Convert to unittest2

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder110.py

diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py
index f9508b4b8873fb438549c814e4abd174f194381a..2397c2a6136e4e109d065685f780c65c4b8721fb 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder110.py
+++ b/htsworkflow/pipelines/test/test_runfolder110.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
-import unittest
+from unittest2 import TestCase
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
@@ -58,7 +58,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald
@@ -205,9 +205,9 @@ class RunfolderTests(unittest.TestCase):
 
             g_eland = g.eland_results
             g2_eland = g2.eland_results
-            for lane in g_eland.results[0].keys():
-                g_results = g_eland.results[0][lane]
-                g2_results = g2_eland.results[0][lane]
+            for key in g_eland:
+                g_results = g_eland[key]
+                g2_results = g2_eland[key]
                 self.failUnlessEqual(g_results.reads,
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
@@ -234,11 +234,11 @@ class RunfolderTests(unittest.TestCase):
                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 
-        for i in range(1,9):
-            lane = eland.results[0][i]
+        for key in eland:
+            lane = eland[key]
             self.failUnlessEqual(lane.reads, 6)
             self.failUnlessEqual(lane.sample_name, "s")
-            self.failUnlessEqual(lane.lane_id, i)
+            self.failUnlessEqual(lane.lane_id, key.lane)
             self.failUnlessEqual(len(lane.mapped_reads), 17)
             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
             self.failUnlessEqual(lane.match_codes['U0'], 3)
@@ -255,9 +255,9 @@ class RunfolderTests(unittest.TestCase):
         xml_str = ElementTree.tostring(xml)
         e2 = gerald.ELAND(xml=xml)
 
-        for i in range(1,9):
-            l1 = eland.results[0][i]
-            l2 = e2.results[0][i]
+        for key in eland:
+            l1 = eland[key]
+            l2 = e2[key]
             self.failUnlessEqual(l1.reads, l2.reads)
             self.failUnlessEqual(l1.sample_name, l2.sample_name)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
@@ -300,8 +300,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite
 
-if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
 
+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")