Convert to unittest2

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_casava_1_7.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index 9f26a43d84648fcc40f4b24b665b393a1da480cf..ae910553bd4fde1dea0b2d5f20e4793cb159120c 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@ -5,7 +5,7 @@ import glob
 import os
 import tempfile
 import shutil
-import unittest
+from unittest2 import TestCase
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
@@ -56,7 +56,7 @@ 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
@@ -177,9 +177,9 @@ 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)
                 if isinstance(g_results, eland.ElandLane):
@@ -210,7 +210,8 @@ class RunfolderTests(unittest.TestCase):
 
         # test fastq
         for i in range(1,4):
-            lane = eland_container.results[0][i]
+            key = eland.SampleKey(lane=i, read=1, sample='s')
+            lane = eland_container[key]
             self.failUnlessEqual(lane.reads, 3)
             self.failUnlessEqual(lane.sample_name, 's')
             self.failUnlessEqual(lane.lane_id, i)
@@ -219,7 +220,8 @@ class RunfolderTests(unittest.TestCase):
 
         # I added sequence lanes to the last 2 lanes of this test case
         for i in range(4,9):
-            lane = eland_container.results[0][i]
+            key = eland.SampleKey(lane=i, read=1, sample='s')
+            lane = eland_container[key]
             self.failUnlessEqual(lane.reads, 28)
             self.failUnlessEqual(lane.sample_name, "s")
             self.failUnlessEqual(lane.lane_id, i)
@@ -240,9 +242,9 @@ class RunfolderTests(unittest.TestCase):
         xml_str = ElementTree.tostring(xml)
         e2 = gerald.ELAND(xml=xml)
 
-        for i in range(1,9):
-            l1 = eland_container.results[0][i]
-            l2 = e2.results[0][i]
+        for key in eland_container:
+            l1 = eland_container[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)
@@ -301,9 +303,12 @@ 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")
-
+    from unittest2 import main
+    main(defaultTest="suite")