Change unittest2 back into unittest.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder026.py

diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py
index 9ab17225a28949331616beee30457d917bfed395..fe52a62060fda3b50d815eaae35c0e3d4fb04d8e 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder026.py
+++ b/htsworkflow/pipelines/test/test_runfolder026.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 firecrest
 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 *
 
@@ -228,7 +228,7 @@ def make_eland_results(gerald_dir):
         f.write(eland_result)
         f.close()
 
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald
@@ -273,6 +273,7 @@ class RunfolderTests(unittest.TestCase):
         Construct a firecrest object
         """
         f = firecrest.firecrest(self.firecrest_dir)
+        self.failUnlessEqual(f.software, 'Firecrest')
         self.failUnlessEqual(f.version, '1.8.28')
         self.failUnlessEqual(f.start, 1)
         self.failUnlessEqual(f.stop, 33)
@@ -284,17 +285,19 @@ class RunfolderTests(unittest.TestCase):
         xml_str = ElementTree.tostring(xml)
 
         f2 = firecrest.Firecrest(xml=xml)
-        self.failUnlessEqual(f.version, f2.version)
-        self.failUnlessEqual(f.start,   f2.start)
-        self.failUnlessEqual(f.stop,    f2.stop)
-        self.failUnlessEqual(f.user,    f2.user)
-        self.failUnlessEqual(f.date,    f2.date)
+        self.failUnlessEqual(f.software, f2.software)
+        self.failUnlessEqual(f.version,  f2.version)
+        self.failUnlessEqual(f.start,    f2.start)
+        self.failUnlessEqual(f.stop,     f2.stop)
+        self.failUnlessEqual(f.user,     f2.user)
+        self.failUnlessEqual(f.date,     f2.date)
 
     def test_bustard(self):
         """
         construct a bustard object
         """
         b = bustard.bustard(self.bustard_dir)
+        self.failUnlessEqual(b.software, 'Bustard')
         self.failUnlessEqual(b.version, '1.8.28')
         self.failUnlessEqual(b.date,    date(2008,4,12))
         self.failUnlessEqual(b.user,    'diane')
@@ -303,9 +306,10 @@ class RunfolderTests(unittest.TestCase):
 
         xml = b.get_elements()
         b2 = bustard.Bustard(xml=xml)
-        self.failUnlessEqual(b.version, b2.version)
-        self.failUnlessEqual(b.date,    b2.date )
-        self.failUnlessEqual(b.user,    b2.user)
+        self.failUnlessEqual(b.software, b2.software)
+        self.failUnlessEqual(b.version,  b2.version)
+        self.failUnlessEqual(b.date,     b2.date )
+        self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         for key in b.phasing.keys():
             self.failUnlessEqual(b.phasing[key].lane,
@@ -319,6 +323,7 @@ class RunfolderTests(unittest.TestCase):
         # need to update gerald and make tests for it
         g = gerald.gerald(self.gerald_dir)
 
+        self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
@@ -381,9 +386,9 @@ 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),
@@ -407,11 +412,11 @@ class RunfolderTests(unittest.TestCase):
                         5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_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, 4)
             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), 3)
             self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
             self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
@@ -423,9 +428,9 @@ 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)
@@ -446,28 +451,32 @@ class RunfolderTests(unittest.TestCase):
 
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
-        self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
+        self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXX_2008-04-19.xml')
 
         # 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)
-        self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
+        self.failUnlessEqual(runs[0].serialization_filename, 'run_207BTAAXY_2008-04-19.xml')
 
         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")