Merge pull request #18433 from nsoranzo/fix_deprecations

Fix some deprecations

lib/galaxy/managers/context.py

@@ -79,11 +79,13 @@ class ProvidesAppContext:
     Mixed in class must provide `app` property.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def app(self) -> MinimalManagerApp:
         """Provide access to the Galaxy ``app`` object."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def url_builder(self) -> Optional[Callable[..., str]]:
         """
         Provide access to Galaxy URLs (if available).
@@ -217,7 +219,8 @@ def async_request_user(self) -> RequestUser:
             raise AuthenticationRequired("The async task requires user authentication.")
         return RequestUser(user_id=self.user.id)
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def user(self):
         """Provide access to the user object."""
 
@@ -290,7 +293,8 @@ class ProvidesHistoryContext(ProvidesUserContext):
     properties.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def history(self) -> Optional[History]:
         """Provide access to the user's current history model object.
 

lib/galaxy/tool_util/deps/container_resolvers/__init__.py

@@ -3,7 +3,6 @@
 from abc import (
     ABCMeta,
     abstractmethod,
-    abstractproperty,
 )
 from typing import (
     Any,
@@ -65,7 +64,8 @@ def resolve(
         of the tool and its requirements.
         """
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def resolver_type(self) -> str:
         """Short label for the type of container resolution."""
 

lib/galaxy/tool_util/deps/resolvers/__init__.py

@@ -5,7 +5,6 @@
 from abc import (
     ABCMeta,
     abstractmethod,
-    abstractproperty,
 )
 from typing import (
     Any,
@@ -237,7 +236,8 @@ def _expand_specs(self, requirement):
 class SpecificationPatternDependencyResolver(SpecificationAwareDependencyResolver):
     """Implement the :class:`SpecificationAwareDependencyResolver` with a regex pattern."""
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def _specification_pattern(self):
         """Pattern of URI to match against."""
 
@@ -275,7 +275,8 @@ def shell_commands(self):
         Return shell commands to enable this dependency.
         """
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def exact(self):
         """Return true if version information wasn't discarded to resolve
         the dependency.

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -21,7 +21,7 @@
     Response,
     status,
 )
-from gxformat2._yaml import ordered_dump
+from gxformat2.yaml import ordered_dump
 from pydantic import (
     UUID1,
     UUID4,

lib/galaxy/work/context.py

@@ -89,15 +89,18 @@ def set_user(self, user):
 class GalaxyAbstractRequest:
     """Abstract interface to provide access to some request properties."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def base(self) -> str:
         """Base URL of the request."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def host(self) -> str:
         """The host address."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def is_secure(self) -> bool:
         """Was this a secure (https) request."""
 
@@ -109,7 +112,8 @@ def get_cookie(self, name):
 class GalaxyAbstractResponse:
     """Abstract interface to provide access to some response utilities."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def headers(self) -> dict:
         """The response headers."""
 

lib/galaxy_test/base/populators.py

@@ -76,7 +76,7 @@
     convert_and_import_workflow,
     ImporterGalaxyInterface,
 )
-from gxformat2._yaml import ordered_load
+from gxformat2.yaml import ordered_load
 from requests import Response
 from rocrate.rocrate import ROCrate
 from typing_extensions import Literal

lib/tool_shed/context.py

@@ -24,7 +24,8 @@ class ProvidesAppContext(Protocol):
     Mixed in class must provide `app` property.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def app(self) -> ToolShedApp:
         """Provide access to the shed ``app`` object."""
 
@@ -54,7 +55,8 @@ class ProvidesUserContext(ProvidesAppContext, Protocol):
     properties.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def user(self) -> Optional[User]:
         """Provide access to the user object."""
 
@@ -74,7 +76,8 @@ def user_is_bootstrap_admin(self) -> bool:
 
 
 class ProvidesRepositoriesContext(ProvidesUserContext, Protocol):
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def repositories_hostname(self) -> str:
         """Provide access to hostname used by target mercurial server."""
 
@@ -86,16 +89,19 @@ def get_galaxy_session(self) -> Optional[GalaxySession]: ...
     @abc.abstractmethod
     def set_galaxy_session(self, galaxy_session: GalaxySession): ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def request(self) -> GalaxyAbstractRequest: ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def response(self) -> GalaxyAbstractResponse: ...
 
     @abc.abstractmethod
     def url_builder(self): ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def session_csrf_token(self) -> str: ...
 
 

lib/tool_shed/test/base/browser.py

@@ -36,7 +36,8 @@ def submit_form(self, form_no=-1, button="runtool_btn", form=None, **kwd):
     def submit_form_with_name(self, form_name: str, button="runtool_btn", **kwd):
         """Submit the target button."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def is_twill(self) -> bool:
         """Return whether this is a twill browser."""
 

lib/tool_shed/test/base/twilltestcase.py

@@ -150,11 +150,13 @@ def update_installed_repository(
     ) -> Dict[str, Any]:
         """"""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def tool_data_path(self) -> str:
         """"""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def shed_tool_data_table_conf(self) -> str:
         """"""