diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 308b9bafc900..fc905ac7ec02 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -5772,6 +5772,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
     __tablename__ = "library_folder"
     __table_args__ = (Index("ix_library_folder_name", "name", mysql_length=200),)
 
+    id: Mapped[int] = mapped_column(primary_key=True)
     parent_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_folder.id"), index=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
@@ -5788,9 +5789,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
         order_by=asc(name),
         back_populates="parent",
     )
-    parent: Mapped[Optional["LibraryFolder"]] = relationship(
-        back_populates="folders", remote_side=["id"]  # type:ignore[list-item]
-    )
+    parent: Mapped[Optional["LibraryFolder"]] = relationship(back_populates="folders", remote_side=[id])
 
     active_folders: Mapped[List["LibraryFolder"]] = relationship(
         primaryjoin=("and_(LibraryFolder.parent_id == LibraryFolder.id, not_(LibraryFolder.deleted))"),
@@ -5910,6 +5909,7 @@ def parent_library(self):
 class LibraryDataset(Base, Serializable):
     __tablename__ = "library_dataset"
 
+    id: Mapped[int] = mapped_column(primary_key=True)
     # current version of dataset, if null, there is not a current version selected
     library_dataset_dataset_association_id: Mapped[Optional[int]] = mapped_column(
         ForeignKey(
@@ -5933,7 +5933,7 @@ class LibraryDataset(Base, Serializable):
         "LibraryDatasetDatasetAssociation", foreign_keys=library_dataset_dataset_association_id, post_update=True
     )
     expired_datasets: Mapped[List["LibraryDatasetDatasetAssociation"]] = relationship(
-        foreign_keys=["id", library_dataset_dataset_association_id],  # type:ignore[list-item]
+        foreign_keys=[id, library_dataset_dataset_association_id],
         primaryjoin=(
             "and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \
              not_(LibraryDataset.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.id))"
@@ -6917,6 +6917,7 @@ class HistoryDatasetCollectionAssociation(
 
     __tablename__ = "history_dataset_collection_association"
 
+    id: Mapped[int] = mapped_column(primary_key=True)
     collection_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset_collection.id"), index=True)
     history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)
     name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
@@ -6940,7 +6941,7 @@ class HistoryDatasetCollectionAssociation(
     copied_from_history_dataset_collection_association = relationship(
         "HistoryDatasetCollectionAssociation",
         primaryjoin=copied_from_history_dataset_collection_association_id == id,
-        remote_side=["id"],  # type:ignore[list-item]
+        remote_side=[id],
         uselist=False,
     )
     implicit_input_collections: Mapped[List["ImplicitlyCreatedDatasetCollectionInput"]] = relationship(
@@ -8462,6 +8463,7 @@ class WorkflowComment(Base, RepresentById):
 
     __tablename__ = "workflow_comment"
 
+    id: Mapped[int] = mapped_column(primary_key=True)
     order_index: Mapped[Optional[int]]
     workflow_id: Mapped[int] = mapped_column(ForeignKey("workflow.id"), index=True)
     position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
@@ -8485,7 +8487,7 @@ class WorkflowComment(Base, RepresentById):
     parent_comment: Mapped[Optional["WorkflowComment"]] = relationship(
         primaryjoin=(lambda: WorkflowComment.id == WorkflowComment.parent_comment_id),
         back_populates="child_comments",
-        remote_side=["id"],  # type:ignore[list-item]
+        remote_side=[id],
     )
 
     child_comments: Mapped[List["WorkflowComment"]] = relationship(
@@ -10591,13 +10593,12 @@ class Tag(Base, RepresentById):
     __tablename__ = "tag"
     __table_args__ = (UniqueConstraint("name"),)
 
+    id: Mapped[int] = mapped_column(primary_key=True)
     type: Mapped[Optional[int]]
     parent_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tag.id"))
     name: Mapped[Optional[str]] = mapped_column(TrimmedString(255))
     children: Mapped[List["Tag"]] = relationship(back_populates="parent")
-    parent: Mapped[Optional["Tag"]] = relationship(
-        back_populates="children", remote_side=["id"]  # type:ignore[list-item]
-    )
+    parent: Mapped[Optional["Tag"]] = relationship(back_populates="children", remote_side=[id])
 
     def __str__(self):
         return f"Tag(id={self.id}, type={self.type or -1}, parent_id={self.parent_id}, name={self.name})"