Fixes for errors reported by mypy 1.11.0 in BaseObjectStore

lib/galaxy/model/__init__.py

@@ -29,6 +29,7 @@
 from typing import (
     Any,
     cast,
+    ClassVar,
     Dict,
     Generic,
     Iterable,
@@ -159,7 +160,6 @@
 )
 from galaxy.model.orm.now import now
 from galaxy.model.orm.util import add_object_to_object_session
-from galaxy.objectstore import ObjectStorePopulator
 from galaxy.objectstore.templates import (
     ObjectStoreConfiguration,
     ObjectStoreTemplate,
@@ -219,6 +219,10 @@
 from galaxy.util.sanitize_html import sanitize_html
 
 if TYPE_CHECKING:
+    from galaxy.objectstore import (
+        BaseObjectStore,
+        ObjectStorePopulator,
+    )
     from galaxy.schema.invocation import InvocationMessageUnion
 
 log = logging.getLogger(__name__)
@@ -4041,7 +4045,7 @@ def flush(self):
                 sa_session.commit()
 
 
-def setup_global_object_store_for_models(object_store):
+def setup_global_object_store_for_models(object_store: "BaseObjectStore") -> None:
     Dataset.object_store = object_store
 
 
@@ -4133,7 +4137,9 @@ class conversion_messages(str, Enum):
 
     permitted_actions = get_permitted_actions(filter="DATASET")
     file_path = "/tmp/"
-    object_store = None  # This get initialized in mapping.py (method init) by app.py
+    object_store: ClassVar[Optional["BaseObjectStore"]] = (
+        None  # This get initialized in mapping.py (method init) by app.py
+    )
     engine = None
 
     def __init__(
@@ -4283,7 +4289,7 @@ def _calculate_size(self) -> int:
             except OSError:
                 return 0
         assert self.object_store
-        return self.object_store.size(self)  # type:ignore[unreachable]
+        return self.object_store.size(self)
 
     @overload
     def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int: ...
@@ -4663,7 +4669,7 @@ def get_quota_source_label(self):
 
     quota_source_label = property(get_quota_source_label)
 
-    def set_skipped(self, object_store_populator: ObjectStorePopulator):
+    def set_skipped(self, object_store_populator: "ObjectStorePopulator") -> None:
         assert self.dataset
         object_store_populator.set_object_store_id(self)
         self.extension = "expression.json"

lib/galaxy/model/mapping.py

@@ -3,6 +3,7 @@
 from typing import (
     Optional,
     Type,
+    TYPE_CHECKING,
 )
 
 from galaxy import model
@@ -16,6 +17,9 @@
 from galaxy.model.security import GalaxyRBACAgent
 from galaxy.model.triggers.update_audit_table import install as install_timestamp_triggers
 
+if TYPE_CHECKING:
+    from galaxy.objectstore import BaseObjectStore
+
 log = logging.getLogger(__name__)
 
 metadata = mapper_registry.metadata
@@ -99,8 +103,11 @@ def _build_model_mapping(engine, map_install_models, thread_local_log) -> Galaxy
 
 
 def init_models_from_config(
-    config: GalaxyAppConfiguration, map_install_models=False, object_store=None, trace_logger=None
-):
+    config: GalaxyAppConfiguration,
+    map_install_models: bool = False,
+    object_store: Optional["BaseObjectStore"] = None,
+    trace_logger=None,
+) -> GalaxyModelMapping:
     model = init(
         config.file_path,
         config.database_connection,

lib/galaxy/objectstore/__init__.py

@@ -235,7 +235,15 @@ def get_data(
 
     @abc.abstractmethod
     def get_filename(
-        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        sync_cache: bool = True,
     ):
         """
         Get the expected filename with absolute path for object with id `obj.id`.
@@ -450,35 +458,161 @@ def _get_object_id(self, obj):
     def _invoke(self, delegate, obj=None, **kwargs):
         return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
 
-    def exists(self, obj, **kwargs):
-        return self._invoke("exists", obj, **kwargs)
+    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        return self._invoke(
+            "exists",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+        )
 
-    def construct_path(self, obj, **kwargs):
-        return self._invoke("construct_path", obj, **kwargs)
+    def construct_path(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None
+    ):
+        return self._invoke(
+            "construct_path",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+        )
 
-    def create(self, obj, **kwargs):
-        return self._invoke("create", obj, **kwargs)
+    def create(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+    ):
+        return self._invoke(
+            "create",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def empty(self, obj, **kwargs):
-        return self._invoke("empty", obj, **kwargs)
+    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        return self._invoke(
+            "empty",
+            obj,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def size(self, obj, **kwargs):
-        return self._invoke("size", obj, **kwargs)
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False) -> int:
+        return self._invoke(
+            "size", obj, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, obj_dir=obj_dir
+        )
 
-    def delete(self, obj, **kwargs):
-        return self._invoke("delete", obj, **kwargs)
+    def delete(
+        self,
+        obj,
+        entire_dir=False,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+    ):
+        return self._invoke(
+            "delete",
+            obj,
+            entire_dir=entire_dir,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def get_data(self, obj, **kwargs):
-        return self._invoke("get_data", obj, **kwargs)
+    def get_data(
+        self,
+        obj,
+        start=0,
+        count=-1,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+    ):
+        return self._invoke(
+            "get_data",
+            obj,
+            start=start,
+            count=count,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def get_filename(self, obj, **kwargs):
-        return self._invoke("get_filename", obj, **kwargs)
+    def get_filename(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        sync_cache: bool = True,
+    ):
+        return self._invoke(
+            "get_filename",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            sync_cache=sync_cache,
+        )
 
-    def update_from_file(self, obj, **kwargs):
-        return self._invoke("update_from_file", obj, **kwargs)
+    def update_from_file(
+        self,
+        obj,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        file_name=None,
+        create=False,
+        preserve_symlinks=False,
+    ):
+        return self._invoke(
+            "update_from_file",
+            obj,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            file_name=file_name,
+            create=create,
+            preserve_symlinks=preserve_symlinks,
+        )
 
-    def get_object_url(self, obj, **kwargs):
-        return self._invoke("get_object_url", obj, **kwargs)
+    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        return self._invoke(
+            "get_object_url",
+            obj,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
     def get_concrete_store_name(self, obj):
         return self._invoke("get_concrete_store_name", obj)
@@ -843,7 +977,7 @@ def _create(self, obj, **kwargs):
 
     def _empty(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by checking file size on disk."""
-        return self.size(obj, **kwargs) == 0
+        return self._size(obj, **kwargs) == 0
 
     def _size(self, obj, **kwargs) -> int:
         """Override `ObjectStore`'s stub by return file size on disk.
@@ -1045,7 +1179,7 @@ def _repr_object_for_exception(self, obj):
     def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         """Check all children object stores for the first one with the dataset."""
         for store in self.backends.values():
-            if store.exists(obj, **kwargs):
+            if store._exists(obj, **kwargs):
                 return store.__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
             raise default(
@@ -1109,22 +1243,22 @@ def __init__(
 
         user_selection_allowed = []
         for backend_def in config_dict["backends"]:
-            backened_id = backend_def["id"]
+            backend_id = backend_def["id"]
             maxpctfull = backend_def.get("max_percent_full", 0)
             weight = backend_def["weight"]
             allow_selection = backend_def.get("allow_selection")
             if allow_selection:
-                user_selection_allowed.append(backened_id)
+                user_selection_allowed.append(backend_id)
             backend = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
 
-            self.backends[backened_id] = backend
-            self.max_percent_full[backened_id] = maxpctfull
+            self.backends[backend_id] = backend
+            self.max_percent_full[backend_id] = maxpctfull
 
             for _ in range(0, weight):
                 # The simplest way to do weighting: add backend ids to a
                 # sequence the number of times equalling weight, then randomly
                 # choose a backend from that sequence at creation
-                self.weighted_backend_ids.append(backened_id)
+                self.weighted_backend_ids.append(backend_id)
 
         self.original_weighted_backend_ids = self.weighted_backend_ids
         self.user_object_store_resolver = user_object_store_resolver
@@ -1340,7 +1474,7 @@ def __get_store_id_for(self, obj, **kwargs):
             # distributed object store, or if the object's store id is invalid,
             # try to locate the object
             for id, store in self.backends.items():
-                if store.exists(obj, **kwargs):
+                if store._exists(obj, **kwargs):
                     log.warning(
                         f"{obj.__class__.__name__} object with ID {obj.id} found in backend object store with ID {id}"
                     )
@@ -1401,7 +1535,7 @@ def __init__(self, config, config_dict, fsmon=False):
         """The default constructor. Extends `NestedObjectStore`."""
         super().__init__(config, config_dict)
 
-        backends: Dict[int, ObjectStore] = {}
+        backends: Dict[int, BaseObjectStore] = {}
         is_private = config_dict.get("private", DEFAULT_PRIVATE)
         for order, backend_def in enumerate(config_dict["backends"]):
             backend_is_private = backend_def.get("private")

test/unit/app/tools/test_metadata.py

@@ -18,7 +18,7 @@ class TestMetadata(TestCase, tools_support.UsesTools):
     def setUp(self):
         super().setUp()
         self.setup_app()
-        model.Dataset.object_store = self.app.object_store  # type: ignore[assignment]
+        model.Dataset.object_store = self.app.object_store
         job = model.Job()
         sa_session = self.app.model.session
         sa_session.add(job)