Merge pull request #413 from tcmitchell/412-namespace-references

Update external references in change_object_namespace

sbol3/document.py

@@ -719,7 +719,9 @@ def migrate(self, top_levels: Iterable[TopLevel]) -> Any:
 
     @staticmethod
     def change_object_namespace(top_levels: Iterable[TopLevel],
-                                new_namespace: str) -> Any:
+                                new_namespace: str,
+                                update_references: Iterable[TopLevel] = None
+                                ) -> Any:
         """Change the namespace of all TopLevel objects in `top_levels` to
         new_namespace, regardless of the previous value, while
         maintaining referential integrity among all the top level
@@ -734,6 +736,8 @@ def change_object_namespace(top_levels: Iterable[TopLevel],
 
         :param top_levels: objects to change
         :param new_namespace: new namespace for objects
+        :param update_references: objects that should have their references
+                                  updated without changing their namespace
         :return: Nothing
         """
         # Validate the objects and build a map of old name to new name
@@ -754,6 +758,12 @@ def change_object_namespace(top_levels: Iterable[TopLevel],
             top_level.namespace = new_namespace
             top_level.set_identity(new_identity)
             top_level.update_all_dependents(identity_map)
+        # Now update any TopLevels in the update_references group. These are
+        # objects that may have references to the objects that had their
+        # namespace changed.
+        if update_references is not None:
+            for top_level in update_references:
+                top_level.update_all_dependents(identity_map)
         return None
 
     def clone(self) -> List[TopLevel]:

test/test_document.py

@@ -616,6 +616,22 @@ def test_change_object_namespace_errors(self):
         with self.assertRaises(ValueError):
             doc.change_object_namespace([i1], new_namespace)
 
+    def test_change_object_namespace_with_references(self):
+        """Test Document.change_object_namespace with outside references.
+
+        See https://github.com/SynBioDex/pySBOL3/issues/412
+        """
+        doc = sbol3.Document()
+        comp = sbol3.Component('http://sbolstandard.org/testfiles/hello',
+                               sbol3.SBO_DNA)
+        seq = sbol3.Sequence('http://sbolstandard.org/testfiles/hello_sequence',
+                             elements='ATGC')
+        doc.add(comp)
+        doc.add(seq)
+        comp.sequences = [seq]
+        doc.change_object_namespace([seq], 'http://parts.igem.org', doc)
+        self.assertEqual(seq.identity, comp.sequences[0])
+
     def test_clone(self):
         namespace = 'https://github.com/synbiodex/pysbol3'
         sbol3.set_namespace(namespace)