Merge pull request #430 from SynBioDex/copy-custom-toplevel

Support copy of custom classes
SynBioDex · Apr 11, 2023 · c84ccd1 · c84ccd1
2 parents f864ff5 + 5fbc4d9
commit c84ccd1
Show file tree

Hide file tree

Showing 2 changed files with 41 additions and 6 deletions.
diff --git a/sbol3/object.py b/sbol3/object.py
@@ -1,3 +1,4 @@
+import logging
 import posixpath
 import uuid
 import warnings
@@ -111,8 +112,12 @@ def copy(self, target_doc=None, target_namespace=None):
                 old_uri = self.identity
                 new_uri = replace_namespace(old_uri, target_namespace, self.getTypeURI())
 
-        new_obj = BUILDER_REGISTER[self.type_uri](**dict(identity=new_uri,
-                                                         type_uri=self.type_uri))
+        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():

diff --git a/test/test_custom.py b/test/test_custom.py
@@ -2,14 +2,14 @@
 import os
 import tempfile
 import unittest
+import warnings
 from typing import Union
 
-import rdflib
-
 import sbol3
 
 
 PYSBOL3_CUSTOM_TOP = 'https://github.com/synbiodex/pysbol3#customTop'
+PYSBOL3_CUSTOM_UNREGISTERED_TOP = 'https://github.com/synbiodex/pysbol3#customUnregisteredTop'
 PYSBOL3_CUSTOM_BOOL = 'https://github.com/synbiodex/pysbol3#customBool'
 PYSBOL3_CUSTOM_CHILD = 'https://github.com/synbiodex/pysbol3#customChildren'
 PYSBOL3_CUSTOM_IDENTIFIED = 'https://github.com/synbiodex/pysbol3#customIdentified'
@@ -26,6 +26,15 @@ def __init__(self, identity, type_uri=PYSBOL3_CUSTOM_TOP):
         self.children = sbol3.OwnedObject(self, PYSBOL3_CUSTOM_CHILD, 0, math.inf)
 
 
+class CustomUnregisteredTopClass(sbol3.CustomTopLevel):
+    def __init__(self, identity, type_uri=PYSBOL3_CUSTOM_UNREGISTERED_TOP):
+        super().__init__(identity, type_uri)
+        # Also test the boolean list while we're here
+        self.foo_bool = sbol3.BooleanProperty(self, PYSBOL3_CUSTOM_BOOL,
+                                              0, math.inf)
+        self.children = sbol3.OwnedObject(self, PYSBOL3_CUSTOM_CHILD, 0, math.inf)
+
+
 class CustomIdentifiedClass(sbol3.CustomIdentified):
     def __init__(self, type_uri=PYSBOL3_CUSTOM_IDENTIFIED, identity=None):
         super().__init__(type_uri, identity=identity)
@@ -85,18 +94,39 @@ def test_round_trip(self):
         obj.foo_bool.append(True)
         obj.foo_bool.append(False)
         self.assertEqual([True, False], obj.foo_bool)
+        obj_unregistered_name = 'bool_test_unregistered'
+        obj_u = CustomUnregisteredTopClass(obj_unregistered_name)
+        obj_u.foo_bool.append(True)
+        self.assertEqual([True], obj_u.foo_bool)
         doc = sbol3.Document()
         doc.add(obj)
+        doc.add(obj_u)
         doc2 = sbol3.Document()
         # Round trip the document
         with tempfile.TemporaryDirectory() as tmpdirname:
             test_file = os.path.join(tmpdirname, 'custom.nt')
             doc.write(test_file, sbol3.NTRIPLES)
             doc2.read(test_file, sbol3.NTRIPLES)
         obj2 = doc2.find(obj_name)
+        obj_u2 = doc2.find(obj_unregistered_name)
         # The lists are necessarily unordered because of RDF
-        # Compare specially
-        self.assertCountEqual([True, False], obj2.foo_bool)
+        self.assertCountEqual([False, True], obj2.foo_bool)
+        unregistered_values = obj_u2._properties['https://github.com/synbiodex/pysbol3#customBool']
+        self.assertEqual(['true'], [str(x) for x in unregistered_values])
+
+        # Finally, make sure the objects can be copied into a new document
+        doc3 = sbol3.Document()
+        # This test deliberately uses the old copy function, as that was where an error previously occurred
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", DeprecationWarning)
+            obj2.copy(doc3)
+            obj_u2.copy(doc3)
+        obj3 = doc3.find(obj_name)
+        obj_u3 = doc3.find(obj_unregistered_name)
+        # The lists are necessarily unordered because of RDF
+        self.assertCountEqual([False, True], obj3.foo_bool)
+        unregistered_values = obj_u3._properties['https://github.com/synbiodex/pysbol3#customBool']
+        self.assertEqual(['true'], [str(x) for x in unregistered_values])
 
     def test_none_identity(self):
         # Make sure a ValueError is raised if None is passed