Mypy fixes: add anno for Lists; type-ignore for HDAs

Note: type-ignore is due to imperative mapping of HDAs (and LDDAs). This
will be removed once we map those models declaratively

lib/galaxy/managers/jobs.py

@@ -5,6 +5,7 @@
     date,
     datetime,
 )
+from typing import List
 
 import sqlalchemy
 from boltons.iterutils import remap
@@ -359,15 +360,15 @@ def replace_dataset_ids(path, key, value):
 
         stmt = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
 
-        data_conditions = []
+        data_conditions: List = []
 
         # We now build the stmt filters that relate to the input datasets
         # that this job uses. We keep track of the requested dataset id in `requested_ids`,
         # the type (hda, hdca or lda) in `data_types`
         # and the ids that have been used in the job that has already been run in `used_ids`.
         requested_ids = []
         data_types = []
-        used_ids = []
+        used_ids: List = []
         for k, input_list in input_data.items():
             # k will be matched against the JobParameter.name column. This can be prefixed depending on whethter
             # the input is in a repeat, or not (section and conditional)
@@ -524,7 +525,7 @@ def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier)
             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).join(c, c.dataset_id == b.dataset_id)
+        stmt = stmt.join(b, a.dataset_id == b.id).join(c, c.dataset_id == b.dataset_id)  # type:ignore[attr-defined]
         name_condition = []
         if identifier:
             stmt = stmt.join(d)
@@ -622,7 +623,7 @@ 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)
+            .outerjoin(e, e.dataset_id == d.dataset_id)  # type:ignore[attr-defined]
         )
         data_conditions.append(
             and_(
@@ -632,7 +633,7 @@ 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,
+                        e.dataset_id == d.dataset_id,  # type:ignore[attr-defined]
                     ),
                 ),
                 c.id == v,