def test_fragment_with_duplicate_in_pair_2(self):
# Ensure the reducer catches a fragment duplicate of pair[1].
p = list(test_utils.pair1())
# Insert the pair into the context
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
# Remove the first read from the pair, reorder so that the None is at index 1,
# the serialize and insert into the context.
test_utils.erase_read1(p)
self.__ctx.add_value(test_utils.make_key(p[1]), proto.serialize_pair( (p[1], None) ))
self.__reducer.reduce(self.__ctx)
# now ensure that nothing was emitted. The pair isn't emitted because
# the key refers to read2, and the fragment isn't emitted because it's a duplicate of
# the one in the pair.
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_fragment_with_duplicate_in_pair_2(self):
# Ensure the reducer catches a fragment duplicate of pair[1].
p = list(test_utils.pair1())
# Insert the pair into the context
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
# Remove the first read from the pair, reorder so that the None is at index 1,
# the serialize and insert into the context.
test_utils.erase_read1(p)
self.__ctx.add_value(test_utils.make_key(p[1]),
proto.serialize_pair((p[1], None)))
self.__reducer.reduce(self.__ctx)
# now ensure that nothing was emitted. The pair isn't emitted because
# the key refers to read2, and the fragment isn't emitted because it's a duplicate of
# the one in the pair.
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
self.assertFalse(
self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(
self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_emit_reverse_fragment1(self): # None in pair[0]. Fragment in pair[1]. self.pair1 = test_utils.erase_read1(list(self.pair1)) self.pair1[1].set_on_reverse(True) self.link.process(self.pair1) self.assertEqual(1, len(self.ctx.emitted.keys())) expected_key = test_utils.make_key(self.pair1[1]) self.assertEqual(1, len(self.ctx.emitted[expected_key])) unserialized = proto.unserialize_pair(self.ctx.emitted[expected_key][0]) self.assertTrue(unserialized[1] is None) self.assertEqual(self.pair1[1].tid, unserialized[0].tid) self.assertEqual(self.pair1[1].pos, unserialized[0].pos) self.assertTrue(unserialized[0].is_on_reverse())
def test_emit_forward_fragment1(self):
# None in pair[0]. Fragment in pair[1].
self.pair1 = test_utils.erase_read1(list(self.pair1))
self.link.process(self.pair1)
self.assertEqual(1, len(self.ctx.emitted.keys()))
expected_key = test_utils.make_key(self.pair1[1])
self.assertEqual(1, len(self.ctx.emitted[expected_key]))
unserialized = proto.unserialize_pair(self.ctx.emitted[expected_key][0])
self.assertTrue(unserialized[1] is None)
self.assertEqual(self.pair1[1].tid, unserialized[0].tid)
self.assertEqual(self.pair1[1].pos, unserialized[0].pos)
self.assertTrue(self.ctx.counters.has_key("Test:MAPPED COORDINATES"))
self.assertEqual(1, self.ctx.counters["Test:MAPPED COORDINATES"])
def test_emit_reverse_fragment1(self):
# None in pair[0]. Fragment in pair[1].
self.pair1 = test_utils.erase_read1(list(self.pair1))
self.pair1[1].set_on_reverse(True)
self.link.process(self.pair1)
self.assertEqual(1, len(self.ctx.emitted.keys()))
expected_key = test_utils.make_key(self.pair1[1])
self.assertEqual(1, len(self.ctx.emitted[expected_key]))
unserialized = proto.unserialize_pair(
self.ctx.emitted[expected_key][0])
self.assertTrue(unserialized[1] is None)
self.assertEqual(self.pair1[1].tid, unserialized[0].tid)
self.assertEqual(self.pair1[1].pos, unserialized[0].pos)
self.assertTrue(unserialized[0].is_on_reverse())
def test_emit_forward_fragment1(self):
# None in pair[0]. Fragment in pair[1].
self.pair1 = test_utils.erase_read1(list(self.pair1))
self.link.process(self.pair1)
self.assertEqual(1, len(self.ctx.emitted.keys()))
expected_key = test_utils.make_key(self.pair1[1])
self.assertEqual(1, len(self.ctx.emitted[expected_key]))
unserialized = proto.unserialize_pair(
self.ctx.emitted[expected_key][0])
self.assertTrue(unserialized[1] is None)
self.assertEqual(self.pair1[1].tid, unserialized[0].tid)
self.assertEqual(self.pair1[1].pos, unserialized[0].pos)
self.assertTrue(self.ctx.counters.has_key("Test:MAPPED COORDINATES"))
self.assertEqual(1, self.ctx.counters["Test:MAPPED COORDINATES"])
def test_empty_read1(self):
# Ensure the reducer raises an exception if the pair[0] is None
p = test_utils.erase_read1(list(test_utils.pair1()))
self.__ctx.add_value(test_utils.make_key(p[1]), proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
def test_empty_read1(self):
# Ensure the reducer raises an exception if the pair[0] is None
p = test_utils.erase_read1(list(test_utils.pair1()))
self.__ctx.add_value(test_utils.make_key(p[1]),
proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
