Merge pull request #117 from tcmitchell/115-write-string

Add Document.write_string()

sbol3/document.py

@@ -225,11 +225,7 @@ def find(self, search_string: str) -> Optional[Identified]:
                 return obj
         return self._find_in_objects(search_string)
 
-    def write(self, fpath: str, file_format: str = None) -> None:
-        if file_format is None:
-            file_format = self._guess_format(fpath)
-        if file_format is None:
-            raise ValueError('Unable to determine file format')
+    def write_string(self, file_format: str) -> bytes:
         graph = self.graph()
         if file_format == SORTED_NTRIPLES:
             # have RDFlib give us the ntriples as a string
@@ -240,14 +236,28 @@ def write(self, fpath: str, file_format: str = None) -> None:
             lines.sort()
             # write out the lines
             # RDFlib gives us bytes, so open file in binary mode
-            with open(fpath, 'wb') as outfile:
-                outfile.writelines(lines)
+            result = b''.join(lines)
         elif file_format == JSONLD:
             context = {f'@{prefix}': uri for prefix, uri in self._namespaces.items()}
             context['@vocab'] = 'https://sbolstandard.org/examples/'
-            graph.serialize(fpath, format=file_format, context=context)
+            result = graph.serialize(format=file_format, context=context)
         else:
-            graph.serialize(fpath, format=file_format)
+            result = graph.serialize(format=file_format)
+        return result
+
+    def write(self, fpath: str, file_format: str = None) -> None:
+        """Write the document to file.
+
+        If file_format is None the desired format is guessed from the
+        extension of fpath. If file_format cannot be guessed a ValueError
+        is raised.
+        """
+        if file_format is None:
+            file_format = self._guess_format(fpath)
+        if file_format is None:
+            raise ValueError('Unable to determine file format')
+        with open(fpath, 'wb') as outfile:
+            outfile.write(self.write_string(file_format))
 
     def graph(self) -> rdflib.Graph:
         """Convert document to an RDF Graph.

test/test_document.py

@@ -19,12 +19,13 @@ def setUpClass(cls) -> None:
 
     def test_read_ntriples(self):
         # Initial test of Document.read
+        filename = 'model.nt'
         test_path = os.path.join(SBOL3_LOCATION, 'entity', 'model',
-                                 'model.nt')
+                                 filename)
         doc = sbol3.Document()
         doc.read(test_path)
         with tempfile.TemporaryDirectory() as tmpdirname:
-            test_file = os.path.join(tmpdirname)
+            test_file = os.path.join(tmpdirname, filename)
             doc.write(test_file, sbol3.NTRIPLES)
 
     def test_read_turtle(self):
@@ -147,6 +148,23 @@ def test_graph(self):
         self.assertIn(sbol3.SBOL_DISPLAY_ID, predicates)
         self.assertIn(sbol3.SBOL_TYPE, predicates)
 
+    def test_write_string(self):
+        # Make sure Document.write_string produces the same output
+        # as Document.write. Must use sorted NTriples for this test
+        # because other formats do not have a guaranteed order.
+        filename = 'model.nt'
+        test_path = os.path.join(SBOL3_LOCATION, 'entity', 'model',
+                                 filename)
+        doc = sbol3.Document()
+        doc.read(test_path)
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            test_file = os.path.join(tmpdirname, filename)
+            doc.write(test_file, sbol3.SORTED_NTRIPLES)
+            with open(test_file, 'rb') as infile:
+                expected = infile.read()
+        actual = doc.write_string(sbol3.SORTED_NTRIPLES)
+        self.assertEqual(expected, actual)
+
 
 if __name__ == '__main__':
     unittest.main()