Merge pull request #373 from tcmitchell/235-copy

Migrate `TopLevel.copy` and `SBOLObject.copy` to `sbol3.copy`

sbol3/object.py

@@ -97,6 +97,9 @@ def find(self, search_string: str) -> Optional['SBOLObject']:
 
     def copy(self, target_doc=None, target_namespace=None):
 
+        # 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
@@ -143,42 +146,12 @@ def copy(self, target_doc=None, target_namespace=None):
 
 
 def replace_namespace(old_uri, target_namespace, rdf_type):
-    """
-    Utility function for mapping an SBOL object's identity into a new namespace. The
-    rdf_type is used to map to and from sbol-typed namespaces.
-    """
 
     # Flag as not working to ensure nobody calls this function thinking
     # it might do something.
     # See https://github.com/SynBioDex/pySBOL3/issues/132
     raise NotImplementedError()
 
-    # Work around an issue where the Document itself is being copied and
-    # doesn't have its own URI, so old_uri is None. Return empty string
-    # because the identity is not allowed to be None.
-    if old_uri is None:
-        return ''
-
-    # If the value is an SBOL-typed URI, replace both the namespace and class name
-    class_name = parseClassName(rdf_type)
-    replacement_target = target_namespace + '/' + class_name
-
-    # If not an sbol typed URI, then just replace the namespace
-    if replacement_target not in old_uri:
-        replacement_target = target_namespace
-
-    if Config.getOption(ConfigOptions.SBOL_TYPED_URIS):
-        # Map into a typed namespace
-        replacement = getHomespace() + '/' + class_name
-    else:
-        # Map into a non-typed namespace
-        replacement = getHomespace()
-
-    new_uri = old_uri.replace(replacement_target, replacement)
-    if type(old_uri) is URIRef:
-        return URIRef(new_uri)
-    return new_uri
-
 
 # Global store for builder methods. Custom SBOL classes
 # register their builders in this store

sbol3/toplevel.py

@@ -5,6 +5,7 @@
 import posixpath
 import urllib.parse
 import uuid
+import warnings
 from typing import Dict, Callable, Optional, Any
 import typing
 
@@ -171,6 +172,8 @@ def update_all_dependents(self, identity_map: dict[str, Identified]) -> Any:
         self.traverse(make_update_references_traverser(identity_map))
 
     def copy(self, target_doc=None, target_namespace=None):
+        # Delete this method in v1.1
+        warnings.warn('Use sbol3.copy() instead', DeprecationWarning)
         new_obj = super().copy(target_doc=target_doc, target_namespace=target_namespace)
         # Need to set `document` on all children recursively. That's what happens when
         # you assign to the `document` property of an Identified

test/test_object.py

@@ -25,7 +25,8 @@ def test_copy_properties(self):
         sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
         root = sbol3.Component('root', sbol3.SBO_DNA)
         root.name = 'foo'
-        root_copy = root.copy()
+        objects = sbol3.copy([root])
+        root_copy = objects[0]
         self.assertEqual(root_copy.name, 'foo')
 
     def test_copy_child_objects(self):
@@ -43,7 +44,8 @@ def test_copy_child_objects(self):
         doc.add(sub2)
 
         doc2 = sbol3.Document()
-        root_copy = root.copy(target_doc=doc2)
+        objects = sbol3.copy([root], into_document=doc2)
+        root_copy = objects[0]
         self.assertIn(root_copy, doc2.objects)
         self.assertEqual([sc.identity for sc in root.features],
                          [sc.identity for sc in root_copy.features])
@@ -57,6 +59,15 @@ def test_replace_namespace(self):
             from sbol3.object import replace_namespace
             replace_namespace(None, None, None)
 
+    def test_copy_is_deprecated(self):
+        namespace = 'https://github.com/synbiodex/pysbol3'
+        sbol3.set_namespace(namespace)
+        name = 'ed1'
+        ed1 = sbol3.ExternallyDefined(types=[sbol3.SBO_DNA],
+                                      definition='https://example.org/other')
+        with self.assertWarns(DeprecationWarning):
+            ed1.copy()
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_toplevel.py

@@ -70,8 +70,7 @@ def check_document(i: sbol3.Identified):
                                  'multicellular.nt')
         doc = sbol3.Document()
         doc.read(test_path)
-        for obj in doc.objects:
-            obj.copy(target_doc=dest_doc)
+        sbol3.copy(doc, into_document=dest_doc)
         self.assertEqual(len(doc), len(dest_doc))
         for obj in dest_doc.objects:
             obj.traverse(check_document)
@@ -172,6 +171,14 @@ def test_clone_bad_rename(self):
         c1_prime = c1.clone(posixpath.join(namespace, clone_name))
         self.assertIsNotNone(c1_prime.find('LocalSubComponent2'))
 
+    def test_copy_is_deprecated(self):
+        namespace = 'https://github.com/synbiodex/pysbol3'
+        sbol3.set_namespace(namespace)
+        name = 'c1'
+        c1 = sbol3.Component(name, types=[sbol3.SBO_DNA])
+        with self.assertWarns(DeprecationWarning):
+            c1.copy()
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_validation.py

@@ -56,7 +56,8 @@ def test_shacl_closure_with_toplevels(self):
         self.assertEqual(len(doc.validate()), 0)
         minidoc = sbol3.Document()
         c = doc.find('https://synbiohub.org/public/igem/BBa_I20270')
-        c.copy(minidoc)
+        self.assertIsInstance(c, sbol3.TopLevel)
+        sbol3.copy([c], into_document=minidoc)
         # this assertion failed before the fix to the shacl rules
         self.assertEqual(len(minidoc.validate()), 0)