Convert to unittest2

Test cases inherit from either unittest2 or django.test.TestCase
I should be able to use skip tests in the future.

I learned inheriting from django.test.TestCase will properly set up
the database for django tests. (Well at least mostly, I'm having
some possible errors on 1.4)

diff --git a/encode_submission/test_encode_find.py b/encode_submission/test_encode_find.py
index 05108955a4d31927b98d395b290ef986a3163d88..6844fa4db99661aba22d6a735d812bdbe0438129 100644 (file)
--- a/encode_submission/test_encode_find.py
+++ b/encode_submission/test_encode_find.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from datetime import datetime
 import os
 #!/usr/bin/env python
 from datetime import datetime
 import os

-import unittest
+from unittest2 import TestCase

 
 import RDF
 
 
 import RDF
 


@@ -14,7 +14,7 @@ from htsworkflow.util.rdfinfer import Infer
 SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
 print SOURCE_PATH
 
 SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
 print SOURCE_PATH
 

-class TestEncodeFind(unittest.TestCase):
+class TestEncodeFind(TestCase):

     def setUp(self):
         self.model = get_model()
         add_default_schemas(self.model)
     def setUp(self):
         self.model = get_model()
         add_default_schemas(self.model)


@@ -163,7 +163,12 @@ _:bnode120970
                              '12097')
 
 def suite():
                              '12097')
 
 def suite():

-    return unittest.makeSuite(TestEncodeFind, "test")
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main()

diff --git a/encode_submission/test_ucsc_gather.py b/encode_submission/test_ucsc_gather.py
index d7d54e6b23ed4e05b3c97af5b8493121ded1ab68..6063951db788a2e9f9562f9a113fae5e335cec7b 100644 (file)
--- a/encode_submission/test_ucsc_gather.py
+++ b/encode_submission/test_ucsc_gather.py
@@ -1,12 +1,15 @@
-import unittest
+from unittest2 import TestCase, TestSuite, defaultTestLoader

 
 import ucsc_gather
 
 
 import ucsc_gather
 

-class testUCSCGather(unittest.TestCase):
+class testUCSCGather(TestCase):

     pass
 
 def suite():
     pass
 
 def suite():

-    return unittest.makeSuite(testUCSCGather,"test")
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testUCSCGather))
+    return suite

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest='suite')

diff --git a/htsworkflow/automation/test/__init__.py b/htsworkflow/automation/test/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/htsworkflow/automation/test/test_runner.py b/htsworkflow/automation/test/test_runner.py
index 1457f9effbb44e764f119184a572cd48d232e940..a60c458401b2f0e8129c72d1a5864b0c11f045a5 100644 (file)
--- a/htsworkflow/automation/test/test_runner.py
+++ b/htsworkflow/automation/test/test_runner.py
@@ -1,5 +1,4 @@
-import unittest
-
+from unittest2 import TestCase

 
 import os
 from htsworkflow.automation.solexa import is_runfolder
 
 import os
 from htsworkflow.automation.solexa import is_runfolder


@@ -17,13 +16,14 @@ def extract_runfolder_path(watchdir, event):
       return runfolder_path
   return None
 
       return runfolder_path
   return None
 

+

 class Event(object):
   def __init__(self, path=None, name=None):
     self.path = path
     self.name = name
 
 class Event(object):
   def __init__(self, path=None, name=None):
     self.path = path
     self.name = name
 

-class testRunner(unittest.TestCase):

 
 

+class testRunner(TestCase):

     def test_extract_runfolder(self):
         watchdir = os.path.join('root', 'server', 'mount')
         runfolder = os.path.join(watchdir, '080909_HWI-EAS229_0052_1234ABCD')
     def test_extract_runfolder(self):
         watchdir = os.path.join('root', 'server', 'mount')
         runfolder = os.path.join(watchdir, '080909_HWI-EAS229_0052_1234ABCD')


@@ -38,9 +38,15 @@ class testRunner(unittest.TestCase):
 
         event = Event( path=other)
         self.failUnlessEqual(extract_runfolder_path(watchdir, event), None )
 
         event = Event( path=other)
         self.failUnlessEqual(extract_runfolder_path(watchdir, event), None )

-        
+
+

 def suite():
 def suite():

-    return unittest.makeSuite(testRunner,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/automation/test/test_solexa_utils.py b/htsworkflow/automation/test/test_solexa_utils.py
index a527ad34f766eb60a8d619a2541d3cc72e1ae3a7..210906ecaf7b1cdf7aa3aeaeea008414dd0b4e14 100644 (file)
--- a/htsworkflow/automation/test/test_solexa_utils.py
+++ b/htsworkflow/automation/test/test_solexa_utils.py
@@ -1,9 +1,8 @@
-
-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.automation import solexa
 
 
 from htsworkflow.automation import solexa
 

-class testSolexaRunfolderUtils(unittest.TestCase):
+class testSolexaRunfolderUtils(TestCase):

     def test_is_runfolder(self):
         self.failUnlessEqual(solexa.is_runfolder(""), False)
         self.failUnlessEqual(solexa.is_runfolder("1345_23"), False)
     def test_is_runfolder(self):
         self.failUnlessEqual(solexa.is_runfolder(""), False)
         self.failUnlessEqual(solexa.is_runfolder("1345_23"), False)


@@ -23,9 +22,14 @@ class testSolexaRunfolderUtils(unittest.TestCase):
         for root, path, response in test_data:
             self.failUnlessEqual(solexa.get_top_dir(root, path), response)
             
         for root, path, response in test_data:
             self.failUnlessEqual(solexa.get_top_dir(root, path), response)
             

+

 def suite():
 def suite():

-    return unittest.makeSuite(testSolexaRunfolderUtils, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
-    
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/frontend/inventory/test_inventory.py b/htsworkflow/frontend/inventory/test_inventory.py
index 024a334cb5ad4bc035e8e2a3d8f76aa72c9c50d3..118c654aaf8463ee638d748414c5c620df9c0d67 100644 (file)
--- a/htsworkflow/frontend/inventory/test_inventory.py
+++ b/htsworkflow/frontend/inventory/test_inventory.py
@@ -1,5 +1,4 @@
 import RDF
 import RDF

-import unittest

 
 from django.test import TestCase
 from django.contrib.auth.models import User
 
 from django.test import TestCase
 from django.contrib.auth.models import User


@@ -110,8 +109,11 @@ class InventoryTestCase(TestCase):
         return flowcells
 
 def suite():
         return flowcells
 
 def suite():

-    return unittest.makeSuite(InventoryTestCase, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(InventoryTestCase))
+    return suite

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
-
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/frontend/labels/test_labels.py b/htsworkflow/frontend/labels/test_labels.py
index 2247054b354559ab535df60bb5dc65c2aa5be686..29354b2b60ff3e14a9191d03f1909dd717e43e8e 100644 (file)
--- a/htsworkflow/frontend/labels/test_labels.py
+++ b/htsworkflow/frontend/labels/test_labels.py
@@ -21,3 +21,12 @@ Another way to test that 1 + 1 is equal to 2.
 True
 """}
 
 True
 """}
 

+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(SimpleTest))
+    return suite
+
+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/frontend/samples/test_samples.py b/htsworkflow/frontend/samples/test_samples.py
index 0320c0ad318f8266ae776ac13b867209ea69866a..2fb394511989b32e6cb97d7a507cf28fce71fc2d 100644 (file)
--- a/htsworkflow/frontend/samples/test_samples.py
+++ b/htsworkflow/frontend/samples/test_samples.py
@@ -1,5 +1,4 @@
 import datetime
 import datetime

-import unittest

 
 try:
     import json
 
 try:
     import json

diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py
index 688d00ef8fe988d3e9b65ad8b1150316405af342..43953fcb71b87079734b37c6abd9da4716dbba77 100644 (file)
--- a/htsworkflow/pipelines/test/test_eland.py
+++ b/htsworkflow/pipelines/test/test_eland.py
@@ -2,12 +2,12 @@
 """More direct synthetic test cases for the eland output file processing
 """
 from StringIO import StringIO
 """More direct synthetic test cases for the eland output file processing
 """
 from StringIO import StringIO

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
      SampleKey, MatchCodes, MappedReads
 
 
 from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
      SampleKey, MatchCodes, MappedReads
 

-class MatchCodeTests(unittest.TestCase):
+class MatchCodeTests(TestCase):

     def test_initializer(self):
         self.assertRaises(ValueError, MatchCodes, {'foo':'bar'})
         self.assertRaises(ValueError, MatchCodes, 3)
     def test_initializer(self):
         self.assertRaises(ValueError, MatchCodes, {'foo':'bar'})
         self.assertRaises(ValueError, MatchCodes, 3)


@@ -38,7 +38,7 @@ class MatchCodeTests(unittest.TestCase):
         self.assertEqual(mc1['U0'], 100)
 
 
         self.assertEqual(mc1['U0'], 100)
 
 

-class TestMappedReads(unittest.TestCase):
+class TestMappedReads(TestCase):

     def test_initializer(self):
         mr1 = MappedReads()
         self.assertEqual(len(mr1), 0)
     def test_initializer(self):
         mr1 = MappedReads()
         self.assertEqual(len(mr1), 0)


@@ -73,7 +73,7 @@ class TestMappedReads(unittest.TestCase):
         mr3['Lambda3'] = 2
         self.assertEqual(mr3['Lambda3'], 2)
 
         mr3['Lambda3'] = 2
         self.assertEqual(mr3['Lambda3'], 2)
 

-class ElandTests(unittest.TestCase):
+class ElandTests(TestCase):

     """Test specific Eland modules
     """
     def compare_match_array(self, current, expected):
     """Test specific Eland modules
     """
     def compare_match_array(self, current, expected):


@@ -244,7 +244,7 @@ class ElandTests(unittest.TestCase):
         self.assertEqual(e_list[1], 'Lane3')
         self.assertEqual(e_list[2], 'Lane5')
 
         self.assertEqual(e_list[1], 'Lane3')
         self.assertEqual(e_list[2], 'Lane5')
 

-class TestElandMatches(unittest.TestCase):
+class TestElandMatches(TestCase):

     def test_eland_replacing(self):
         key = SampleKey(1, 1, 's')
         e = ELAND()
     def test_eland_replacing(self):
         key = SampleKey(1, 1, 's')
         e = ELAND()


@@ -276,5 +276,16 @@ class TestElandMatches(unittest.TestCase):
         self.assertEqual(len(em[key11111]), 3)
         self.assertEqual(len(em[key11112]), 2)
 
         self.assertEqual(len(em[key11111]), 3)
         self.assertEqual(len(em[key11112]), 2)
 

+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(ElandTests))
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestElandMatches))
+    return suite
+
+

 if __name__ == "__main__":
 if __name__ == "__main__":

-    unittest.main()
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_extract_results.py b/htsworkflow/pipelines/test/test_extract_results.py
index b64bd0f7f9a8cc4bfcf0a3715efeff05029bf300..6f2b4238fe7d648896bd4c3c3bffce3697dc8cf5 100644 (file)
--- a/htsworkflow/pipelines/test/test_extract_results.py
+++ b/htsworkflow/pipelines/test/test_extract_results.py
@@ -6,7 +6,7 @@ import os
 import tempfile
 import shutil
 import sys
 import tempfile
 import shutil
 import sys

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -60,7 +60,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         obj.gerald_dir = gerald_dir
 
 

-class RunfolderExtractTests(unittest.TestCase):
+class RunfolderExtractTests(TestCase):

     """
     Test the extract result code.
     """
     """
     Test the extract result code.
     """


@@ -79,10 +79,15 @@ class RunfolderExtractTests(unittest.TestCase):
         self.failUnlessEqual(len(archive), 34)
         self.failUnless('asite_090608_HWI-EAS229_0117_4286GAAXX_l6_r1.tar.bz2' in archive)
 
         self.failUnlessEqual(len(archive), 34)
         self.failUnless('asite_090608_HWI-EAS229_0117_4286GAAXX_l6_r1.tar.bz2' in archive)
 

-        
+

 def suite():
 def suite():

-    return unittest.makeSuite(RunfolderExtractTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

 
 

diff --git a/htsworkflow/pipelines/test/test_genome_mapper.py b/htsworkflow/pipelines/test/test_genome_mapper.py
index 8ba1ba5ff4daec281d15ac92fdf389c3c16495ab..1101305effd80ede9a09d4db99abe3566b31c8ca 100644 (file)
--- a/htsworkflow/pipelines/test/test_genome_mapper.py
+++ b/htsworkflow/pipelines/test/test_genome_mapper.py
@@ -1,9 +1,9 @@
-import unittest
+from unittest2 import TestCase

 
 from StringIO import StringIO
 from htsworkflow.pipelines import genome_mapper
 
 
 from StringIO import StringIO
 from htsworkflow.pipelines import genome_mapper
 

-class testGenomeMapper(unittest.TestCase):
+class testGenomeMapper(TestCase):

     def test_construct_mapper(self):
         genomes = {
         'Arabidopsis thaliana': {'v01212004': '/arabidopsis'},
     def test_construct_mapper(self):
         genomes = {
         'Arabidopsis thaliana': {'v01212004': '/arabidopsis'},


@@ -27,7 +27,12 @@ class testGenomeMapper(unittest.TestCase):
         
         
 def suite():
         
         
 def suite():

-    return unittest.makeSuite(testGenomeMapper,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py
index d0c1e660e5a786c50794d278f164678026a5cb74..aa2f618f9324faca633dae27a0053ad76c14b54b 100644 (file)
--- a/htsworkflow/pipelines/test/test_genomemap.py
+++ b/htsworkflow/pipelines/test/test_genomemap.py
@@ -5,7 +5,7 @@ import os
 from StringIO import StringIO
 import shutil
 import tempfile
 from StringIO import StringIO
 import shutil
 import tempfile

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines.runfolder import ElementTree
 from htsworkflow.pipelines import genomemap
 
 from htsworkflow.pipelines.runfolder import ElementTree
 from htsworkflow.pipelines import genomemap


@@ -15,7 +15,7 @@ MINI_GENOME_XML = '''<sequenceSizes>
         <chromosome fileName="chr1.fa" contigName="chr1" totalBases="197195432"/>
 </sequenceSizes>
 '''
         <chromosome fileName="chr1.fa" contigName="chr1" totalBases="197195432"/>
 </sequenceSizes>
 '''

-class TestGenomeMap(unittest.TestCase):
+class TestGenomeMap(TestCase):

     def test_genomesizes_xml(self):
         xml = ElementTree.fromstring(MINI_GENOME_XML)
         g = genomemap.GenomeMap()
     def test_genomesizes_xml(self):
         xml = ElementTree.fromstring(MINI_GENOME_XML)
         g = genomemap.GenomeMap()


@@ -76,5 +76,13 @@ class TestGenomeMap(unittest.TestCase):
         self.assertEqual(g['chr1.fa'], '{0}/chr1.fa'.format(tempgenome))
 
 
         self.assertEqual(g['chr1.fa'], '{0}/chr1.fa'.format(tempgenome))
 
 

+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap))
+    return suite
+
+

 if __name__ == "__main__":
 if __name__ == "__main__":

-    unittest.main()
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py
index 85926459f11b7eb7a4cffd463895ea809fbb1164..8b28b9e9cc88eb34d687865fc6ad5b78a1a4a19c 100644 (file)
--- a/htsworkflow/pipelines/test/test_run_xml.py
+++ b/htsworkflow/pipelines/test/test_run_xml.py
@@ -1,13 +1,14 @@
 import os
 import os

-import unittest
+from unittest2 import TestCase

 from StringIO import StringIO
 
 from simulate_runfolder import TESTDATA_DIR
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 
 from htsworkflow.pipelines.eland import SampleKey
 from StringIO import StringIO
 
 from simulate_runfolder import TESTDATA_DIR
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 
 from htsworkflow.pipelines.eland import SampleKey

-class testLoadRunXML(unittest.TestCase):

 
 

+
+class testLoadRunXML(TestCase):

     def _check_run_xml(self, run_xml_name, results, eland_results=8):
         run_xml_path = os.path.join(TESTDATA_DIR, run_xml_name)
         run = load_pipeline_run_xml(run_xml_path)
     def _check_run_xml(self, run_xml_name, results, eland_results=8):
         run_xml_path = os.path.join(TESTDATA_DIR, run_xml_name)
         run = load_pipeline_run_xml(run_xml_path)


@@ -94,8 +95,14 @@ class testLoadRunXML(unittest.TestCase):
                    }
         self._check_run_xml(run_xml_name, results, eland_results=8)
 
                    }
         self._check_run_xml(run_xml_name, results, eland_results=8)
 

+

 def suite():
 def suite():

-    return unittest.makeSuite(testLoadRunXML,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py
index f6162dee06436b72891679fbb2f491587f78ded6..8eef13096d3694a11c3f80e0704a6d6cdea7ee6b 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder026.py
+++ b/htsworkflow/pipelines/test/test_runfolder026.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -228,7 +228,7 @@ def make_eland_results(gerald_dir):
         f.write(eland_result)
         f.close()
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -471,8 +471,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py
index 2a060d13810d3a41bdcb53dc80b9a7b93a88a3ac..a571944d834a2e897832f777d137ed707369b5df 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder030.py
+++ b/htsworkflow/pipelines/test/test_runfolder030.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -678,7 +678,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -895,8 +895,11 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 def suite():

-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
-
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py
index 3e1bf87a62c81c04ee2229aaf213f99b1eb89862..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 os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -58,7 +58,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -300,8 +300,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index 12fec6df50a3277daf6cabf702fe59799d583484..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 os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland


@@ -56,7 +56,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -303,9 +303,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 def suite():

-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite

 
 
 if __name__ == "__main__":
 
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
-
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
index fff9a7f8ccef578f7aafcd2c14a211d51a399808..1e956326fa5cebc5f515934fa623a5661f3db5fe 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import bustard


@@ -58,7 +58,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -299,8 +299,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
index eb018d87db908ba69e31c01f8e8e81b0361f6b96..07c87784fadd9062c977843566511accbf0f8a57 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -56,7 +56,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -337,8 +337,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py
index 97ba6f44d2afca3f8216029d858f8c14c3714e48..b159c5fd9d953e5eff625a996b84ca9b7d9fa6f3 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_pair.py
+++ b/htsworkflow/pipelines/test/test_runfolder_pair.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -59,7 +59,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -325,8 +325,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta.py b/htsworkflow/pipelines/test/test_runfolder_rta.py
index 90126d8ac461ae1664400c6030bb4845e7e617f8..2c82041f4e18e37956661b08f11e2afaf2d3a808 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -56,7 +56,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -299,8 +299,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta160.py b/htsworkflow/pipelines/test/test_runfolder_rta160.py
index caf82a0d7cc811facd6ef155d236abcaf16fc303..9d4879a47f498c70c850bf90cf1332933ffd790a 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta160.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta160.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -56,7 +56,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -275,10 +275,13 @@ class RunfolderTests(unittest.TestCase):
         self.failIfEqual(r2.gerald, None)
 
 
         self.failIfEqual(r2.gerald, None)
 
 

-

 def suite():
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py
index b803787d81d86b899e71ffbe4d416c0db5fa953c..be83c3fbdaf06557912e661f6d6c5e8d1a68ffb6 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta180.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta180.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -57,7 +57,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
         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
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -284,8 +284,12 @@ class RunfolderTests(unittest.TestCase):
 
 
 def suite():
 
 
 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")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
index fdb60011df9f12785ba224ccc29a62617c0a30d1..6933157d5691917bb9bf7a1ff7be3993535b2453 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
@@ -5,7 +5,7 @@ import logging
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines.samplekey import SampleKey
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines.samplekey import SampleKey


@@ -63,7 +63,7 @@ def make_runfolder(obj=None):
         obj.reads = 2
 
 
         obj.reads = 2
 
 

-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):

     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald


@@ -274,9 +274,12 @@ class RunfolderTests(unittest.TestCase):
         self.failIfEqual(r2.gerald, None)
 
 def suite():
         self.failIfEqual(r2.gerald, None)
 
 def suite():

-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite

 
 

-if __name__ == "__main__":
-    logging.basicConfig(level=logging.WARN)
-    unittest.main(defaultTest="suite")

 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_samplekey.py b/htsworkflow/pipelines/test/test_samplekey.py
index a4287d34b113825e5b6621ac8c8fedfd78dc66e3..ecd273dedd1c3eab53fc0c6b94b720ecadb5145f 100644 (file)
--- a/htsworkflow/pipelines/test/test_samplekey.py
+++ b/htsworkflow/pipelines/test/test_samplekey.py
@@ -2,11 +2,11 @@
 """More direct synthetic test cases for the eland output file processing
 """
 from StringIO import StringIO
 """More direct synthetic test cases for the eland output file processing
 """
 from StringIO import StringIO

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines.samplekey import SampleKey
 
 
 from htsworkflow.pipelines.samplekey import SampleKey
 

-class TestSampleKey(unittest.TestCase):
+class TestSampleKey(TestCase):

     def test_equality(self):
         k1 = SampleKey(lane=1, read='1', sample='12345')
         k2 = SampleKey(lane=1, read=1, sample='12345')
     def test_equality(self):
         k1 = SampleKey(lane=1, read='1', sample='12345')
         k2 = SampleKey(lane=1, read=1, sample='12345')


@@ -43,5 +43,13 @@ class TestSampleKey(unittest.TestCase):
         self.assertTrue(k2.matches(q3))
         self.assertTrue(k3.matches(q3))
 
         self.assertTrue(k2.matches(q3))
         self.assertTrue(k3.matches(q3))
 

+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestSampleKey))
+    return suite
+
+

 if __name__ == "__main__":
 if __name__ == "__main__":

-    unittest.main()
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_sequences.py b/htsworkflow/pipelines/test/test_sequences.py
index accd43ecf8786b4d25a96683bf861940006cf44f..522a9aafdf1ff7f3364a99f70cbb530a622eeae8 100644 (file)
--- a/htsworkflow/pipelines/test/test_sequences.py
+++ b/htsworkflow/pipelines/test/test_sequences.py
@@ -2,7 +2,7 @@
 import os
 import shutil
 import tempfile
 import os
 import shutil
 import tempfile

-import unittest
+from unittest2 import TestCase

 
 import RDF
 
 
 import RDF
 


@@ -10,7 +10,7 @@ from htsworkflow.pipelines import sequences
 from htsworkflow.util.rdfhelp import get_model, load_string_into_model, \
      rdfNS, libraryOntology, dump_model, fromTypedNode
 
 from htsworkflow.util.rdfhelp import get_model, load_string_into_model, \
      rdfNS, libraryOntology, dump_model, fromTypedNode
 

-class SequenceFileTests(unittest.TestCase):
+class SequenceFileTests(TestCase):

     """
     Make sure the sequence archive class works
     """
     """
     Make sure the sequence archive class works
     """


@@ -612,7 +612,12 @@ class SimulateSimpleTree(SimulateTree):
 
 
 def suite():
 
 
 def suite():

-    return unittest.makeSuite(SequenceFileTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_summary.py b/htsworkflow/pipelines/test/test_summary.py
index af0e90854bf30310b764f8ba75ae4ac5e0200813..1f7e46108856a737846c93996212a3d9cf80b69c 100644 (file)
--- a/htsworkflow/pipelines/test/test_summary.py
+++ b/htsworkflow/pipelines/test/test_summary.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 import os
 from StringIO import StringIO
 #!/usr/bin/env python
 import os
 from StringIO import StringIO

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.pipelines import summary
 from simulate_runfolder import TESTDATA_DIR
 
 
 from htsworkflow.pipelines import summary
 from simulate_runfolder import TESTDATA_DIR
 

-class SummaryTests(unittest.TestCase):
+class SummaryTests(TestCase):

     """Test elements of the summary file parser
     """
     def test_is_xml(self):
     """Test elements of the summary file parser
     """
     def test_is_xml(self):


@@ -34,8 +34,14 @@ class SummaryTests(unittest.TestCase):
         pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
         s = summary.SummaryGA(pathname)
 
         pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
         s = summary.SummaryGA(pathname)
 

+

 def suite():
 def suite():

-    return unittest.makeSuite(SummaryTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/submission/test/test_condorfastq.py b/htsworkflow/submission/test/test_condorfastq.py
index cffb5ac17175f59a3a4fc10219c5e151f578882b..ffb9f88620356ba0e61800db60fa4715463515e2 100644 (file)
--- a/htsworkflow/submission/test/test_condorfastq.py
+++ b/htsworkflow/submission/test/test_condorfastq.py
@@ -5,7 +5,8 @@ import os
 from pprint import pprint
 import shutil
 import tempfile
 from pprint import pprint
 import shutil
 import tempfile

-import unittest
+
+from django.test import TestCase

 
 from htsworkflow.submission.condorfastq import CondorFastqExtract
 from htsworkflow.submission.results import ResultMap
 
 from htsworkflow.submission.condorfastq import CondorFastqExtract
 from htsworkflow.submission.results import ResultMap


@@ -411,7 +412,7 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
 """
 HOST = "http://localhost"
 
 """
 HOST = "http://localhost"
 

-class TestCondorFastq(unittest.TestCase):
+class TestCondorFastq(TestCase):

     def setUp(self):
         self.cwd = os.getcwd()
 
     def setUp(self):
         self.cwd = os.getcwd()
 


@@ -676,9 +677,11 @@ class TestCondorFastq(unittest.TestCase):
 
 
 def suite():
 
 
 def suite():

-    suite = unittest.makeSuite(TestCondorFastq, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq))

     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
-
+    from unittest2 import main
+    main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index 95dc1d9064688f4b63ca4c7b1a70866587deb9f7..c7227216e42d2582129c8dae9dacc1d88638b499 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -3,7 +3,7 @@ import os
 from StringIO import StringIO
 import shutil
 import tempfile
 from StringIO import StringIO
 import shutil
 import tempfile

-import unittest
+from unittest2 import TestCase, TestSuite, defaultTestLoader

 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \
 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \


@@ -80,7 +80,7 @@ required         no
 """
 
 
 """
 
 

-class TestDAF(unittest.TestCase):
+class TestDAF(TestCase):

     def test_parse(self):
 
         parsed = daf.fromstring(test_daf)
     def test_parse(self):
 
         parsed = daf.fromstring(test_daf)


@@ -165,7 +165,7 @@ def dump_model(model):
     print turtle
 
 
     print turtle
 
 

-class TestUCSCSubmission(unittest.TestCase):
+class TestUCSCSubmission(TestCase):

     def setUp(self):
         test_results.generate_sample_results_tree(self)
 
     def setUp(self):
         test_results.generate_sample_results_tree(self)
 


@@ -329,11 +329,11 @@ def mktempfile(suffix='', prefix='tmp', dir=None):
     os.close(fd)
     os.unlink(pathname)
 
     os.close(fd)
     os.unlink(pathname)
 

-

 def suite():
 def suite():

-    suite = unittest.makeSuite(TestDAF, 'test')
-    suite.addTest(unittest.makeSuite(TestUCSCSubmission, 'test'))
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCInfo))

     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
+    from unittest2 import main
+    main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_results.py b/htsworkflow/submission/test/test_results.py
index 2d8cd57c30dbc661a88733a5d1af36efd9ecd3e9..3487b69d7e410f1734887f6afd0969013f0466ff 100644 (file)
--- a/htsworkflow/submission/test/test_results.py
+++ b/htsworkflow/submission/test/test_results.py
@@ -5,7 +5,8 @@ import os
 from pprint import pprint
 import shutil
 import tempfile
 from pprint import pprint
 import shutil
 import tempfile

-import unittest
+
+from unittest2 import TestCase, defaultTestLoader

 
 from htsworkflow.submission.results import ResultMap
 
 
 from htsworkflow.submission.results import ResultMap
 


@@ -41,7 +42,7 @@ def generate_sample_results_tree(obj):
         stream.write(f)
         stream.close()
 
         stream.write(f)
         stream.close()
 

-class TestResultMap(unittest.TestCase):
+class TestResultMap(TestCase):

     def setUp(self):
         generate_sample_results_tree(self)
 
     def setUp(self):
         generate_sample_results_tree(self)
 


@@ -91,12 +92,10 @@ class TestResultMap(unittest.TestCase):
                     os.path.join(self.resultdir, f)))
 
 
                     os.path.join(self.resultdir, f)))
 
 

-
-

 def suite():
 def suite():

-    suite = unittest.makeSuite(TestResultMap, 'test')
+    suite = defaultTestLoader.loadTestsFromTestCase(TestResultMap)

     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
-
+    from unittest2 import main
+    main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_ucsc.py b/htsworkflow/submission/test/test_ucsc.py
index 53ac287a5f0b876eb18df0638277493e7e106604..fad690e27f5ee638d315c593336dbd110a84fa96 100644 (file)
--- a/htsworkflow/submission/test/test_ucsc.py
+++ b/htsworkflow/submission/test/test_ucsc.py
@@ -1,4 +1,4 @@
-import unittest
+from unittest2 import TestCase, TestSuite, defaultTestLoader

 from StringIO import StringIO
 
 from htsworkflow.submission import ucsc
 from StringIO import StringIO
 
 from htsworkflow.submission import ucsc


@@ -9,7 +9,7 @@ wgEncodeCaltechRnaSeqGm12878R2x75Il200FastqRd2Rep1.fastq.tgz    project=wgEncode; g
 """
 
 
 """
 
 

-class TestUCSCInfo(unittest.TestCase):
+class TestUCSCInfo(TestCase):

     def test_parse_encodedcc_file(self):
         stream = StringIO(ENCODE_FILES)
         file_index = ucsc.parse_ucsc_file_index(stream, 'http://example.com/files')
     def test_parse_encodedcc_file(self):
         stream = StringIO(ENCODE_FILES)
         file_index = ucsc.parse_ucsc_file_index(stream, 'http://example.com/files')


@@ -21,9 +21,10 @@ class TestUCSCInfo(unittest.TestCase):
             self.assertEquals(attributes['project'], 'wgEncode')
 
 def suite():
             self.assertEquals(attributes['project'], 'wgEncode')
 
 def suite():

-    suite = unittest.makeSuite(TestUCSCInfo, 'test')
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCInfo))

     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
-
+    from unittest2 import main
+    main(defaultTest='suite')

diff --git a/htsworkflow/util/test/__init__.py b/htsworkflow/util/test/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/htsworkflow/util/test/test_alphanum.py b/htsworkflow/util/test/test_alphanum.py
index 3fd60250cbe392f9208c077076253fd6aed10f94..29a53859a6bcb70699f0e028039759c15882540d 100644 (file)
--- a/htsworkflow/util/test/test_alphanum.py
+++ b/htsworkflow/util/test/test_alphanum.py
@@ -1,10 +1,10 @@
 import copy
 import os
 import copy
 import os

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util.alphanum import alphanum
 
 
 from htsworkflow.util.alphanum import alphanum
 

-class testAlphanum(unittest.TestCase):
+class testAlphanum(TestCase):

     def test_string(self):
       unsorted = ['z5', 'b3', 'b10', 'a001', 'a2']
       sorted = [ 'a001', 'a2', 'b3', 'b10', 'z5']
     def test_string(self):
       unsorted = ['z5', 'b3', 'b10', 'a001', 'a2']
       sorted = [ 'a001', 'a2', 'b3', 'b10', 'z5']


@@ -42,7 +42,12 @@ class testAlphanum(unittest.TestCase):
 
 
 def suite():
 
 
 def suite():

-    return unittest.makeSuite(testAlphanum, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_api.py b/htsworkflow/util/test/test_api.py
index 4cbe3831405916266493a3c62cd7f5af67f61749..dadd6afd198fa841c19f81a56f3f6249becbdd47 100644 (file)
--- a/htsworkflow/util/test/test_api.py
+++ b/htsworkflow/util/test/test_api.py
@@ -1,10 +1,10 @@
 import copy
 import os
 import copy
 import os

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util import api
 
 
 from htsworkflow.util import api
 

-class testApi(unittest.TestCase):
+class testApi(TestCase):

     def test_make_key(self):
         k1 = api.make_django_secret_key()
         k2 = api.make_django_secret_key()
     def test_make_key(self):
         k1 = api.make_django_secret_key()
         k2 = api.make_django_secret_key()


@@ -14,7 +14,12 @@ class testApi(unittest.TestCase):
         self.failUnless(k1 != k2)
 
 def suite():
         self.failUnless(k1 != k2)
 
 def suite():

-    return unittest.makeSuite(testApi, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestApi))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_conversion.py b/htsworkflow/util/test/test_conversion.py
index 9100625fb598ab75ed0eb6aadbab682e7705bcbe..4919e56a4c4a6527e4af1c185403e0a6952946ca 100644 (file)
--- a/htsworkflow/util/test/test_conversion.py
+++ b/htsworkflow/util/test/test_conversion.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
 #!/usr/bin/env python
 

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util import conversion
 
 
 from htsworkflow.util import conversion
 

-class TestConversion(unittest.TestCase):
+class TestConversion(TestCase):

     def test_parse_slice(self):
         s = conversion.parse_slice("1:")
         self.failUnlessEqual(s.start, 1)
     def test_parse_slice(self):
         s = conversion.parse_slice("1:")
         self.failUnlessEqual(s.start, 1)


@@ -15,8 +15,12 @@ class TestConversion(unittest.TestCase):
         self.failUnlessEqual(s.stop, 2)
 
 def suite():
         self.failUnlessEqual(s.stop, 2)
 
 def suite():

-    return unittest.makeSuite(TestConversion, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestConversion))
+    return suite

 
 

-if __name__ == "__main__":
-    unittest.main(defaultTest="suite")

 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_ethelp.py b/htsworkflow/util/test/test_ethelp.py
index 63f0ac3ee6ee1d5e5c91b8008437cd666890deab..461a564ab8f8d325dbb41f0f908555bc0b5d036b 100644 (file)
--- a/htsworkflow/util/test/test_ethelp.py
+++ b/htsworkflow/util/test/test_ethelp.py
@@ -1,5 +1,5 @@
 import os
 import os

-import unittest
+from unittest2 import TestCase

 
 try:
   from xml.etree import ElementTree
 
 try:
   from xml.etree import ElementTree


@@ -8,7 +8,7 @@ except ImportError, e:
 
 from htsworkflow.util.ethelp import indent, flatten
 
 
 from htsworkflow.util.ethelp import indent, flatten
 

-class testETHelper(unittest.TestCase):
+class testETHelper(TestCase):

     def setUp(self):
         self.foo = '<foo><bar>asdf</bar><br/></foo>'
         self.foo_tree = ElementTree.fromstring(self.foo)
     def setUp(self):
         self.foo = '<foo><bar>asdf</bar><br/></foo>'
         self.foo_tree = ElementTree.fromstring(self.foo)


@@ -25,11 +25,12 @@ class testETHelper(unittest.TestCase):
         self.failUnless(flatten(self.foo_tree), 'asdf')
 
 def suite():
         self.failUnless(flatten(self.foo_tree), 'asdf')
 
 def suite():

-    return unittest.makeSuite(testETHelper, 'test')
-
-if __name__ == "__main__":
-    unittest.main(defaultTest='suite')
-
-
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testETHelper))
+    return suite

 
 
 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py
index b5d3026578fe967cee0fbf0d9fe5dd48042b1a7c..b701e08a5fec656f0705449e3b9a4352e1269d2a 100644 (file)
--- a/htsworkflow/util/test/test_makebed.py
+++ b/htsworkflow/util/test/test_makebed.py
@@ -1,10 +1,10 @@
 import os
 from StringIO import StringIO
 import os
 from StringIO import StringIO

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util import makebed
 
 
 from htsworkflow.util import makebed
 

-class testMakeBed(unittest.TestCase):
+class testMakeBed(TestCase):

     def test_multi_1_0_0_limit_1(self):
       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383    TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0   mm9_chr13_random.fa:1240R0')
       out = StringIO()
     def test_multi_1_0_0_limit_1(self):
       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383    TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0   mm9_chr13_random.fa:1240R0')
       out = StringIO()


@@ -46,10 +46,14 @@ class testMakeBed(unittest.TestCase):
       print out
       self.failUnlessEqual(len(out), 1)
 
       print out
       self.failUnlessEqual(len(out), 1)
 

-def suite():
-    return unittest.makeSuite(testMakeBed, 'test')

 
 

-if __name__ == "__main__":
-    unittest.main(defaultTest='suite')
+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testMakeBed))
+    return suite

 
 
 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_queuecommands.py b/htsworkflow/util/test/test_queuecommands.py
index dc745a6ff6d2c6d60d4a8274281c4989fd65b2a2..5885f73515e4422f3acaa39723f57dc1564ab26a 100644 (file)
--- a/htsworkflow/util/test/test_queuecommands.py
+++ b/htsworkflow/util/test/test_queuecommands.py
@@ -1,17 +1,15 @@
 import os
 import logging
 import time
 import os
 import logging
 import time

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util.queuecommands import QueueCommands
 
 
 from htsworkflow.util.queuecommands import QueueCommands
 

-class testQueueCommands(unittest.TestCase):
+class testQueueCommands(TestCase):

     def setUp(self):
         logging.basicConfig(level=logging.DEBUG,
                             format='%(asctime)s %(name)-8s %(message)s')
 
     def setUp(self):
         logging.basicConfig(level=logging.DEBUG,
                             format='%(asctime)s %(name)-8s %(message)s')
 

-
-

     def test_unlimited_run_slow(self):
         """
         Run everything at once
     def test_unlimited_run_slow(self):
         """
         Run everything at once


@@ -44,12 +42,14 @@ class testQueueCommands(unittest.TestCase):
         self.failUnless( end > 3.9 and end < 4.1,
                          "took %s seconds, expected ~4" % (end,))
 
         self.failUnless( end > 3.9 and end < 4.1,
                          "took %s seconds, expected ~4" % (end,))
 

-def suite():
-    return unittest.makeSuite(testQueueCommands, 'test')
-
-if __name__ == "__main__":
-    unittest.main(defaultTest='suite')
-

 
 

+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testQueueCommands))
+    return suite

 
 
 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index dfa4b971c70c1bcd28723d8b3b416c331d6d84c5..a477b95c9adacbb4a15c1997d29e712750b0d452 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -1,7 +1,6 @@
 import os
 import os

-import unittest

 import types
 import types

-
+from unittest2 import TestCase

 
 from datetime import datetime
 
 
 from datetime import datetime
 


@@ -28,7 +27,7 @@ from htsworkflow.util.rdfhelp import \
 try:
     import RDF
 
 try:
     import RDF
 

-    class TestRDFHelp(unittest.TestCase):
+    class TestRDFHelp(TestCase):

         def test_from_none(self):
           self.failUnlessEqual(fromTypedNode(None), None)
 
         def test_from_none(self):
           self.failUnlessEqual(fromTypedNode(None), None)
 


@@ -224,7 +223,7 @@ _:a owl:imports "{loc}extra.turtle" .
             for contenttype, url, parser in DATA:
                 self.assertEqual(guess_parser(contenttype, url), parser)
 
             for contenttype, url, parser in DATA:
                 self.assertEqual(guess_parser(contenttype, url), parser)
 

-    class TestRDFSchemas(unittest.TestCase):
+    class TestRDFSchemas(TestCase):

         def test_rdf_schema(self):
             """Does it basically work?
             """
         def test_rdf_schema(self):
             """Does it basically work?
             """


@@ -256,13 +255,17 @@ _:a owl:imports "{loc}extra.turtle" .
             self.assertTrue(model.contains_statement(s))
 
 
             self.assertTrue(model.contains_statement(s))
 
 

-    def suite():
-        return unittest.makeSuite(TestRDFHelp, 'test')

 except ImportError, e:
     print "Unable to test rdfhelp"
 
 except ImportError, e:
     print "Unable to test rdfhelp"
 

-    def suite():
-        return None
+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFHelp))
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFSchemas))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_rdfinfer.py b/htsworkflow/util/test/test_rdfinfer.py
index faa76727cf21a5f59f2c26b056579af1ba8a0f18..b40f46151f2d45c1243318fdd79d7720fcb3ee07 100644 (file)
--- a/htsworkflow/util/test/test_rdfinfer.py
+++ b/htsworkflow/util/test/test_rdfinfer.py
@@ -1,4 +1,4 @@
-import unittest
+from unittest2 import TestCase

 
 import RDF
 
 
 import RDF
 


@@ -88,7 +88,7 @@ _:me
      foaf:depicts _:me .
 """
 
      foaf:depicts _:me .
 """
 

-class TestInfer(unittest.TestCase):
+class TestInfer(TestCase):

     def setUp(self):
         self.model = get_model()
         add_default_schemas(self.model)
     def setUp(self):
         self.model = get_model()
         add_default_schemas(self.model)


@@ -228,8 +228,14 @@ class TestInfer(unittest.TestCase):
         print errmsg
         self.failUnlessEqual(len(errmsg), 0)
 
         print errmsg
         self.failUnlessEqual(len(errmsg), 0)
 

+

 def suite():
 def suite():

-    return unittest.makeSuite(TestInfer, 'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest='suite')
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_validate.py b/htsworkflow/util/test/test_validate.py
index 513a3a396221149e8fbadee0457638fdd7865be4..cc05f3c56641e645ccbabb8c5006f83c3b7168da 100644 (file)
--- a/htsworkflow/util/test/test_validate.py
+++ b/htsworkflow/util/test/test_validate.py
@@ -1,10 +1,10 @@
 import os
 from StringIO import StringIO
 import os
 from StringIO import StringIO

-import unittest
+from unittest2 import TestCase

 
 from htsworkflow.util import validate
 
 
 from htsworkflow.util import validate
 

-class TestValidate(unittest.TestCase):
+class TestValidate(TestCase):

     def test_phred33_works(self):
         q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n")
         errors = validate.validate_fastq(q)
     def test_phred33_works(self):
         q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n")
         errors = validate.validate_fastq(q)


@@ -45,10 +45,14 @@ class TestValidate(unittest.TestCase):
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 

-def suite():
-    return unittest.makeSuite(testValidate, 'test')

 
 

-if __name__ == "__main__":
-    unittest.main(defaultTest='suite')
+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate))
+    return suite

 
 
 
 

+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/test/test_copier.py b/test/test_copier.py
index 36078dc438b083b7fec43dcbe932bc2bdab21225..3e26cc679605f36d45d5f24016a99f959df63b4e 100644 (file)
--- a/test/test_copier.py
+++ b/test/test_copier.py
@@ -1,10 +1,10 @@
-import unittest
+from unittest2 import TestCase

 
 from StringIO import StringIO
 from htsworkflow.automation import copier
 from htsworkflow.automation.solexa import is_runfolder
 
 
 from StringIO import StringIO
 from htsworkflow.automation import copier
 from htsworkflow.automation.solexa import is_runfolder
 

-class testCopier(unittest.TestCase):        
+class testCopier(TestCase):

     def test_empty_config(self):
         cfg = StringIO("""[fake]
 something: unrelated
     def test_empty_config(self):
         cfg = StringIO("""[fake]
 something: unrelated


@@ -74,8 +74,14 @@ notify_users: user3@example.fake
        self.failUnlessEqual(len(result), 1)
        self.failUnlessEqual(result[0][-1], '4')
 
        self.failUnlessEqual(len(result), 1)
        self.failUnlessEqual(result[0][-1], '4')
 

+

 def suite():
 def suite():

-    return unittest.makeSuite(testCopier,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")

diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py
index 74e031ca7324174362de8695fb99ba4c50d830c7..9185fffde9d516d8651a5ade40723645ab82fa26 100644 (file)
--- a/test/test_srf2fastq.py
+++ b/test/test_srf2fastq.py
@@ -1,7 +1,7 @@
 import os
 from StringIO import StringIO
 import sys
 import os
 from StringIO import StringIO
 import sys

-import unittest
+from unittest2 import TestCase

 
 _module_path, _module_name = os.path.split(__file__)
 sys.path.append(os.path.join(_module_path, '..', 'scripts'))
 
 _module_path, _module_name = os.path.split(__file__)
 sys.path.append(os.path.join(_module_path, '..', 'scripts'))


@@ -10,7 +10,7 @@ from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 
 from htsworkflow.pipelines import srf2fastq
 
 
 from htsworkflow.pipelines import srf2fastq
 

-class testSrf2Fastq(unittest.TestCase):
+class testSrf2Fastq(TestCase):

     def test_split_good(self):
         source = StringIO("""@header
 AGCTTTTT
     def test_split_good(self):
         source = StringIO("""@header
 AGCTTTTT


@@ -135,8 +135,14 @@ IIIIB+++
         self.failUnlessEqual(is_cnf1(cnf4_path), False)
         self.failUnlessEqual(is_cnf1(cnf1_path), True)
 
         self.failUnlessEqual(is_cnf1(cnf4_path), False)
         self.failUnlessEqual(is_cnf1(cnf1_path), True)
 

+

 def suite():
 def suite():

-    return unittest.makeSuite(testSrf2Fastq,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
+    return suite
+

 
 if __name__ == "__main__":
 
 if __name__ == "__main__":

-    unittest.main(defaultTest="suite")
+    from unittest2 import main
+    main(defaultTest="suite")