Testing addNamespace in conjunction with a custom annotation property

SynBioDex · Jan 23, 2020 · 2fb31df · 2fb31df
1 parent e879c78
commit 2fb31df
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Showing 2 changed files with 18 additions and 6 deletions.
diff --git a/sbol/document.py b/sbol/document.py
@@ -91,7 +91,6 @@ def __init__(self, filename=None):
         # Initialized when parsing a graph.
         # Updated when writing a graph.
         self.graph = rdflib.Graph()
-        self.graph.namespace_manager = rdflib.namespace.NamespaceManager(self.graph)
         # The Document's register of objects
         self.objectCache = {}  # Needed?
         self.SBOLObjects = {}  # Needed?
@@ -218,8 +217,13 @@ def addNamespace(self, namespace, prefix):
         :param prefix: The namespace prefix, eg. sbol
         :return:
         """
-        namespace = rdflib.namespace.Namespace(namespace)
-        self.graph.namespace_manager.bind(prefix, namespace, override=False)
+        if namespace[-1] != '#' and namespace[-1] != '/':
+            raise ValueError('Invalid namespace. Namespace must end with # or /')
+        namespace = rdflib.term.URIRef(namespace)
+        # Overwrite the prefix, if the namespace already has a conflicting one
+        inv_namespace_map = {ns: p for p, ns in self._namespaces.items()}
+        inv_namespace_map[namespace] = prefix
+        self._namespaces = {p: ns for ns, p in inv_namespace_map.items()}
 
     def addComponentDefinition(self, sbol_obj):
         """

diff --git a/sbol/test/test_document.py b/sbol/test/test_document.py
@@ -164,14 +164,22 @@ def test_find_property_value(self):
     def test_add_namespace(self):
         doc = sbol.Document()
         cd = doc.componentDefinitions.create('cd')
-        cd.foo = sbol.property.LiteralProperty(cd, 'http://examples.org#', '0', '1', 'bar')
+        cd.foo = sbol.property.LiteralProperty(cd, 'http://examples.org#foo', '0', '1', None, 'bar')
         doc.readString(doc.writeString())
         namespaces = [n[1] for n in doc.graph.namespace_manager.namespaces()]
         self.assertFalse('http://examples.org#' in namespaces)
-        doc.addNamespace('http://examples.org#', 'foo')
+        doc.addNamespace('http://examples.org#', 'examples')
+        cd.foo = sbol.property.LiteralProperty(cd, 'http://examples.org#foo', '0', '1', None, 'bar')
+        namespaces = [n for n in doc.graph.namespace_manager.namespaces()]
         doc.readString(doc.writeString())
         namespaces = [n for n in doc.graph.namespace_manager.namespaces()]
-        self.assertTrue(('foo', URIRef('http://examples.org#')) in namespaces)
+        self.assertTrue(('examples', URIRef('http://examples.org#')) in namespaces)
+
+    def test_namespace_fail(self):
+        doc = sbol.Document()
+        with self.assertRaises(ValueError):
+            doc.addNamespace('http://examples.org', 'foo')
+
 
 if __name__ == '__main__':
     unittest.main()