def test_filter_single_subset_exclude(self):
exps = [(None, ['sample2']), ("Study='A'", ['sample2']),
("Study='A' OR Study='B'", ['sample2'])]
for (where, exp) in exps:
dir_fmt = filter_samples(self.sample_single, self.md_single_subset,
where, True)
self._assert_single_contains(dir_fmt, exp)
def test_filter_paired_subset(self):
exps = [(None, ['sample1R1', 'sample1R2']),
("Study='A'", ['sample1R1', 'sample1R2']),
("Study='A' OR Study='B'", ['sample1R1', 'sample1R2'])]
for (where, exp) in exps:
dir_fmt = filter_samples(self.sample_paired,
self.md_paired_subset, where, False)
self._assert_paired_contains(dir_fmt, exp)
def test_filter_single_all(self):
exps = [(None, ['sample1', 'sample2']), ("Study='A'", ['sample1']),
("Study='B'", ['sample2']),
("Study='A' OR Study='B'", ['sample1', 'sample2'])]
for (where, exp) in exps:
dir_fmt = filter_samples(self.sample_single, self.md_single_all,
where, False)
self._assert_single_contains(dir_fmt, exp)
def test_filter_paired_all_exclude(self):
exps = [(None, []), ("Study='A'", ['sample2R1', 'sample2R2']),
("Study='B'", ['sample1R1', 'sample1R2']),
("Study='A' OR Study='B'", [])]
for (where, exp) in exps:
dir_fmt = filter_samples(self.sample_paired, self.md_paired_all,
where, True)
self._assert_paired_contains(dir_fmt, exp)
def test_filter_single_subset_no_filter(self):
wheres = ["Study='B'", "Study='A' AND Study='B'"]
for where in wheres:
with self.assertRaisesRegex(ValueError, 'No'):
filter_samples(self.sample_single, self.md_single_subset,
where, False)
def test_filter_paired_none_exclude_no_filter(self):
wheres = ["Study='B'", "Study='A' AND Study='B'"]
for where in wheres:
with self.assertRaisesRegex(ValueError, 'No'):
filter_samples(self.sample_paired, self.md_paired_none, where,
True)
def test_filter_paired_id_not_present(self):
wheres = [None, "Study='A'", "Study='A' OR Study='B'"]
for where in wheres:
with self.assertRaisesRegex(ValueError, '1'):
filter_samples(self.sample_paired, self.md_paired_none, where,
False)
