def test_job_conf_getters(self):
values = ['int', '1', 'float', '2.3', 'bool', 'false']
conv_values = [1, 2.3, False]
jc = JobConf(values)
for i, k in enumerate(values[::2]):
getter = getattr(jc, 'get_%s' % k)
self.assertEqual(getter(k), conv_values[i])
for jc in JobConf([]), JobConf(['x', 'foo']):
for d in False, True:
self.assertEqual(jc.get_bool('x', default=d), d)
self.assertRaises(RuntimeError, JobConf(['x', 'foo']).get_bool, 'x')
def test_job_conf(self):
job_conf = {}
for k in mrv1_to_mrv2:
job_conf[k] = k
jc = JobConf(
[item for sublist in job_conf.iteritems() for item in sublist])
for k in mrv2_to_mrv1:
self.assertEqual(jc[k], job_conf[mrv2_to_mrv1[k]])
def setUp(self):
self._map_batch_size = 6
self._log = logging.getLogger(__name__)
self._old_cwd = os.getcwd()
self._jc = JobConf([
'seal.seqal.log.level',
'DEBUG',
'seal.seqal.fastq-subformat',
'fastq-sanger',
#'seal.seqal.alignment.max.isize', None,
#'seal.seqal.alignment.min.isize', None,
'seal.seqal.pairing.batch.size',
self._map_batch_size,
'seal.seqal.min_hit_quality',
0,
'seal.seqal.remove_unmapped',
False,
'seal.seqal.nthreads',
1,
'seal.seqal.trim.qual',
0,
'mapred.reduce.tasks',
0,
'mapred.cache.archives',
(os.path.join("file://", tseal_utils.MiniRefMemDir,
"mini_ref_bwamem_0.7.8.tar") + "#reference"),
])
self._things_to_clean_up = []
workdir = tempfile.mkdtemp("seqal_mapper_test_workdir")
self._things_to_clean_up.append(workdir)
os.chdir(workdir)
self._ctx = sam_map_context(self._jc, [])
try:
self._setup_ref(self._jc.get('mapred.cache.archives'))
self._mapper = mapper(self._ctx)
except StandardError:
# call tearDown ourselves because unittest doesn't call it if setUp fails
self.tearDown()
raise
def test_missing_key(self):
jc = JobConf(((1, 2), (3, 4)))
self.assertRaises(RuntimeError, jc.get, 'no_key')
def test_missing_key(self):
jc = JobConf(('a', 'b', 'c', 'd'))
self.assertRaises(RuntimeError, jc.get, 'no_key')
def setUp(self):
self.__jc = JobConf([])
self.__ctx = reduce_context(self.__jc, [])
self.__reducer = reducer(self.__ctx)
self.__reducer.discard_duplicates = True
self.__clean_reducer = reducer(self.__ctx) # unmodified
