Use distinct only for dataset states/extensions summary

lib/galaxy/model/__init__.py

@@ -6203,9 +6203,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
             if entity == DatasetCollectionElement:
                 q = q.filter(entity.id == dce.c.id)
 
-        q = q.distinct().order_by(*order_by_columns)
-        # With DISTINCT, all columns that appear in the ORDER BY clause must appear in the SELECT clause.
-        q = q.add_columns(*order_by_columns)
+        q = q.order_by(*order_by_columns)
         return q
 
     @property
@@ -6214,11 +6212,15 @@ def dataset_states_and_extensions_summary(self):
             stmt = self._build_nested_collection_attributes_stmt(
                 hda_attributes=("extension",), dataset_attributes=("state",)
             )
+            # With DISTINCT, all columns that appear in the ORDER BY clause must appear in the SELECT clause.
+            stmt = stmt.add_columns(*stmt._order_by_clauses)
+            stmt = stmt.distinct()
+
             tuples = object_session(self).execute(stmt)
 
             extensions = set()
             states = set()
-            for extension, state, *_ in tuples:
+            for extension, state, *_ in tuples:  # we discard the added columns from the order-by clause
                 states.add(state)
                 extensions.add(extension)
 
@@ -6234,8 +6236,7 @@ def has_deferred_data(self):
                 # TODO: Optimize by just querying without returning the states...
                 stmt = self._build_nested_collection_attributes_stmt(dataset_attributes=("state",))
                 tuples = object_session(self).execute(stmt)
-
-                for state, *_ in tuples:
+                for (state,) in tuples:
                     if state == Dataset.states.DEFERRED:
                         has_deferred_data = True
                         break
@@ -6283,28 +6284,13 @@ def dataset_action_tuples(self):
         if not hasattr(self, "_dataset_action_tuples"):
             stmt = self._build_nested_collection_attributes_stmt(dataset_permission_attributes=("action", "role_id"))
             tuples = object_session(self).execute(stmt)
-            self._dataset_action_tuples = [(action, role_id) for action, role_id, *_ in tuples if action is not None]
+            self._dataset_action_tuples = [(action, role_id) for action, role_id in tuples if action is not None]
         return self._dataset_action_tuples
 
     @property
     def element_identifiers_extensions_paths_and_metadata_files(
         self,
     ) -> List[List[Any]]:
-        def find_identifiers(row):
-            # Assume row has this structure: [id1, id2, ..., idn, extension, model, anything];
-            # model is an instance of a Dataset or a HistoryDatasetAssociation;
-            # extension is a string that always preceeds the model;
-            # we look for the first model, then pick the preceeding items minus the extention.
-            identifiers = []
-            i = 0
-            while i + 1 < len(row):
-                item, next_item = row[i], row[i + 1]
-                if isinstance(next_item, HistoryDatasetAssociation) or isinstance(next_item, Dataset):
-                    break
-                identifiers.append(item)
-                i += 1
-            return tuple(identifiers)
-
         results = []
         if object_session(self):
             stmt = self._build_nested_collection_attributes_stmt(
@@ -6315,7 +6301,7 @@ def find_identifiers(row):
             tuples = object_session(self).execute(stmt)
             # element_identifiers, extension, path
             for row in tuples:
-                result = [find_identifiers(row), row.extension, row.Dataset.get_file_name()]
+                result = [row[:-3], row.extension, row.Dataset.get_file_name()]
                 hda = row.HistoryDatasetAssociation
                 result.append(hda.get_metadata_file_paths_and_extensions())
                 results.append(result)
@@ -6468,7 +6454,6 @@ def replace_failed_elements(self, replacements):
             return_entities=[DatasetCollectionElement], hda_attributes=["id"]
         )
         tuples = object_session(self).execute(stmt).all()
-        tuples = [(element, id) for element, id, *_ in tuples]
         hda_id_to_element = dict(tuples)
         for failed, replacement in replacements.items():
             element = hda_id_to_element.get(failed.id)

test/unit/data/test_galaxy_mapping.py

@@ -414,25 +414,25 @@ def test_nested_collection_attributes(self):
         )
         result = self.model.session.execute(stmt).all()
         assert [(r._fields) for r in result] == [
-            ("element_identifier_0", "element_identifier_1", "extension", "state", "element_index", "element_index_1"),
-            ("element_identifier_0", "element_identifier_1", "extension", "state", "element_index", "element_index_1"),
+            ("element_identifier_0", "element_identifier_1", "extension", "state"),
+            ("element_identifier_0", "element_identifier_1", "extension", "state"),
         ]
 
         stmt = c2._build_nested_collection_attributes_stmt(
             element_attributes=("element_identifier",), hda_attributes=("extension",), dataset_attributes=("state",)
         )
         result = self.model.session.execute(stmt).all()
-        assert result == [("inner_list", "forward", "bam", "new", 0, 0), ("inner_list", "reverse", "txt", "new", 0, 1)]
+        assert result == [("inner_list", "forward", "bam", "new"), ("inner_list", "reverse", "txt", "new")]
 
         stmt = c2._build_nested_collection_attributes_stmt(return_entities=(model.HistoryDatasetAssociation,))
         result = self.model.session.execute(stmt).all()
-        assert result == [(d1, 0, 0), (d2, 0, 1)]
+        assert result == [(d1,), (d2,)]
 
         stmt = c2._build_nested_collection_attributes_stmt(
             return_entities=(model.HistoryDatasetAssociation, model.Dataset)
         )
         result = self.model.session.execute(stmt).all()
-        assert result == [(d1, d1.dataset, 0, 0), (d2, d2.dataset, 0, 1)]
+        assert result == [(d1, d1.dataset), (d2, d2.dataset)]
         # Assert properties that use _get_nested_collection_attributes return correct content
         assert c2.dataset_instances == [d1, d2]
         assert c2.dataset_elements == [dce1, dce2]
@@ -455,8 +455,8 @@ def test_nested_collection_attributes(self):
         stmt = c4._build_nested_collection_attributes_stmt(element_attributes=("element_identifier",))
         result = self.model.session.execute(stmt).all()
         assert result == [
-            ("outer_list", "inner_list", "forward", 0, 0, 0),
-            ("outer_list", "inner_list", "reverse", 0, 0, 1),
+            ("outer_list", "inner_list", "forward"),
+            ("outer_list", "inner_list", "reverse"),
         ]
         assert c4.dataset_elements == [dce1, dce2]