Fix order of dataset instances

lib/galaxy/model/__init__.py

@@ -4302,17 +4302,19 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
 
             depth_collection_type = self.collection_type
             select_from = dc.outerjoin(de, de.c.dataset_collection_id == dc.c.id)
+            order_by_columns = [de.c.element_index]
 
             while ":" in depth_collection_type:
                 child_collection = alias(DatasetCollection.table)
                 child_collection_element = alias(DatasetCollectionElement.table)
                 select_from = select_from.outerjoin(child_collection, child_collection.c.id == de.c.child_collection_id)
                 select_from = select_from.outerjoin(child_collection_element, child_collection_element.c.dataset_collection_id == child_collection.c.id)
+                order_by_columns.append(child_collection_element.c.element_index)
 
                 de = child_collection_element
                 depth_collection_type = depth_collection_type.split(":", 1)[1]
             select_from = select_from.outerjoin(hda, hda.c.id == de.c.hda_id)
-            select_stmt = select([hda]).select_from(select_from).where(dc.c.id == self.id).distinct()
+            select_stmt = select([hda]).select_from(select_from).where(dc.c.id == self.id).distinct(*order_by_columns).order_by(*order_by_columns)
             return db_session.query(HistoryDatasetAssociation).select_entity_from(select_stmt).filter(HistoryDatasetAssociation.id.isnot(None)).all()
         else:
             # Sessionless context

test/unit/data/test_galaxy_mapping.py

@@ -1,5 +1,6 @@
 import collections
 import os
+import random
 import unittest
 import uuid
 
@@ -288,6 +289,42 @@ class MappingTests(BaseModelTestCase):
         for i in range(elements):
             assert c1[i] == dces[i]
 
+    def test_dataset_instance_order(self):
+        model = self.model
+        u = model.User(email="mary@example.com", password="password")
+        h1 = model.History(name="History 1", user=u)
+        elements = []
+        list_pair = model.DatasetCollection(collection_type="list:paired")
+        for i in range(20):
+            pair = model.DatasetCollection(collection_type="pair")
+            forward = model.HistoryDatasetAssociation(extension="txt", history=h1, name=f"forward_{i}", create_dataset=True, sa_session=model.session)
+            reverse = model.HistoryDatasetAssociation(extension="bam", history=h1, name=f"reverse_{i}", create_dataset=True, sa_session=model.session)
+            dce1 = model.DatasetCollectionElement(collection=pair, element=forward, element_identifier=f"forward_{i}", element_index=1)
+            dce2 = model.DatasetCollectionElement(collection=pair, element=reverse, element_identifier=f"reverse_{i}", element_index=2)
+            to_persist = [(forward, reverse), (dce1, dce2)]
+            self.persist(pair)
+            for item in to_persist:
+                if i % 2:
+                    self.persist(item[0])
+                    self.persist(item[1])
+                else:
+                    self.persist(item[1])
+                    self.persist(item[0])
+            elements.append(model.DatasetCollectionElement(collection=list_pair, element=pair, element_index=i, element_identifier=str(i)))
+        self.persist(list_pair)
+        random.shuffle(elements)
+        for item in elements:
+            self.persist(item)
+        forward = []
+        reverse = []
+        for i, dataset_instance in enumerate(list_pair.dataset_instances):
+            if i % 2:
+                reverse.append(dataset_instance)
+            else:
+                forward.append(dataset_instance)
+        assert all(d.name == f"forward_{i}" for i, d in enumerate(forward))
+        assert all(d.name == f"reverse_{i}" for i, d in enumerate(reverse))
+
     def test_collections_in_histories(self):
         model = self.model