Merge pull request #388 from tcmitchell/385-variable-component

Add variable component unit testing

sbol2/__init__.py

@@ -10,7 +10,7 @@
 # symbols are also exported.
 from .attachment import Attachment
 from .collection import Collection
-from .combinatorialderivation import CombinatorialDerivation
+from .combinatorialderivation import CombinatorialDerivation, VariableComponent
 from .component import Component
 from .component import FunctionalComponent
 from .componentdefinition import ComponentDefinition

test/test_combderiv.py

@@ -0,0 +1,48 @@
+import os
+import posixpath
+import unittest
+
+import sbol2
+
+MODULE_LOCATION = os.path.dirname(os.path.abspath(__file__))
+SBOL_TEST_SUITE = os.path.join(MODULE_LOCATION, 'SBOLTestSuite')
+
+
+class MyTestCase(unittest.TestCase):
+
+    def test_exported(self):
+        self.assertIn('CombinatorialDerivation', dir(sbol2))
+        self.assertIn('VariableComponent', dir(sbol2))
+
+    def test_read(self):
+        fname = os.path.join(SBOL_TEST_SUITE,
+                             'SBOL2_ic/gfp_reporter_template.xml')
+        doc = sbol2.Document(fname)
+        uri = 'http://michael.zhang/GFP_Reporter_Template_CombinatorialDerivation'
+        cd: sbol2.CombinatorialDerivation = doc.find(uri)
+        self.assertIsNotNone(cd)
+        self.assertEqual(1, len(cd.variableComponents))
+        vc_uri = posixpath.join(uri, 'CDS_Component_VariableComponent')
+        vc: sbol2.VariableComponent = doc.find(vc_uri)
+        self.assertEqual(vc.identity, cd.variableComponents[0].identity)
+        self.assertIsInstance(vc, sbol2.VariableComponent)
+        self.assertEqual(3, len(vc.variants))
+
+    def test_read2(self):
+        fname = os.path.join(SBOL_TEST_SUITE,
+                             'SBOL2_ic/eukaryotic_transcriptional_unit.xml')
+        doc = sbol2.Document(fname)
+        uri = posixpath.join('http://michael.zhang',
+                             'Eukaryotic_Transcriptional_Unit_CombinatorialDerivation')
+        cd: sbol2.CombinatorialDerivation = doc.find(uri)
+        self.assertIsNotNone(cd)
+        self.assertEqual(2, len(cd.variableComponents))
+        vc_uri = posixpath.join(uri, 'Pro_Component_VariableComponent')
+        vc: sbol2.VariableComponent = doc.find(vc_uri)
+        self.assertIsNotNone(vc)
+        self.assertIsInstance(vc, sbol2.VariableComponent)
+        self.assertEqual(1, len(vc.variantDerivations))
+
+
+if __name__ == '__main__':
+    unittest.main()

test/test_partshop.py

@@ -160,7 +160,13 @@ def test_submit(self):
         doc.name = "SBOL Test Collection"
         doc.description = "A scratch collection for automated testing of the sbol."
         sbh = sbol.PartShop(RESOURCE, SPOOFED_RESOURCE)
-        sbh.login(username, password)
+        try:
+            sbh.login(username, password)
+        except sbol2.SBOLError as sbol_error:
+            if sbol_error.error_code() == sbol2.SBOLErrorCode.SBOL_ERROR_BAD_HTTP_REQUEST:
+                if '503' in sbol_error.what():
+                    return
+            raise
         try:
             sbh.submit(doc)
         except Exception: