From 6ea8652c57937ff48c18fc3990ae7f2ee0875ab9 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 27 Nov 2012 16:37:55 -0800 Subject: [PATCH] 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) --- encode_submission/test_encode_find.py | 13 +++++++---- encode_submission/test_ucsc_gather.py | 11 +++++---- htsworkflow/automation/test/__init__.py | 0 htsworkflow/automation/test/test_runner.py | 18 ++++++++++----- .../automation/test/test_solexa_utils.py | 16 ++++++++----- .../frontend/inventory/test_inventory.py | 10 ++++---- htsworkflow/frontend/labels/test_labels.py | 9 ++++++++ htsworkflow/frontend/samples/test_samples.py | 1 - htsworkflow/pipelines/test/test_eland.py | 23 ++++++++++++++----- .../pipelines/test/test_extract_results.py | 15 ++++++++---- .../pipelines/test/test_genome_mapper.py | 13 +++++++---- htsworkflow/pipelines/test/test_genomemap.py | 14 ++++++++--- htsworkflow/pipelines/test/test_run_xml.py | 15 ++++++++---- .../pipelines/test/test_runfolder026.py | 14 +++++++---- .../pipelines/test/test_runfolder030.py | 13 +++++++---- .../pipelines/test/test_runfolder110.py | 14 +++++++---- .../test/test_runfolder_casava_1_7.py | 13 +++++++---- .../pipelines/test/test_runfolder_ipar100.py | 14 +++++++---- .../pipelines/test/test_runfolder_ipar130.py | 14 +++++++---- .../pipelines/test/test_runfolder_pair.py | 14 +++++++---- .../pipelines/test/test_runfolder_rta.py | 14 +++++++---- .../pipelines/test/test_runfolder_rta160.py | 15 +++++++----- .../pipelines/test/test_runfolder_rta180.py | 14 +++++++---- .../pipelines/test/test_runfolder_rta1_12.py | 15 +++++++----- htsworkflow/pipelines/test/test_samplekey.py | 14 ++++++++--- htsworkflow/pipelines/test/test_sequences.py | 13 +++++++---- htsworkflow/pipelines/test/test_summary.py | 14 +++++++---- .../submission/test/test_condorfastq.py | 13 +++++++---- htsworkflow/submission/test/test_daf.py | 14 +++++------ htsworkflow/submission/test/test_results.py | 13 +++++------ htsworkflow/submission/test/test_ucsc.py | 11 +++++---- htsworkflow/util/test/__init__.py | 0 htsworkflow/util/test/test_alphanum.py | 13 +++++++---- htsworkflow/util/test/test_api.py | 13 +++++++---- htsworkflow/util/test/test_conversion.py | 14 +++++++---- htsworkflow/util/test/test_ethelp.py | 17 +++++++------- htsworkflow/util/test/test_makebed.py | 16 ++++++++----- htsworkflow/util/test/test_queuecommands.py | 20 ++++++++-------- htsworkflow/util/test/test_rdfhelp.py | 21 +++++++++-------- htsworkflow/util/test/test_rdfinfer.py | 14 +++++++---- htsworkflow/util/test/test_validate.py | 16 ++++++++----- test/__init__.py | 0 test/test_copier.py | 14 +++++++---- test/test_srf2fastq.py | 14 +++++++---- 44 files changed, 373 insertions(+), 203 deletions(-) create mode 100644 htsworkflow/automation/test/__init__.py create mode 100644 htsworkflow/util/test/__init__.py create mode 100644 test/__init__.py diff --git a/encode_submission/test_encode_find.py b/encode_submission/test_encode_find.py index 0510895..6844fa4 100644 --- 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 -import unittest +from unittest2 import TestCase 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 -class TestEncodeFind(unittest.TestCase): +class TestEncodeFind(TestCase): def setUp(self): self.model = get_model() add_default_schemas(self.model) @@ -163,7 +163,12 @@ _:bnode120970 '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__": - 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 d7d54e6..6063951 100644 --- 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 -class testUCSCGather(unittest.TestCase): +class testUCSCGather(TestCase): pass def suite(): - return unittest.makeSuite(testUCSCGather,"test") + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testUCSCGather)) + return suite 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 index 0000000..e69de29 diff --git a/htsworkflow/automation/test/test_runner.py b/htsworkflow/automation/test/test_runner.py index 1457f9e..a60c458 100644 --- 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 @@ -17,13 +16,14 @@ def extract_runfolder_path(watchdir, event): return runfolder_path return None + 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') @@ -38,9 +38,15 @@ class testRunner(unittest.TestCase): event = Event( path=other) self.failUnlessEqual(extract_runfolder_path(watchdir, event), None ) - + + def suite(): - return unittest.makeSuite(testRunner,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner)) + return suite + 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 a527ad3..210906e 100644 --- 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 -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) @@ -23,9 +22,14 @@ class testSolexaRunfolderUtils(unittest.TestCase): for root, path, response in test_data: self.failUnlessEqual(solexa.get_top_dir(root, path), response) + def suite(): - return unittest.makeSuite(testSolexaRunfolderUtils, 'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils)) + return suite + 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 024a334..118c654 100644 --- a/htsworkflow/frontend/inventory/test_inventory.py +++ b/htsworkflow/frontend/inventory/test_inventory.py @@ -1,5 +1,4 @@ import RDF -import unittest from django.test import TestCase from django.contrib.auth.models import User @@ -110,8 +109,11 @@ class InventoryTestCase(TestCase): 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__": - 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 2247054..29354b2 100644 --- 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 """} +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 0320c0a..2fb3945 100644 --- a/htsworkflow/frontend/samples/test_samples.py +++ b/htsworkflow/frontend/samples/test_samples.py @@ -1,5 +1,4 @@ import datetime -import unittest try: import json diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py index 688d00e..43953fc 100644 --- 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 -import unittest +from unittest2 import TestCase 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) @@ -38,7 +38,7 @@ class MatchCodeTests(unittest.TestCase): self.assertEqual(mc1['U0'], 100) -class TestMappedReads(unittest.TestCase): +class TestMappedReads(TestCase): 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) -class ElandTests(unittest.TestCase): +class ElandTests(TestCase): """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') -class TestElandMatches(unittest.TestCase): +class TestElandMatches(TestCase): 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) +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__": - 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 b64bd0f..6f2b423 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -60,7 +60,7 @@ def make_runfolder(obj=None): obj.gerald_dir = gerald_dir -class RunfolderExtractTests(unittest.TestCase): +class RunfolderExtractTests(TestCase): """ 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) - + def suite(): - return unittest.makeSuite(RunfolderExtractTests,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests)) + return suite + 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 8ba1ba5..1101305 100644 --- 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 -class testGenomeMapper(unittest.TestCase): +class testGenomeMapper(TestCase): def test_construct_mapper(self): genomes = { 'Arabidopsis thaliana': {'v01212004': '/arabidopsis'}, @@ -27,7 +27,12 @@ class testGenomeMapper(unittest.TestCase): def suite(): - return unittest.makeSuite(testGenomeMapper,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper)) + return suite + 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 d0c1e66..aa2f618 100644 --- 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 -import unittest +from unittest2 import TestCase from htsworkflow.pipelines.runfolder import ElementTree from htsworkflow.pipelines import genomemap @@ -15,7 +15,7 @@ MINI_GENOME_XML = ''' ''' -class TestGenomeMap(unittest.TestCase): +class TestGenomeMap(TestCase): 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)) +def suite(): + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap)) + return suite + + 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 8592645..8b28b9e 100644 --- a/htsworkflow/pipelines/test/test_run_xml.py +++ b/htsworkflow/pipelines/test/test_run_xml.py @@ -1,13 +1,14 @@ 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 -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) @@ -94,8 +95,14 @@ class testLoadRunXML(unittest.TestCase): } self._check_run_xml(run_xml_name, results, eland_results=8) + def suite(): - return unittest.makeSuite(testLoadRunXML,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML)) + return suite + 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 f6162de..8eef130 100644 --- 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 unittest +from unittest2 import TestCase 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() -class RunfolderTests(unittest.TestCase): +class RunfolderTests(TestCase): """ Test components of the runfolder processing code which includes firecrest, bustard, and gerald @@ -471,8 +471,12 @@ 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") +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 2a060d1..a571944 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -678,7 +678,7 @@ 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 @@ -895,8 +895,11 @@ 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") diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py index 3e1bf87..2397c2a 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -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 @@ -300,8 +300,12 @@ 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") +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 12fec6d..ae91055 100644 --- 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 @@ -303,9 +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") diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py index fff9a7f..1e95632 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import ipar from htsworkflow.pipelines import bustard @@ -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 @@ -299,8 +299,12 @@ 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") +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 eb018d8..07c8778 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -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 @@ -337,8 +337,12 @@ 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") +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 97ba6f4..b159c5f 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import firecrest from htsworkflow.pipelines import bustard @@ -59,7 +59,7 @@ 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 @@ -325,8 +325,12 @@ 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") +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 90126d8..2c82041 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -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 @@ -299,8 +299,12 @@ 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") +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 caf82a0..9d4879a 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -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 @@ -275,10 +275,13 @@ class RunfolderTests(unittest.TestCase): 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__": - 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 b803787..be83c3f 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines import ipar @@ -57,7 +57,7 @@ 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 @@ -284,8 +284,12 @@ 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") +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 fdb6001..6933157 100644 --- 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 unittest +from unittest2 import TestCase from htsworkflow.pipelines import eland from htsworkflow.pipelines.samplekey import SampleKey @@ -63,7 +63,7 @@ def make_runfolder(obj=None): obj.reads = 2 -class RunfolderTests(unittest.TestCase): +class RunfolderTests(TestCase): """ 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(): - 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 a4287d3..ecd273d 100644 --- 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 -import unittest +from unittest2 import TestCase 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') @@ -43,5 +43,13 @@ class TestSampleKey(unittest.TestCase): 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__": - 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 accd43e..522a9aa 100644 --- 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 unittest +from unittest2 import TestCase 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 -class SequenceFileTests(unittest.TestCase): +class SequenceFileTests(TestCase): """ Make sure the sequence archive class works """ @@ -612,7 +612,12 @@ class SimulateSimpleTree(SimulateTree): def suite(): - return unittest.makeSuite(SequenceFileTests,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests)) + return suite + 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 af0e908..1f7e461 100644 --- 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 -import unittest +from unittest2 import TestCase 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): @@ -34,8 +34,14 @@ class SummaryTests(unittest.TestCase): pathname = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm') s = summary.SummaryGA(pathname) + def suite(): - return unittest.makeSuite(SummaryTests,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests)) + return suite + 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 cffb5ac..ffb9f88 100644 --- 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 -import unittest + +from django.test import TestCase from htsworkflow.submission.condorfastq import CondorFastqExtract from htsworkflow.submission.results import ResultMap @@ -411,7 +412,7 @@ lib_turtle = """@prefix : . """ HOST = "http://localhost" -class TestCondorFastq(unittest.TestCase): +class TestCondorFastq(TestCase): def setUp(self): self.cwd = os.getcwd() @@ -676,9 +677,11 @@ class TestCondorFastq(unittest.TestCase): def suite(): - suite = unittest.makeSuite(TestCondorFastq, 'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq)) 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 95dc1d9..c722721 100644 --- 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 -import unittest +from unittest2 import TestCase, TestSuite, defaultTestLoader 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) @@ -165,7 +165,7 @@ def dump_model(model): print turtle -class TestUCSCSubmission(unittest.TestCase): +class TestUCSCSubmission(TestCase): 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) - 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__": - 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 2d8cd57..3487b69 100644 --- 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 -import unittest + +from unittest2 import TestCase, defaultTestLoader from htsworkflow.submission.results import ResultMap @@ -41,7 +42,7 @@ def generate_sample_results_tree(obj): stream.write(f) stream.close() -class TestResultMap(unittest.TestCase): +class TestResultMap(TestCase): def setUp(self): generate_sample_results_tree(self) @@ -91,12 +92,10 @@ class TestResultMap(unittest.TestCase): os.path.join(self.resultdir, f))) - - def suite(): - suite = unittest.makeSuite(TestResultMap, 'test') + suite = defaultTestLoader.loadTestsFromTestCase(TestResultMap) 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 53ac287..fad690e 100644 --- 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 @@ -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') @@ -21,9 +21,10 @@ class TestUCSCInfo(unittest.TestCase): self.assertEquals(attributes['project'], 'wgEncode') def suite(): - suite = unittest.makeSuite(TestUCSCInfo, 'test') + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCInfo)) 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 index 0000000..e69de29 diff --git a/htsworkflow/util/test/test_alphanum.py b/htsworkflow/util/test/test_alphanum.py index 3fd6025..29a5385 100644 --- a/htsworkflow/util/test/test_alphanum.py +++ b/htsworkflow/util/test/test_alphanum.py @@ -1,10 +1,10 @@ import copy import os -import unittest +from unittest2 import TestCase 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'] @@ -42,7 +42,12 @@ class testAlphanum(unittest.TestCase): def suite(): - return unittest.makeSuite(testAlphanum, 'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum)) + return suite + 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 4cbe383..dadd6af 100644 --- a/htsworkflow/util/test/test_api.py +++ b/htsworkflow/util/test/test_api.py @@ -1,10 +1,10 @@ import copy import os -import unittest +from unittest2 import TestCase 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() @@ -14,7 +14,12 @@ class testApi(unittest.TestCase): 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__": - 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 9100625..4919e56 100644 --- a/htsworkflow/util/test/test_conversion.py +++ b/htsworkflow/util/test/test_conversion.py @@ -1,10 +1,10 @@ #!/usr/bin/env python -import unittest +from unittest2 import TestCase 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) @@ -15,8 +15,12 @@ class TestConversion(unittest.TestCase): 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 63f0ac3..461a564 100644 --- a/htsworkflow/util/test/test_ethelp.py +++ b/htsworkflow/util/test/test_ethelp.py @@ -1,5 +1,5 @@ import os -import unittest +from unittest2 import TestCase try: from xml.etree import ElementTree @@ -8,7 +8,7 @@ except ImportError, e: from htsworkflow.util.ethelp import indent, flatten -class testETHelper(unittest.TestCase): +class testETHelper(TestCase): def setUp(self): self.foo = 'asdf
' self.foo_tree = ElementTree.fromstring(self.foo) @@ -25,11 +25,12 @@ class testETHelper(unittest.TestCase): 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 b5d3026..b701e08 100644 --- 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 unittest +from unittest2 import TestCase 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() @@ -46,10 +46,14 @@ class testMakeBed(unittest.TestCase): 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 dc745a6..5885f73 100644 --- 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 unittest +from unittest2 import TestCase 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 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,)) -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 dfa4b97..a477b95 100644 --- a/htsworkflow/util/test/test_rdfhelp.py +++ b/htsworkflow/util/test/test_rdfhelp.py @@ -1,7 +1,6 @@ import os -import unittest import types - +from unittest2 import TestCase from datetime import datetime @@ -28,7 +27,7 @@ from htsworkflow.util.rdfhelp import \ try: import RDF - class TestRDFHelp(unittest.TestCase): + class TestRDFHelp(TestCase): 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) - class TestRDFSchemas(unittest.TestCase): + class TestRDFSchemas(TestCase): 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)) - def suite(): - return unittest.makeSuite(TestRDFHelp, 'test') 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__": - 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 faa7672..b40f461 100644 --- 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 @@ -88,7 +88,7 @@ _:me foaf:depicts _:me . """ -class TestInfer(unittest.TestCase): +class TestInfer(TestCase): 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) + def suite(): - return unittest.makeSuite(TestInfer, 'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer)) + return suite + 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 513a3a3..cc05f3c 100644 --- 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 unittest +from unittest2 import TestCase 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) @@ -45,10 +45,14 @@ class TestValidate(unittest.TestCase): 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 index 0000000..e69de29 diff --git a/test/test_copier.py b/test/test_copier.py index 36078dc..3e26cc6 100644 --- 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 -class testCopier(unittest.TestCase): +class testCopier(TestCase): 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') + def suite(): - return unittest.makeSuite(testCopier,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier)) + return suite + 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 74e031c..9185fff 100644 --- a/test/test_srf2fastq.py +++ b/test/test_srf2fastq.py @@ -1,7 +1,7 @@ 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')) @@ -10,7 +10,7 @@ from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR from htsworkflow.pipelines import srf2fastq -class testSrf2Fastq(unittest.TestCase): +class testSrf2Fastq(TestCase): 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) + def suite(): - return unittest.makeSuite(testSrf2Fastq,'test') + from unittest2 import TestSuite, defaultTestLoader + suite = TestSuite() + suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq)) + return suite + if __name__ == "__main__": - unittest.main(defaultTest="suite") + from unittest2 import main + main(defaultTest="suite") -- 2.30.2