def _test_missing_key(self):
host=Host(config_file, 'clutch')
try:
self.assertEqual(host.environ('imaginary_key'), '/usr/local/lib') # key provided
self.fail()
except ConfigParser.NoOptionError:
pass
def test_localhost(self):
try:
host=Host(config_file, 'clutch')
except Excption:
self.fail('clutch not found')
self.assertEquals(host.get('n_procs'), '2')
def _test_missing_key(self):
host = Host(config_file, 'clutch')
try:
self.assertEqual(host.environ('imaginary_key'),
'/usr/local/lib') # key provided
self.fail()
except ConfigParser.NoOptionError:
pass
def _test_environ(self):
host = Host(config_file, 'clutch')
environ = host.environ()
self.assertEqual(environ['ld_library_path'],
'/usr/local/lib') # no key provided
self.assertEqual(host.environ('ld_library_path'),
'/usr/local/lib') # key provided
def test_variant_splitter(self):
host=Host(hostname=self.args.host)
pipeline=Pipeline('mock', host, working_dir, True)
data_basename='data/rawdata/1047-COPD.10K'
variants_fn='data/trip_neg_Vic/triple_negativ_mut_seq'
output_dir=os.path.join(root_dir, 't', 'fixtures', 'var2reads')
cmd=RunVariantSplitter(pipeline, data_basename, variants_fn, output_dir)
cmd=cmd.cmd_string()
print cmd
self.assertIn(host.get('variant_splitter.script'), cmd)
self.assertIn(data_basename, cmd)
self.assertIn(variants_fn, cmd)
def test_graph(self):
buffy = Host(hostname='buffy')
p = Pipeline('test_graph', buffy, root)
def test_empty_environ(self):
host=Host(config_file, 'imaginary_host')
self.assertEqual(str(host), 'imaginary_host')
env=host.environ()
self.assertEqual(type(env), type({}))
self.assertEqual(len(env), 0)
def _test_environ(self):
host=Host(config_file, 'clutch')
environ=host.environ()
self.assertEqual(environ['ld_library_path'], '/usr/local/lib') # no key provided
self.assertEqual(host.environ('ld_library_path'), '/usr/local/lib') # key provided
def test_empty_environ(self):
host = Host(config_file, 'imaginary_host')
self.assertEqual(str(host), 'imaginary_host')
env = host.environ()
self.assertEqual(type(env), type({}))
self.assertEqual(len(env), 0)
