Initial port to python3

[htsworkflow.git] / htsworkflow / submission / test / test_daf.py

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index 95dc1d9064688f4b63ca4c7b1a70866587deb9f7..3e960265f93fac6872382dd06aff1f0117ed175b 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -1,9 +1,9 @@
 from contextlib import contextmanager
 import os
-from StringIO import StringIO
+from io import StringIO
 import shutil
 import tempfile
-import unittest
+from unittest import TestCase, TestSuite, defaultTestLoader
 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \
@@ -80,7 +80,7 @@ required         no
 """
 
 
-class TestDAF(unittest.TestCase):
+class TestDAF(TestCase):
     def test_parse(self):
 
         parsed = daf.fromstring(test_daf)
@@ -121,7 +121,7 @@ class TestDAF(unittest.TestCase):
                 signal_view_node, None, None)))
         self.failUnlessEqual(len(statements), 6)
         name = model.get_target(signal_view_node, dafTermOntology['name'])
-        self.failUnlessEqual(fromTypedNode(name), u'Signal')
+        self.failUnlessEqual(fromTypedNode(name), 'Signal')
 
     def test_get_view_namespace_from_string(self):
         url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
@@ -162,10 +162,10 @@ def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
 def dump_model(model):
     writer = get_serializer()
     turtle =  writer.serialize_model_to_string(model)
-    print turtle
+    print(turtle)
 
 
-class TestUCSCSubmission(unittest.TestCase):
+class TestUCSCSubmission(TestCase):
     def setUp(self):
         test_results.generate_sample_results_tree(self)
 
@@ -247,7 +247,7 @@ thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
         # server is 500 for this library
         self.failUnlessEqual(gel_cut, 100)
 
-        species = daf_mapper._get_library_attribute(libNode, 'species')
+        species = daf_mapper._get_library_attribute(libNode, 'species_name')
         self.failUnlessEqual(species, "Homo sapiens")
 
         with mktempdir('analysis') as analysis_dir:
@@ -329,11 +329,11 @@ def mktempfile(suffix='', prefix='tmp', dir=None):
     os.close(fd)
     os.unlink(pathname)
 
-
 def suite():
-    suite = unittest.makeSuite(TestDAF, 'test')
-    suite.addTest(unittest.makeSuite(TestUCSCSubmission, 'test'))
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCInfo))
     return suite
 
 if __name__ == "__main__":
-    unittest.main(defaultTest='suite')
+    from unittest import main
+    main(defaultTest='suite')