def test_natsort_keygen_splits_input_with_locale():
load_locale('en_US')
strxfrm = get_strxfrm()
with patch('natsort.compat.locale.dumb_sort', return_value=False):
assert natsort_keygen(alg=ns.L)(INPUT) == ((null_string_locale, 6, strxfrm('A-'), 5, strxfrm('.'), 34, strxfrm('e+'), 1), (strxfrm('/Folder ('), 1, strxfrm(')/Foo')), (null_string_locale, 56.7))
with patch('natsort.compat.locale.dumb_sort', return_value=True):
assert natsort_keygen(alg=ns.L)(INPUT) == ((null_string_locale, 6, strxfrm('aa--'), 5, strxfrm('..'), 34, strxfrm('eE++'), 1), (strxfrm('//ffoOlLdDeErR (('), 1, strxfrm('))//ffoOoO')), (null_string_locale, 56.7))
if PY_VERSION >= 3: assert natsort_keygen(alg=ns.LA)(b'6A-5.034e+1') == (b'6A-5.034e+1',)
locale.setlocale(locale.LC_ALL, str(''))
def test_natsort_keygen_splits_input_with_locale_and_capitalfirst():
load_locale('en_US')
strxfrm = get_strxfrm()
with patch('natsort.compat.locale.dumb_sort', return_value=False):
assert natsort_keygen(alg=ns.LA | ns.C)(INPUT) == ((('',), (null_string_locale, 6, strxfrm('A-'), 5, strxfrm('.'), 34, strxfrm('e+'), 1)), (('/',), (strxfrm('/Folder ('), 1, strxfrm(')/Foo'))), (('',), (null_string_locale, 56.7)))
if PY_VERSION >= 3: assert natsort_keygen(alg=ns.LA | ns.C)(b'6A-5.034e+1') == (b'6A-5.034e+1',)
locale.setlocale(locale.LC_ALL, str(''))
def test_sort_and_print_entries_excludes_paths_between_of_20_to_100_with_reverse_filter_option():
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a130/path1
sort_and_print_entries(entries, Args(None, [(20, 100)], False, True, False))
e = [call(entries[i]) for i in [2, 3, 4]]
p.assert_has_calls(e)
def test_fetch(self):
try:
nds_buffer = mockutils.mock_nds2_buffer(
'X1:TEST', self.data, 1000000000, self.data.shape[0], 'm')
except ImportError as e:
self.skipTest(str(e))
nds_connection = mockutils.mock_nds2_connection([nds_buffer])
with mock.patch('nds2.connection') as mock_connection, \
mock.patch('nds2.buffer', nds_buffer):
mock_connection.return_value = nds_connection
# use verbose=True to hit more lines
ts = TimeSeries.fetch('X1:TEST', 1000000000, 1000000001,
verbose=True)
nptest.assert_array_equal(ts.value, self.data)
self.assertEqual(ts.sample_rate, self.data.shape[0] * units.Hz)
self.assertTupleEqual(ts.span, (1000000000, 1000000001))
self.assertEqual(ts.unit, units.meter)
def test_fetch(self):
try:
nds_buffer = mockutils.mock_nds2_buffer(
'X1:TEST', self.data, 1000000000, self.data.shape[0], 'm')
except ImportError as e:
self.skipTest(str(e))
nds_connection = mockutils.mock_nds2_connection([nds_buffer])
with mock.patch('nds2.connection') as mock_connection, \
mock.patch('nds2.buffer', nds_buffer):
mock_connection.return_value = nds_connection
# use verbose=True to hit more lines
ts = TimeSeries.fetch('X1:TEST', 1000000000, 1000000001,
verbose=True)
nptest.assert_array_equal(ts.value, self.data)
self.assertEqual(ts.sample_rate, self.data.shape[0] * units.Hz)
self.assertTupleEqual(ts.span, (1000000000, 1000000001))
self.assertEqual(ts.unit, units.meter)
def test_sort_and_print_entries_keeps_only_paths_between_of_20_to_100_with_filter_option():
with patch(mock_print) as p:
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
sort_and_print_entries(entries, Args([(20, 100)], None, False, False, False))
e = [call(entries[i]) for i in [1, 0, 5, 6]]
p.assert_has_calls(e)
def test_natsort_keygen_splits_input_with_locale():
load_locale("en_US")
strxfrm = get_strxfrm()
with patch("natsort.compat.locale.dumb_sort", return_value=False):
assert natsort_keygen(alg=ns.L)(INPUT) == (
(null_string, 6, strxfrm("A-"), 5, strxfrm("."), 34, strxfrm("e+"), 1),
(strxfrm("/Folder ("), 1, strxfrm(")/Foo")),
(null_string, 56.7),
)
with patch("natsort.compat.locale.dumb_sort", return_value=True):
assert natsort_keygen(alg=ns.L)(INPUT) == (
(null_string, 6, strxfrm("aa--"), 5, strxfrm(".."), 34, strxfrm("eE++"), 1),
(strxfrm("//ffoOlLdDeErR (("), 1, strxfrm("))//ffoOoO")),
(null_string, 56.7),
)
if PY_VERSION >= 3:
assert natsort_keygen(alg=ns.LA)(b"6A-5.034e+1") == (b"6A-5.034e+1",)
locale.setlocale(locale.LC_ALL, str(""))
def test_sort_and_print_entries_excludes_paths_between_of_20_to_100_with_reverse_filter_option(
):
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a130/path1
sort_and_print_entries(entries,
Args(None, [(20, 100)], False, True, False))
e = [call(entries[i]) for i in [2, 3, 4]]
p.assert_has_calls(e)
def test_sort_and_print_entries_excludes_paths_23_or_130_with_exclude_option_list():
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
sort_and_print_entries(entries, Args(None, None, [23, 130], True, False))
e = [call(entries[i]) for i in [2, 3, 0, 5, 6]]
p.assert_has_calls(e)
def test__keys_are_being_cached():
natcmp.cached_keys = {}
assert len(natcmp.cached_keys) == 0
natcmp(0, 0)
assert len(natcmp.cached_keys) == 1
natcmp(0, 0)
assert len(natcmp.cached_keys) == 1
with patch('natsort.compat.locale.dumb_sort', return_value=False):
natcmp(0, 0, alg=ns.L)
assert len(natcmp.cached_keys) == 2
natcmp(0, 0, alg=ns.L)
assert len(natcmp.cached_keys) == 2
with patch('natsort.compat.locale.dumb_sort', return_value=True):
natcmp(0, 0, alg=ns.L)
assert len(natcmp.cached_keys) == 3
natcmp(0, 0, alg=ns.L)
assert len(natcmp.cached_keys) == 3
def test_iter_channel_names(self):
# maybe need something better?
from types import GeneratorType
names = gwf.iter_channel_names(TEST_GWF_FILE)
self.assertIsInstance(names, GeneratorType)
self.assertSequenceEqual(list(names), TEST_CHANNELS)
with mock.patch('gwpy.utils.shell.call', mock_call):
names = gwf.iter_channel_names(TEST_GWF_FILE)
self.assertIsInstance(names, GeneratorType)
self.assertSequenceEqual(list(names), TEST_CHANNELS)
def test_iter_channel_names(self):
# maybe need something better?
from types import GeneratorType
names = datafind.iter_channel_names(TEST_GWF_FILE)
self.assertIsInstance(names, GeneratorType)
self.assertSequenceEqual(list(names), TEST_CHANNELS)
with mock.patch('gwpy.utils.shell.call', mock_call):
names = datafind.iter_channel_names(TEST_GWF_FILE)
self.assertIsInstance(names, GeneratorType)
self.assertSequenceEqual(list(names), TEST_CHANNELS)
def test_sort_and_print_entries_keeps_only_paths_between_of_20_to_100_with_filter_option(
):
with patch(mock_print) as p:
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
sort_and_print_entries(entries,
Args([(20, 100)], None, False, False, False))
e = [call(entries[i]) for i in [1, 0, 5, 6]]
p.assert_has_calls(e)
def test_sort_and_print_entries_excludes_paths_23_or_130_with_exclude_option_list(
):
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
sort_and_print_entries(entries, Args(None, None, [23, 130], True,
False))
e = [call(entries[i]) for i in [2, 3, 0, 5, 6]]
p.assert_has_calls(e)
def _mock_query_versionless(self, cm, result, *args, **kwargs):
"""Query for segments using a mock of the dqsegdb API
"""
try:
return cm(*args, **kwargs)
except (UnboundLocalError, AttributeError, URLError) as e:
warnings.warn("Test query failed with %s: %s, "
"rerunning with mock..." %
(type(e).__name__, str(e)))
with mock.patch('dqsegdb.apicalls.dqsegdbCascadedQuery',
mockutils.mock_dqsegdb_cascaded_query(result)):
return cm(*args, **kwargs)
def test_natsort_keygen_splits_input_with_locale_and_capitalfirst():
load_locale("en_US")
strxfrm = get_strxfrm()
with patch("natsort.compat.locale.dumb_sort", return_value=False):
assert natsort_keygen(alg=ns.LA | ns.C)(INPUT) == (
(("",), (null_string, 6, strxfrm("A-"), 5, strxfrm("."), 34, strxfrm("e+"), 1)),
(("/",), (strxfrm("/Folder ("), 1, strxfrm(")/Foo"))),
(("",), (null_string, 56.7)),
)
if PY_VERSION >= 3:
assert natsort_keygen(alg=ns.LA | ns.C)(b"6A-5.034e+1") == (b"6A-5.034e+1",)
locale.setlocale(locale.LC_ALL, str(""))
def test_randomly_selects_correct_amount_of_items(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam', 10, 'chr1:1-10',
)
self.assertEqual(set(self.samview_lines), r)
def test_sort_and_print_entries_reverses_order_with_reverse_option():
with patch(mock_print) as p:
# tmp/a130/path1
# tmp/a64/path2
# tmp/a64/path1
# tmp/a57/path2
# tmp/a23/path1
# tmp/a1 (1)/path1
# tmp/a1/path1
sort_and_print_entries(entries, Args(None, None, False, True, True))
e = [call(entries[i]) for i in reversed([2, 3, 1, 0, 5, 6, 4])]
p.assert_has_calls(e)
def test_sort_and_print_entries_uses_default_algorithm_with_all_options_false():
with patch(mock_print) as p:
# tmp/a1 (1)/path1
# tmp/a1/path1
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
# tmp/a130/path1
sort_and_print_entries(entries, Args(None, None, False, False, False))
e = [call(entries[i]) for i in [3, 2, 1, 0, 5, 6, 4]]
p.assert_has_calls(e)
def _mock_query_versionless(self, cm, result, *args, **kwargs):
"""Query for segments using a mock of the dqsegdb API
"""
try:
return cm(*args, **kwargs)
except (UnboundLocalError, AttributeError, URLError) as e:
warnings.warn("Test query failed with %s: %s, "
"rerunning with mock..."
% (type(e).__name__, str(e)))
with mock.patch('dqsegdb.apicalls.dqsegdbCascadedQuery',
mockutils.mock_dqsegdb_cascaded_query(result)):
return cm(*args, **kwargs)
def test_sort_and_print_entries_uses_PATH_algorithm_with_path_option_true_to_properly_sort_OS_generated_path_names():
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
# tmp/a130/path1
sort_and_print_entries(entries, Args(None, None, False, True, False))
e = [call(entries[i]) for i in [2, 3, 1, 0, 5, 6, 4]]
p.assert_has_calls(e)
def test_sort_and_print_entries_reverses_order_with_reverse_option():
with patch(mock_print) as p:
# tmp/a130/path1
# tmp/a64/path2
# tmp/a64/path1
# tmp/a57/path2
# tmp/a23/path1
# tmp/a1 (1)/path1
# tmp/a1/path1
sort_and_print_entries(entries, Args(None, None, False, True, True))
e = [call(entries[i]) for i in reversed([2, 3, 1, 0, 5, 6, 4])]
p.assert_has_calls(e)
def test_handles_missing_depth_error(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam', 11, 'chr1:1-10',
)
self.assertEqual(set([]), r)
for i in range(1,11):
msys.stderr.write.assert_has_call('Depth for chr1:{0}-{0} is only 10\n'.format(i))
def test_missing_samtools(self, margparser, msys, mpool):
mpool.return_value.map = map
args = mock.Mock()
margparser.return_value.parse_args.return_value = args
args.bamfile = 'foo.bam'
args.subsample = 10
args.regionstr = 'chr1:1-10'
with mock.patch('subsamplebam.samtools_is_available') as mocky:
mocky.return_value = False
msys.exit.side_effect = SystemExit
self.assertRaises(SystemExit, subsamplebam.main)
def test_sort_and_print_entries_uses_PATH_algorithm_with_path_option_true_to_properly_sort_OS_generated_path_names(
):
with patch(mock_print) as p:
# tmp/a1/path1
# tmp/a1 (1)/path1
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
# tmp/a130/path1
sort_and_print_entries(entries, Args(None, None, False, True, False))
e = [call(entries[i]) for i in [2, 3, 1, 0, 5, 6, 4]]
p.assert_has_calls(e)
def test_missing_samtools(self, margparser, msys, mpool):
mpool.return_value.map = map
args = mock.Mock()
margparser.return_value.parse_args.return_value = args
args.bamfile = 'foo.bam'
args.subsample = 10
args.regionstr = 'chr1:1-10'
with mock.patch('subsamplebam.samtools_is_available') as mocky:
mocky.return_value = False
msys.exit.side_effect = SystemExit
self.assertRaises(SystemExit, subsamplebam.main)
def test_sort_and_print_entries_uses_default_algorithm_with_all_options_false(
):
with patch(mock_print) as p:
# tmp/a1 (1)/path1
# tmp/a1/path1
# tmp/a23/path1
# tmp/a57/path2
# tmp/a64/path1
# tmp/a64/path2
# tmp/a130/path1
sort_and_print_entries(entries, Args(None, None, False, False, False))
e = [call(entries[i]) for i in [3, 2, 1, 0, 5, 6, 4]]
p.assert_has_calls(e)
def test_main_passes_default_arguments_with_no_command_line_options():
with patch('natsort.__main__.sort_and_print_entries') as p:
sys.argv[1:] = ['num-2', 'num-6', 'num-1']
main()
args = p.call_args[0][1]
assert not args.paths
assert args.filter is None
assert args.reverse_filter is None
assert args.exclude is None
assert not args.reverse
assert args.number_type == 'int'
assert not args.signed
assert args.exp
assert not args.locale
def test_main_passes_default_arguments_with_no_command_line_options():
with patch('natsort.__main__.sort_and_print_entries') as p:
sys.argv[1:] = ['num-2', 'num-6', 'num-1']
main()
args = p.call_args[0][1]
assert not args.paths
assert args.filter is None
assert args.reverse_filter is None
assert args.exclude is None
assert not args.reverse
assert args.number_type == 'int'
assert not args.signed
assert args.exp
assert not args.locale
def test_randomly_selects_correct_amount_of_items(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[
1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[
0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam',
10,
'chr1:1-10',
)
self.assertEqual(set(self.samview_lines), r)
def test_handles_missing_depth_error(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[
1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[
0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam',
11,
'chr1:1-10',
)
self.assertEqual(set([]), r)
for i in range(1, 11):
msys.stderr.write.assert_has_call(
'Depth for chr1:{0}-{0} is only 10\n'.format(i))
def test_main_passes_arguments_with_all_command_line_options():
with patch('natsort.__main__.sort_and_print_entries') as p:
sys.argv[1:] = ['--paths', '--reverse', '--locale',
'--filter', '4', '10',
'--reverse-filter', '100', '110',
'--number-type', 'float', '--noexp', '--sign',
'--exclude', '34', '--exclude', '35',
'num-2', 'num-6', 'num-1']
main()
args = p.call_args[0][1]
assert args.paths
assert args.filter == [(4.0, 10.0)]
assert args.reverse_filter == [(100.0, 110.0)]
assert args.exclude == [34, 35]
assert args.reverse
assert args.number_type == 'float'
assert args.signed
assert not args.exp
assert args.locale
def test_main_passes_arguments_with_all_command_line_options():
with patch('natsort.__main__.sort_and_print_entries') as p:
sys.argv[1:] = [
'--paths', '--reverse', '--locale', '--filter', '4', '10',
'--reverse-filter', '100', '110', '--number-type', 'float',
'--noexp', '--sign', '--exclude', '34', '--exclude', '35', 'num-2',
'num-6', 'num-1'
]
main()
args = p.call_args[0][1]
assert args.paths
assert args.filter == [(4.0, 10.0)]
assert args.reverse_filter == [(100.0, 110.0)]
assert args.exclude == [34, 35]
assert args.reverse
assert args.number_type == 'float'
assert args.signed
assert not args.exp
assert args.locale