correcting 'io.Reader.run' with 'group_objects_by_model'=False to mat…

…ch behavior of 'obj_tables.io.Reader' with the same option (i.e. return list of objects rather than dictionary)

tests/test_io.py

@@ -379,6 +379,7 @@ class TestModel(obj_tables.Model):
         finally:
             core.KnowledgeBase.Meta.related_attributes.pop('test')
 
+    @unittest.skip('Assertions need to be uncommented')
     def test_seq_path_consistency(self):
         pass
 
@@ -387,3 +388,20 @@ def test_seq_path_consistency(self):
         #kb = io.Reader().run(core_path, seq_path=self.seq_path)[core.KnowledgeBase][0]
         #core_path = os.path.join(self.dir, 'core2.xlsx')
         #seq_path = os.path.join(self.dir, 'seq2.fna')
+
+    def test_read_flat_list_of_objects(self):
+        core_path = os.path.join(self.dir, 'core.xlsx')
+
+        writer = io.Writer()
+        writer.run(core_path, self.kb, data_repo_metadata=False)
+
+        reader = io.Reader()
+
+        objs = reader.run(core_path, seq_path=self.seq_path)
+        self.assertIsInstance(objs, dict)
+
+        objs = reader.run(core_path, seq_path=self.seq_path, 
+                          group_objects_by_model=False)
+        self.assertIsInstance(objs, list)
+        kb = next(obj for obj in objs if isinstance(obj, core.KnowledgeBase))
+        self.assertTrue(kb.is_equal(self.kb))

wc_kb/io.py

@@ -322,7 +322,7 @@ def run(self, core_path,
                                           ignore_missing_attributes=ignore_missing_attributes,
                                           ignore_extra_attributes=ignore_extra_attributes,
                                           ignore_attribute_order=ignore_attribute_order,
-                                          group_objects_by_model=group_objects_by_model,
+                                          group_objects_by_model=True,
                                           validate=False)
 
         # Check if sequence pathes are consistent
@@ -381,6 +381,13 @@ def run(self, core_path,
                 raise ValueError(
                     indent_forest(['The knowledge base cannot be loaded because it fails to validate:', [errors]]))
 
+        # if `group_objects_by_model` is False, flatten objects into list
+        if not group_objects_by_model:
+            flat_objects = []
+            for model_objs in objects.values():
+                flat_objects.extend(list(model_objs))
+            objects = flat_objects
+
         return objects