Change unittest2 back into unittest.

[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..99364205c7f1412a38a1b60c0b292a8894bd753f 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 unittest import TestCase
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
@@ -13,7 +13,7 @@ from htsworkflow.pipelines import gerald
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines import srf
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
@@ -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):
@@ -197,7 +197,6 @@ class RunfolderTests(unittest.TestCase):
 
 
     def test_eland(self):
-        ls_tree(self.runfolder_dir)
         hg_map = {'Lambda.fa': 'Lambda.fa'}
         for i in range(1,22):
           short_name = 'chr%d.fa' % (i,)
@@ -210,7 +209,8 @@ 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 +219,8 @@ 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 +241,9 @@ 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)
@@ -267,21 +268,21 @@ class RunfolderTests(unittest.TestCase):
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, 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, FCID)
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, 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)
@@ -297,13 +298,14 @@ class RunfolderTests(unittest.TestCase):
             glob.fnmatch.fnmatch("s_1_0001_qseq.txt", pattern),
             False)
 
-        print pattern
-
 
 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")
-
+    from unittest import main
+    main(defaultTest="suite")