.10 instead of 3.8 Clean up unused deprecated typing imports after pyupgrade Remove now-unused typing imports (Dict, List, Optional, Set, Tuple, Type, Union) that became dead after pyupgrade --py310-plus converted annotations to use built-in types and | syntax. Also run ruff check --fix --select=UP007,UP045 across the entire codebase to convert remaining Optional[X] -> X | None and Union[X, Y] -> X | Y patterns. Enable ruff UP007/UP045 for Python 3.10 union syntax Remove UP007 (Union[X,Y] -> X | Y) and UP045 (Optional[X] -> X | None) from the ruff ignore list and convert all type aliases across the codebase. These rules were deferred while Python 3.9 was supported; requires-python is now >=3.10. A custom script was used because neither ruff --fix nor pyupgrade --py310-plus converts Optional[X]/Union[X,Y] in type alias positions (e.g. X = Union[A, B]) — they only handle annotation positions (e.g. def f(x: Optional[int])). All 167 violations were module-level type aliases. A few edge cases were fixed manually: single-element Union[X,], typing.Union qualified refs, runtime Optional[type] calls, and Annotated[Optional[...]] pydantic fields. Fix UP007 autofix regression with string forward reference type aliases Commit fa6bd955a0 enabled ruff UP007/UP045 and auto-fixed module-level type aliases using Union with string forward references, producing invalid 'str | str' expressions. This was a known ruff bug (charliermarsh/ruff#826) that has since been fixed in later ruff versions, but this codebase was converted before the fix was in place. Revert to Union syntax and restore TYPE_CHECKING imports that ruff's TCH rule cleaned up as a side effect when it thought the forward references were unused.
182 lines
4.8 KiB
Python
182 lines
4.8 KiB
Python
import abc
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from sqlalchemy.orm import scoped_session
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from typing_extensions import Protocol
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from galaxy.security.idencoding import IdEncodingHelper
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from galaxy.work.context import (
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GalaxyAbstractRequest,
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GalaxyAbstractResponse,
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)
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from tool_shed.structured_app import ToolShedApp
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from tool_shed.webapp.model import (
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GalaxySession,
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User,
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)
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from tool_shed.webapp.model.mapping import ToolShedModelMapping
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class ProvidesAppContext(Protocol):
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"""For transaction-like objects to provide the shed convenience layer for
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database and event handling.
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Mixed in class must provide `app` property.
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"""
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@property
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@abc.abstractmethod
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def app(self) -> ToolShedApp:
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"""Provide access to the shed ``app`` object."""
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@property
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def security(self) -> IdEncodingHelper:
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return self.app.security
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@property
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def sa_session(self) -> scoped_session:
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"""Provide access to Galaxy's SQLAlchemy session.
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:rtype: galaxy.model.scoped_session.galaxy_scoped_session
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"""
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return self.model.session
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@property
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def model(self) -> ToolShedModelMapping:
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"""Provide access to Tool Shed's model mapping class."""
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return self.app.model
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class ProvidesUserContext(ProvidesAppContext, Protocol):
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"""For transaction-like objects to provide Galaxy convenience layer for
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reasoning about users.
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Mixed in class must provide `user` and `app`
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properties.
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"""
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@property
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@abc.abstractmethod
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def user(self) -> User | None:
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"""Provide access to the user object."""
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@property
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def anonymous(self) -> bool:
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return self.user is None
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@property
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def user_is_admin(self) -> bool:
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return self.app.config.is_admin_user(self.user)
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@property
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def user_is_bootstrap_admin(self) -> bool:
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"""Master key provided so there is no real user"""
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user = self.user
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return not self.anonymous and user is not None and user.bootstrap_admin_user
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class ProvidesRepositoriesContext(ProvidesUserContext, Protocol):
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@property
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@abc.abstractmethod
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def repositories_hostname(self) -> str:
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"""Provide access to hostname used by target mercurial server."""
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class SessionRequestContext(ProvidesRepositoriesContext, Protocol):
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@abc.abstractmethod
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def get_galaxy_session(self) -> GalaxySession | None: ...
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@abc.abstractmethod
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def set_galaxy_session(self, galaxy_session: GalaxySession): ...
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@property
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@abc.abstractmethod
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def request(self) -> GalaxyAbstractRequest: ...
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@property
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@abc.abstractmethod
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def response(self) -> GalaxyAbstractResponse: ...
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@abc.abstractmethod
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def url_builder(self): ...
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@property
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@abc.abstractmethod
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def session_csrf_token(self) -> str: ...
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class SessionRequestContextImpl(SessionRequestContext):
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_app: ToolShedApp
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_user: User | None
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_galaxy_session: GalaxySession | None
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def __init__(
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self,
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app: ToolShedApp,
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request: GalaxyAbstractRequest,
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response: GalaxyAbstractResponse,
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user: User | None = None,
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galaxy_session: GalaxySession | None = None,
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url_builder=None,
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):
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self._app = app
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self._user = user
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self._galaxy_session = galaxy_session
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self._url_builder = url_builder
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self.__request = request
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self.__response = response
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@property
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def app(self) -> ToolShedApp:
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return self._app
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@property
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def url_builder(self):
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return self._url_builder
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@property
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def user(self) -> User | None:
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return self._user
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def get_galaxy_session(self) -> GalaxySession | None:
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return self._galaxy_session
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def set_galaxy_session(self, galaxy_session: GalaxySession):
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self._galaxy_session = galaxy_session
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if galaxy_session.user:
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self._user = galaxy_session.user
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@property
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def repositories_hostname(self) -> str:
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# Use configured tool_shed_url if available
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if tool_shed_url := self.app.config.tool_shed_url:
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return tool_shed_url.rstrip("/")
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# Fall back to request-based URL
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return str(self.request.base).rstrip("/")
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@property
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def host(self):
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return self.__request.host
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@property
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def request(self) -> GalaxyAbstractRequest:
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return self.__request
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@property
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def response(self) -> GalaxyAbstractResponse:
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return self.__response
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# Following three things added v2.0 frontend
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@property
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def session_csrf_token(self):
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token = ""
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if self._galaxy_session:
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token = self.security.encode_id(self._galaxy_session.id, kind="csrf")
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return token
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@property
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def galaxy_session(self) -> GalaxySession | None:
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return self._galaxy_session
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def log_event(self, str):
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pass
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