#!/usr/bin/env python
from datetime import datetime
import os
-from unittest2 import TestCase
+from unittest import TestCase
import RDF
'12097')
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main()
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader
import ucsc_gather
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
-from unittest2 import TestCase
+from unittest import TestCase
import os
from htsworkflow.automation.solexa import is_runfolder
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.automation import solexa
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
self.assertEqual(len(errmsgs), 0)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
for testcase in [ClusterStationTestCases,
SequencerTestCases,
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
return flowcells
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(InventoryTestCase))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
"""}
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(SimpleTest))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
return model
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
self.assertEqual(run.runfolder_name, '130508_SN787_0146_BC23KDACXX')
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(AlignmentFreeRunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
"""More direct synthetic test cases for the eland output file processing
"""
from StringIO import StringIO
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
SampleKey, MatchCodes, MappedReads
self.assertEqual(len(em[key11112]), 2)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import tempfile
import shutil
import sys
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase
+from unittest import TestCase
from StringIO import StringIO
from htsworkflow.pipelines import genome_mapper
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
from StringIO import StringIO
import shutil
import tempfile
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import ElementTree
from htsworkflow.pipelines import genomemap
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
-from unittest2 import TestCase
+from unittest import TestCase
from StringIO import StringIO
from simulate_runfolder import TESTDATA_DIR
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import eland
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import ipar
from htsworkflow.pipelines import bustard
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import tempfile
import shutil
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines.samplekey import SampleKey
self.failIfEqual(r2.gerald, None)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader
from htsworkflow.pipelines import runfolder
class TestRunfolderUtilities(TestCase):
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
"""More direct synthetic test cases for the eland output file processing
"""
from StringIO import StringIO
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines.samplekey import SampleKey
self.assertTrue(k3.matches(q3))
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestSampleKey))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import shutil
import tempfile
-from unittest2 import TestCase
+from unittest import TestCase
import RDF
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
#!/usr/bin/env python
import os
from StringIO import StringIO
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import summary
from simulate_runfolder import TESTDATA_DIR
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
from StringIO import StringIO
import shutil
import tempfile
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader
from htsworkflow.submission import daf, results
from htsworkflow.util.rdfhelp import \
if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
import json
import os
from pprint import pprint
-from unittest2 import TestCase, TestSuite, defaultTestLoader, skip
+from unittest import TestCase, TestSuite, defaultTestLoader, skip
from htsworkflow.submission.encoded import (ENCODED,
ENCODED_CONTEXT,
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.submission.fastqname import FastqName
class TestFastqName(TestCase):
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
from pprint import pprint
import shutil
-from unittest2 import TestCase, defaultTestLoader
+from unittest import TestCase, defaultTestLoader
from htsworkflow.submission.results import ResultMap
from submission_test_common import *
if __name__ == "__main__":
import logging
logging.basicConfig(level=logging.DEBUG)
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
from StringIO import StringIO
import shutil
import tempfile
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader
from htsworkflow.submission import daf, results
from htsworkflow.util.rdfhelp import \
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader
from StringIO import StringIO
from htsworkflow.submission import ucsc
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
import copy
import os
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util.alphanum import alphanum
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import copy
import os
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util import api
self.failUnless(k1 != k2)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestApi))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
#!/usr/bin/env python
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util import conversion
self.failUnlessEqual(s.stop, 2)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestConversion))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
-from unittest2 import TestCase
+from unittest import TestCase
try:
from xml.etree import ElementTree
self.failUnless(flatten(self.foo_tree), 'asdf')
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testETHelper))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
from StringIO import StringIO
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util import makebed
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testMakeBed))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import logging
import time
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util.queuecommands import QueueCommands
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testQueueCommands))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
import types
-from unittest2 import TestCase
+from unittest import TestCase
from datetime import datetime
print "Unable to test rdfhelp"
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFHelp))
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFSchemas))
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase
+from unittest import TestCase
import RDF
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase, TestSuite, defaultTestLoader, skip
+from unittest import TestCase, TestSuite, defaultTestLoader, skip
from htsworkflow.util.rdfjsonld import load_into_model, to_node, triple_to_statement
from htsworkflow.util.rdfhelp import get_model
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')
"""Test wrappers around ucsc file formats
"""
import os
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util.test import TEST_DATA_DIR
from htsworkflow.util.ucsc import bigWigInfo
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util.url import normalize_url, parse_ssh_url
self.assertRaises(ValueError, parse_ssh_url, 'hello')
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestURLUtilities))
return suite
if __name__ == '__main__':
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
from StringIO import StringIO
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util import validate
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.util import version
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTest(defaultTestLoader.loadTestsFromTestCase(TestVersion))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")
import os
from StringIO import StringIO
import sys
-from unittest2 import TestCase
+from unittest import TestCase
_module_path, _module_name = os.path.split(__file__)
sys.path.append(os.path.join(_module_path, '..', 'scripts'))
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")