from contextlib import contextmanager
+import logging
import os
from StringIO import StringIO
import shutil
import tempfile
-import unittest
+from unittest 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)
+ test_results.generate_sample_results_tree(self, 'daf_results')
def tearDown(self):
# see things created by temp_results.generate_sample_results_tree
# server is 500 for this library
self.failUnlessEqual(gel_cut, 100)
- species = daf_mapper._get_library_attribute(libNode, 'species')
+ species = daf_mapper._get_library_attribute(libNode, 'species_name')
self.failUnlessEqual(species, "Homo sapiens")
with mktempdir('analysis') as analysis_dir:
result_map = results.ResultMap()
result_dir = os.path.join(self.sourcedir,
test_results.S1_NAME)
- result_map.add_result('1000', result_dir)
+ result_map['1000'] = result_dir
submission.link_daf(result_map)
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(TestDAF))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCSubmission))
return suite
if __name__ == "__main__":
- unittest.main(defaultTest='suite')
+ logging.basicConfig(level=logging.DEBUG)
+ from unittest import main
+ main(defaultTest='suite')