Fix various mypy issues around mapped attributes

lib/galaxy/celery/tasks.py

@@ -199,7 +199,7 @@ def set_metadata(
     try:
         if overwrite:
             hda_manager.overwrite_metadata(dataset_instance)
-        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore [arg-type]
+        dataset_instance.datatype.set_meta(dataset_instance)
         dataset_instance.set_peek()
         # Reset SETTING_METADATA state so the dataset instance getter picks the dataset state
         dataset_instance.set_metadata_success_state()

lib/galaxy/datatypes/protocols.py

@@ -2,10 +2,16 @@
 Location of protocols used in datatypes
 """
 
-from typing import Any
+from typing import (
+    Any,
+    TYPE_CHECKING,
+)
 
 from typing_extensions import Protocol
 
+if TYPE_CHECKING:
+    from sqlalchemy.orm import Mapped
+
 
 class HasClearAssociatedFiles(Protocol):
     def clear_associated_files(self, metadata_safe: bool = False, purge: bool = False) -> None: ...
@@ -17,7 +23,7 @@ def creating_job(self): ...
 
 
 class HasDeleted(Protocol):
-    deleted: bool
+    deleted: "Mapped[bool]"
 
 
 class HasExt(Protocol):
@@ -39,7 +45,7 @@ class HasHid(Protocol):
 
 
 class HasId(Protocol):
-    id: int
+    id: "Mapped[int]"
 
 
 class HasInfo(Protocol):

lib/galaxy/managers/hdas.py

@@ -371,7 +371,7 @@ def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
             .where(
                 and_(
                     HistoryDatasetAssociation.deleted == true(),
-                    HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
+                    HistoryDatasetAssociation.purged == false(),
                     model.History.user_id == user.id,
                 )
             )
@@ -401,7 +401,7 @@ def get_discarded(
             .where(
                 and_(
                     HistoryDatasetAssociation.deleted == true(),
-                    HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
+                    HistoryDatasetAssociation.purged == false(),
                     model.History.user_id == user.id,
                 )
             )

lib/galaxy/managers/jobs.py

@@ -623,14 +623,14 @@ def _build_stmt_for_hda(self, stmt: S, data_conditions, used_ids, k, v, identifi
         c = aliased(model.HistoryDatasetAssociation)
         d = aliased(model.JobParameter)
         e = aliased(model.HistoryDatasetAssociationHistory)
-        stmt = stmt.add_columns(a.dataset_id)
+        stmt = cast(S, stmt.add_columns(a.dataset_id))
         used_ids.append(a.dataset_id)
         stmt = stmt.join(a, a.job_id == model.Job.id)
         hda_stmt = select(model.HistoryDatasetAssociation.id).where(
             model.HistoryDatasetAssociation.id == e.history_dataset_association_id
         )
         # b is the HDA used for the job
-        stmt = stmt.join(b, a.dataset_id == b.id)  # type:ignore[attr-defined]
+        stmt = stmt.join(b, a.dataset_id == b.id)
         stmt = has_same_source(stmt, b, c)
         name_condition = []
         if identifier:
@@ -729,7 +729,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
                 ),
             )
             .outerjoin(d, d.id == c.hda_id)
-            .outerjoin(e, e.dataset_id == d.dataset_id)  # type:ignore[attr-defined]
+            .outerjoin(e, e.dataset_id == d.dataset_id)
         )
         data_conditions.append(
             and_(
@@ -739,7 +739,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
                     and_(
                         c.hda_id == b.hda_id,
                         d.id == c.hda_id,
-                        e.dataset_id == d.dataset_id,  # type:ignore[attr-defined]
+                        e.dataset_id == d.dataset_id,
                     ),
                 ),
                 c.id == v,

lib/galaxy/model/__init__.py

@@ -3152,8 +3152,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     active_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship(
         primaryjoin=(
             lambda: and_(
-                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[arg-type]
-                not_(HistoryDatasetAssociation.deleted),  # type: ignore[has-type]
+                HistoryDatasetAssociation.history_id == History.id,
+                not_(HistoryDatasetAssociation.deleted),
             )
         ),
         order_by=lambda: asc(HistoryDatasetAssociation.hid),  # type: ignore[has-type]
@@ -3165,7 +3165,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
             lambda: (
                 and_(
                     HistoryDatasetCollectionAssociation.history_id == History.id,
-                    not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[arg-type]
+                    not_(HistoryDatasetCollectionAssociation.deleted),
                 )
             )
         ),
@@ -3175,8 +3175,8 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     visible_datasets: Mapped[List["HistoryDatasetAssociation"]] = relationship(
         primaryjoin=(
             lambda: and_(
-                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[arg-type]
-                not_(HistoryDatasetAssociation.deleted),  # type: ignore[has-type]
+                HistoryDatasetAssociation.history_id == History.id,
+                not_(HistoryDatasetAssociation.deleted),
                 HistoryDatasetAssociation.visible,  # type: ignore[has-type]
             )
         ),
@@ -3187,7 +3187,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         primaryjoin=(
             lambda: and_(
                 HistoryDatasetCollectionAssociation.history_id == History.id,
-                not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[arg-type]
+                not_(HistoryDatasetCollectionAssociation.deleted),
                 HistoryDatasetCollectionAssociation.visible,  # type: ignore[arg-type]
             )
         ),
@@ -4110,27 +4110,27 @@ class Dataset(Base, StorableObject, Serializable):
     active_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(
         primaryjoin=(
             lambda: and_(
-                Dataset.id == HistoryDatasetAssociation.dataset_id,  # type: ignore[attr-defined]
-                HistoryDatasetAssociation.deleted == false(),  # type: ignore[has-type]
-                HistoryDatasetAssociation.purged == false(),  # type: ignore[arg-type]
+                Dataset.id == HistoryDatasetAssociation.dataset_id,
+                HistoryDatasetAssociation.deleted == false(),
+                HistoryDatasetAssociation.purged == false(),
             )
         ),
         viewonly=True,
     )
     purged_history_associations: Mapped[List["HistoryDatasetAssociation"]] = relationship(
         primaryjoin=(
             lambda: and_(
-                Dataset.id == HistoryDatasetAssociation.dataset_id,  # type: ignore[attr-defined]
-                HistoryDatasetAssociation.purged == true(),  # type: ignore[arg-type]
+                Dataset.id == HistoryDatasetAssociation.dataset_id,
+                HistoryDatasetAssociation.purged == true(),
             )
         ),
         viewonly=True,
     )
     active_library_associations: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship(
         primaryjoin=(
             lambda: and_(
-                Dataset.id == LibraryDatasetDatasetAssociation.dataset_id,  # type: ignore[attr-defined]
-                LibraryDatasetDatasetAssociation.deleted == false(),  # type: ignore[has-type]
+                Dataset.id == LibraryDatasetDatasetAssociation.dataset_id,
+                LibraryDatasetDatasetAssociation.deleted == false(),
             )
         ),
         viewonly=True,
@@ -4596,11 +4596,13 @@ def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
 class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
     """A base class for all 'dataset instances', HDAs, LDDAs, etc"""
 
+    purged: Mapped[Optional[bool]]
+    deleted: Mapped[bool]
+    dataset_id: Mapped[Optional[int]]
+    _state: Mapped[Optional[str]]
     states = Dataset.states
-    _state: Optional[str]
     conversion_messages = Dataset.conversion_messages
     permitted_actions = Dataset.permitted_actions
-    purged: bool
     creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]
     copied_from_history_dataset_association: Optional["HistoryDatasetAssociation"]
     copied_from_library_dataset_dataset_association: Optional["LibraryDatasetDatasetAssociation"]
@@ -5055,9 +5057,7 @@ def find_conversion_destination(
         self, accepted_formats: List[str], **kwd
     ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """Returns ( target_ext, existing converted dataset )"""
-        return self.datatype.find_conversion_destination(
-            self, accepted_formats, _get_datatypes_registry(), **kwd  # type:ignore[arg-type]
-        )
+        return self.datatype.find_conversion_destination(self, accepted_formats, _get_datatypes_registry(), **kwd)
 
     def add_validation_error(self, validation_error):
         self.validation_errors.append(validation_error)
@@ -5260,7 +5260,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
     Resource class that creates a relation between a dataset and a user history.
     """
 
-    history_id: Optional[int]
+    history_id: Mapped[Optional[int]]
 
     def __init__(
         self,
@@ -6947,7 +6947,7 @@ class HistoryDatasetCollectionAssociation(
     name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     hid: Mapped[Optional[int]]
     visible: Mapped[Optional[bool]]
-    deleted: Mapped[Optional[bool]] = mapped_column(default=False)
+    deleted: Mapped[bool] = mapped_column(default=False)
     copied_from_history_dataset_collection_association_id: Mapped[Optional[int]] = mapped_column(
         ForeignKey("history_dataset_collection_association.id")
     )

lib/galaxy/model/store/__init__.py

@@ -718,7 +718,7 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                                 # Try to set metadata directly. @mvdbeek thinks we should only record the datasets
                                 try:
                                     if dataset_instance.has_metadata_files:
-                                        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore[arg-type]
+                                        dataset_instance.datatype.set_meta(dataset_instance)
                                 except Exception:
                                     log.debug(f"Metadata setting failed on {dataset_instance}", exc_info=True)
                                     dataset_instance.state = dataset_instance.dataset.states.FAILED_METADATA