Restore deprecated copy because too many tests still depend on it

Author: Bryan Bartley

sbol3/object.py

@@ -110,6 +110,76 @@ def _resolve_references(self, new_obj):
         resolve_references = make_resolve_references_traverser(new_obj)
         self.traverse(resolve_references)
 
+    def copy(self, target_doc=None, target_namespace=None):  # pylint: disable=R0912
+
+        # Delete this method in v1.1
+        warnings.warn('Use sbol3.copy() instead', DeprecationWarning)
+
+        new_uri = self.identity
+
+        # If caller specified a target_namespace argument, then copy the object into this
+        # new namespace.
+        if target_namespace:
+
+            # Map the identity of self into the target namespace
+            if hasattr(self, 'identity'):
+                old_uri = self.identity
+                new_uri = replace_namespace(old_uri, target_namespace, self.getTypeURI())
+
+        try:
+            builder = BUILDER_REGISTER[self.type_uri]
+        except KeyError:
+            logging.warning(f'No builder found for {self.type_uri}; assuming {self.__class__.__name__}')
+            builder = self.__class__
+        new_obj = builder(**dict(identity=new_uri, type_uri=self.type_uri))
+
+        # Copy properties
+        for property_uri, value_store in self._properties.items():
+            new_obj._properties[property_uri] = value_store.copy()
+
+            # TODO: Map into new namespace
+
+        # Assign the new object to the target Document
+        if target_doc is not None:
+            try:
+                target_doc.add(new_obj)
+            except TypeError:
+                pass  # object is not TopLevel
+
+        # When an object is simply being cloned, the value of wasDerivedFrom should be
+        # copied exactly as is from self. However, when copy is being used to generate
+        # a new entity, the wasDerivedFrom should point back to self.
+        if self.identity == new_obj.identity:
+            new_obj.derived_from = self.derived_from
+        else:
+            new_obj.derived_from = self.identity
+
+        # Copy child objects recursively
+        for property_uri, object_list in self._owned_objects.items():
+            for o in object_list:
+                o_copy = o.copy(target_doc, target_namespace)
+                new_obj._owned_objects[property_uri].append(o_copy)
+                o_copy.parent = self
+
+        # After we have copied all the owned objects, copy the referenced objects
+        # and attempt to resolve the references
+        if target_doc:
+            for property_uri, object_store in self._referenced_objects.items():
+                for o in object_store:
+                    referenced_obj = target_doc.find(o.identity)
+                    if referenced_obj:
+                        new_obj._referenced_objects[property_uri].append(referenced_obj)
+                    else:
+                        new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity))
+        else:
+            # If the copy does not belong to a Document, then treat all references
+            # like external references
+            for property_uri, object_store in self._referenced_objects.items():
+                for o in object_store:
+                    new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity))
+
+        return new_obj
+
     def lookup(self):
         return self