#!/usr/bin/env python
from datetime import datetime
import os
-import unittest
+from unittest2 import TestCase
import RDF
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)
'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()
-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')
-import unittest
-
+from unittest2 import TestCase
import os
from htsworkflow.automation.solexa import is_runfolder
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')
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")
-
-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)
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")
import RDF
-import unittest
from django.test import TestCase
from django.contrib.auth.models import User
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")
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")
import datetime
-import unittest
try:
import json
"""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)
self.assertEqual(mc1['U0'], 100)
-class TestMappedReads(unittest.TestCase):
+class TestMappedReads(TestCase):
def test_initializer(self):
mr1 = MappedReads()
self.assertEqual(len(mr1), 0)
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):
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()
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")
import tempfile
import shutil
import sys
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
obj.gerald_dir = gerald_dir
-class RunfolderExtractTests(unittest.TestCase):
+class RunfolderExtractTests(TestCase):
"""
Test the extract result code.
"""
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")
-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'},
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")
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
<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()
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")
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)
}
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import eland
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import ipar
from htsworkflow.pipelines import bustard
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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
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")
import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines.samplekey import SampleKey
obj.reads = 2
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
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")
"""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')
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")
import os
import shutil
import tempfile
-import unittest
+from unittest2 import TestCase
import RDF
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
"""
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")
#!/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):
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")
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
"""
HOST = "http://localhost"
-class TestCondorFastq(unittest.TestCase):
+class TestCondorFastq(TestCase):
def setUp(self):
self.cwd = os.getcwd()
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')
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 \
"""
-class TestDAF(unittest.TestCase):
+class TestDAF(TestCase):
def test_parse(self):
parsed = daf.fromstring(test_daf)
print turtle
-class TestUCSCSubmission(unittest.TestCase):
+class TestUCSCSubmission(TestCase):
def setUp(self):
test_results.generate_sample_results_tree(self)
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')
from pprint import pprint
import shutil
import tempfile
-import unittest
+
+from unittest2 import TestCase, defaultTestLoader
from htsworkflow.submission.results import ResultMap
stream.write(f)
stream.close()
-class TestResultMap(unittest.TestCase):
+class TestResultMap(TestCase):
def setUp(self):
generate_sample_results_tree(self)
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')
-import unittest
+from unittest2 import TestCase, TestSuite, defaultTestLoader
from StringIO import StringIO
from htsworkflow.submission import ucsc
"""
-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')
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')
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']
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")
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()
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")
#!/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)
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")
import os
-import unittest
+from unittest2 import TestCase
try:
from xml.etree import ElementTree
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)
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")
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()
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")
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
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")
import os
-import unittest
import types
-
+from unittest2 import TestCase
from datetime import datetime
try:
import RDF
- class TestRDFHelp(unittest.TestCase):
+ class TestRDFHelp(TestCase):
def test_from_none(self):
self.failUnlessEqual(fromTypedNode(None), None)
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?
"""
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")
-import unittest
+from unittest2 import TestCase
import RDF
foaf:depicts _:me .
"""
-class TestInfer(unittest.TestCase):
+class TestInfer(TestCase):
def setUp(self):
self.model = get_model()
add_default_schemas(self.model)
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")
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)
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")
-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
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")
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'))
from htsworkflow.pipelines import srf2fastq
-class testSrf2Fastq(unittest.TestCase):
+class testSrf2Fastq(TestCase):
def test_split_good(self):
source = StringIO("""@header
AGCTTTTT
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")
projects / htsworkflow.git / commitdiff