def test_query(self, api):
if api == 'dqsegdb':
result = query_dqsegdb(self.TEST_CLASS.query, QUERY_FLAGS,
0, 10)
RESULT = QUERY_RESULTC
else:
result = query_segdb(self.TEST_CLASS.query, QUERY_FLAGS,
0, 10, url='https://geosegdb.does.not.exist')
RESULT = QUERY_RESULT
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
def test_query(self, api):
if api == 'dqsegdb':
result = query_dqsegdb(self.TEST_CLASS.query, QUERY_FLAGS, 0, 10)
RESULT = QUERY_RESULTC
else:
result = query_segdb(self.TEST_CLASS.query,
QUERY_FLAGS,
0,
10,
url='https://segdb.does.not.exist')
RESULT = QUERY_RESULT
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
def test_populate(self):
def fake():
return self.TEST_CLASS({
x: self.ENTRY_CLASS(name=x, known=y.known)
for x, y in QUERY_RESULT.items()
})
# build fake veto definer file
vdf = fake()
vdf2 = fake()
vdf3 = fake()
flag = QUERY_FLAGS[0]
vdf2[flag].padding = (-1, 1)
span = SegmentList([Segment(0, 2)])
# and populate using a mocked query
with mock.patch('dqsegdb.apicalls.dqsegdbQueryTimes',
mocks.dqsegdb_query_times(QUERY_RESULT)):
vdf.populate()
vdf2.populate()
vdf3.populate(segments=span)
# test warnings on bad entries
vdf['TEST'] = self.ENTRY_CLASS('X1:BLAHBLAHBLAH:1', known=[(0, 1)])
with pytest.warns(UserWarning) as record:
vdf.populate(on_error='warn')
vdf.populate(on_error='ignore')
assert len(record) == 1
vdf.pop('TEST')
with pytest.raises(ValueError):
vdf.populate(on_error='blah')
# check basic populate worked
utils.assert_dict_equal(vdf, QUERY_RESULTC, utils.assert_flag_equal)
# check padded populate worked
utils.assert_flag_equal(vdf2[flag], QUERY_RESULTC[flag].pad(-1, 1))
# check segment-restricted populate worked
for flag in vdf3:
utils.assert_segmentlist_equal(vdf3[flag].known,
QUERY_RESULTC[flag].known & span)
utils.assert_segmentlist_equal(vdf3[flag].active,
QUERY_RESULTC[flag].active & span)
def test_populate(self):
def fake():
return self.TEST_CLASS({
x: self.ENTRY_CLASS(name=x, known=y.known) for
x, y in QUERY_RESULT.items()})
# build fake veto definer file
vdf = fake()
vdf2 = fake()
vdf3 = fake()
flag = QUERY_FLAGS[0]
vdf2[flag].padding = (-1, 1)
span = SegmentList([Segment(0, 2)])
# and populate using a mocked query
with mock.patch('dqsegdb.apicalls.dqsegdbQueryTimes',
mocks.dqsegdb_query_times(QUERY_RESULT)):
vdf.populate()
vdf2.populate()
vdf3.populate(segments=span)
# test warnings on bad entries
vdf['TEST'] = self.ENTRY_CLASS('X1:BLAHBLAHBLAH:1', known=[(0, 1)])
with pytest.warns(UserWarning) as record:
vdf.populate(on_error='warn')
vdf.populate(on_error='ignore')
assert len(record) == 1
vdf.pop('TEST')
with pytest.raises(ValueError):
vdf.populate(on_error='blah')
# check basic populate worked
utils.assert_dict_equal(vdf, QUERY_RESULTC, utils.assert_flag_equal)
# check padded populate worked
utils.assert_flag_equal(vdf2[flag], QUERY_RESULTC[flag].pad(-1, 1))
# check segment-restricted populate worked
for flag in vdf3:
utils.assert_segmentlist_equal(
vdf3[flag].known, QUERY_RESULTC[flag].known & span)
utils.assert_segmentlist_equal(
vdf3[flag].active, QUERY_RESULTC[flag].active & span)
def test_query_dqsegdb(self):
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb, QUERY_FLAGS,
0, 10)
RESULT = QUERY_RESULTC
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
# check all values of on_error
with pytest.warns(UserWarning) as record:
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb,
QUERY_FLAGS + ['X1:BLAHBLAH:1'], 0, 10,
on_error='warn')
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb,
QUERY_FLAGS + ['X1:BLAHBLAH:1'], 0, 10,
on_error='ignore')
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
assert len(record) == 1 # check on_error='ignore' didn't warn
with pytest.raises(ValueError):
self.TEST_CLASS.query_dqsegdb(QUERY_FLAGS, 0, 10, on_error='blah')
def test_query_dqsegdb(self):
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb, QUERY_FLAGS, 0,
10)
RESULT = QUERY_RESULTC
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
# check all values of on_error
with pytest.warns(UserWarning) as record:
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb,
QUERY_FLAGS + ['X1:BLAHBLAH:1'],
0,
10,
on_error='warn')
result = query_dqsegdb(self.TEST_CLASS.query_dqsegdb,
QUERY_FLAGS + ['X1:BLAHBLAH:1'],
0,
10,
on_error='ignore')
utils.assert_dict_equal(result, RESULT, utils.assert_flag_equal)
assert len(record) == 1 # check on_error='ignore' didn't warn
with pytest.raises(ValueError):
self.TEST_CLASS.query_dqsegdb(QUERY_FLAGS, 0, 10, on_error='blah')
def test_sub(self, instance, reverse):
a = instance.copy()
a -= reverse
utils.assert_dict_equal(a, instance - reverse, utils.assert_flag_equal)
def _assert(a, b):
return utils.assert_dict_equal(a, b, utils.assert_flag_equal)
def test_invert(self, instance):
inverse = type(instance)()
for key in instance:
inverse[key] = ~instance[key]
utils.assert_dict_equal(~instance, inverse, utils.assert_flag_equal)
def test_xor(self, instance, reverse):
a = instance.copy(deep=True)
a ^= reverse
utils.assert_dict_equal(a, instance ^ reverse, utils.assert_flag_equal)
def test_sub(self, instance, reverse):
a = instance.copy(deep=True)
a -= reverse
utils.assert_dict_equal(a, instance - reverse, utils.assert_flag_equal)
def test_or(self, instance, reverse):
a = instance.copy()
a |= reverse
utils.assert_dict_equal(a, instance | reverse, utils.assert_flag_equal)
def test_or(self, instance, reverse):
a = instance.copy()
a |= reverse
utils.assert_dict_equal(a, instance | reverse, utils.assert_flag_equal)
def test_query_segdb(self):
result = query_segdb(self.TEST_CLASS.query_segdb, QUERY_FLAGS, 0, 10)
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, QUERY_RESULT, utils.assert_flag_equal)
def test_query_segdb(self):
result = query_segdb(self.TEST_CLASS.query_segdb, QUERY_FLAGS, 0, 10)
assert isinstance(result, self.TEST_CLASS)
utils.assert_dict_equal(result, QUERY_RESULT, utils.assert_flag_equal)
def test_invert(self, instance):
inverse = type(instance)()
for key in instance:
inverse[key] = ~instance[key]
utils.assert_dict_equal(~instance, inverse, utils.assert_flag_equal)
def _assert(a, b):
return utils.assert_dict_equal(a, b, utils.assert_flag_equal)
def test_and(self, instance, reverse):
a = instance.copy()
a &= reverse
utils.assert_dict_equal(a, instance & reverse, utils.assert_flag_equal)
def test_and(self, instance, reverse):
a = instance.copy()
a &= reverse
utils.assert_dict_equal(a, instance & reverse, utils.assert_flag_equal)
