Merge pull request #116 from tcmitchell/114-document-graph

Add Document.graph()

sbol3/document.py

@@ -230,11 +230,7 @@ def write(self, fpath: str, file_format: str = None) -> None:
             file_format = self._guess_format(fpath)
         if file_format is None:
             raise ValueError('Unable to determine file format')
-        graph = rdflib.Graph()
-        for prefix, uri in self._namespaces.items():
-            graph.bind(prefix, uri)
-        for obj in self.objects:
-            obj.serialize(graph)
+        graph = self.graph()
         if file_format == SORTED_NTRIPLES:
             # have RDFlib give us the ntriples as a string
             nt_text = graph.serialize(format='nt')
@@ -253,6 +249,19 @@ def write(self, fpath: str, file_format: str = None) -> None:
         else:
             graph.serialize(fpath, format=file_format)
 
+    def graph(self) -> rdflib.Graph:
+        """Convert document to an RDF Graph.
+
+        The returned graph is a snapshot of the document and will
+        not be updated by subsequent changes to the document.
+        """
+        graph = rdflib.Graph()
+        for prefix, uri in self._namespaces.items():
+            graph.bind(prefix, uri)
+        for obj in self.objects:
+            obj.serialize(graph)
+        return graph
+
     def bind(self, prefix: str, uri: str) -> None:
         """Bind a prefix to an RDF namespace in the written RDF document.
 

test/test_document.py

@@ -3,6 +3,8 @@
 import tempfile
 import unittest
 
+import rdflib
+
 import sbol3
 
 MODULE_LOCATION = os.path.dirname(os.path.abspath(__file__))
@@ -119,6 +121,32 @@ def test_guess_format(self):
         with self.assertRaises(ValueError):
             doc.write('test.foo')
 
+    def test_empty_graph(self):
+        # Ensure that an empty document generates an empty RDF graph
+        doc = sbol3.Document()
+        g = doc.graph()
+        self.assertEqual(0, len(g))
+
+    def test_graph(self):
+        doc = sbol3.Document()
+        doc.add(sbol3.Component('foo', sbol3.SBO_DNA))
+        graph = doc.graph()
+        self.assertEqual(3, len(graph))
+        subjects = set()
+        predicates = set()
+        for s, p, _ in graph:
+            subjects.add(s)
+            predicates.add(p)
+        # Expecting 1 subject, the component
+        self.assertEqual(1, len(subjects))
+        # Expecting 3 predicates
+        self.assertEqual(3, len(predicates))
+        self.assertIn(rdflib.RDF.type, predicates)
+        # Convert predicates to strings for the remaining assertions
+        predicates = [str(p) for p in predicates]
+        self.assertIn(sbol3.SBOL_DISPLAY_ID, predicates)
+        self.assertIn(sbol3.SBOL_TYPE, predicates)
+
 
 if __name__ == '__main__':
     unittest.main()