Change unittest2 back into unittest.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_ipar100.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
index 7913ed079a045c64e910a51addf625a4132c223b..9de36535e2bd3cff21809570c794b525b719f62f 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
@@ -4,13 +4,13 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
-import unittest
+from unittest import TestCase
 
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import gerald
 from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
@@ -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
@@ -202,9 +202,9 @@ 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),
@@ -231,11 +231,11 @@ 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.mapped_reads['spike.fa/sample1'], 1)
@@ -254,9 +254,9 @@ 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)
@@ -278,29 +278,33 @@ class RunfolderTests(unittest.TestCase):
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
         name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         # do we get the flowcell id from the FlowcellId.xml file
         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)
 
         r2 = runfolder.PipelineRun(xml=xml)
-        self.failUnlessEqual(r1.name, r2.name)
+        self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
         self.failIfEqual(r2.image_analysis, None)
         self.failIfEqual(r2.bustard, None)
         self.failIfEqual(r2.gerald, None)
 
 
 def suite():
-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite
 
-if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
 
+if __name__ == "__main__":
+    from unittest import main
+    main(defaultTest="suite")