class CoreDbTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run = (
u"2015-10-11", u"HiSeq", u"Nextera XT", 1,
u"run_file.fastq", u"Bob's run",
)
self.run_acc = self.db.register_run(*self.run)
self.sample_bcs = [
("Sample1", "ABC"),
("Sample2", "DEF"),
("My.Sample3", "GHI"),
]
self.single_sample = self.sample_bcs[0]
self.annotations = {
"SampleType": "Oral swab",
"SubjectID": "Subj23",
"study_group": "Healthy",
"study_day": "1",
}
def test_register_run(self):
self.assertEqual(self.run_acc, 1)
self.assertTrue(self.db.query_run_exists(self.run_acc))
obs_run = self.db._query_run(self.run_acc)
self.assertEqual(self.run, obs_run)
# Registering the run twice should raise an error
self.assertRaises(ValueError, self.db.register_run, *self.run)
def test_query_run_exists(self):
self.assertTrue(self.db.query_run_exists(1))
def test_register_samples(self):
# Here, accessions given by database cursor. In other tests,
# we double-check that we can actually find the samples in a
# query
registered_accessions = self.db.register_samples(
1, self.sample_bcs)
self.assertEqual(registered_accessions, [1, 2, 3])
# Registering the samples again should raise an error
self.assertRaises(
ValueError, self.db.register_samples, 1, self.sample_bcs)
def test_query_barcoded_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_barcoded_sample_accessions(1, self.sample_bcs),
[1, 2, 3])
def test_query_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_sample_accessions(1), [1, 2, 3])
def test_remove_samples(self):
self.db.register_samples(1, self.sample_bcs)
self.db.remove_samples([1, 2, 3])
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_register_and_remove_annotations(self):
sample_accessions = self.db.register_samples(1, self.sample_bcs)
for acc in sample_accessions:
ann = [(acc, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.db.remove_annotations(sample_accessions)
for acc in sample_accessions:
self.assertEqual(
self.db.query_sample_annotations(acc), {})
def test_register_and_query_annotations(self):
self.db.register_samples(1, [("Sample1", "GGCCTT")])
ann = [(1, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.assertEqual(
self.db.query_sample_annotations(1), self.annotations)
def test_collect_standard_annotations(self):
a = [
(1, "SampleType", "a"),
(1, "HostSpecies", "b"),
(2, "SubjectID", "c"),
]
obs = CoreDb._collect_standard_annotations(a)
self.assertEqual(obs, {1: ["a", None, "b"], 2: [None, "c", None]})
class CoreDbTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run = (
u"2015-10-11",
u"HiSeq",
u"Nextera XT",
1,
u"run_file.fastq",
u"Bob's run",
)
self.run_acc = self.db.register_run(*self.run)
self.sample_bcs = [
("Sample1", "ABC"),
("Sample2", "DEF"),
("My.Sample3", "GHI"),
]
self.single_sample = self.sample_bcs[0]
self.annotations = {
"SampleType": "Oral swab",
"SubjectID": "Subj23",
"study_group": "Healthy",
"study_day": "1",
}
def test_register_run(self):
self.assertEqual(self.run_acc, 1)
self.assertTrue(self.db.query_run_exists(self.run_acc))
obs_run = self.db._query_run(self.run_acc)
self.assertEqual(self.run, obs_run)
# Registering the run twice should raise an error
self.assertRaises(ValueError, self.db.register_run, *self.run)
def test_query_run_exists(self):
self.assertTrue(self.db.query_run_exists(1))
def test_register_samples(self):
# Here, accessions given by database cursor. In other tests,
# we double-check that we can actually find the samples in a
# query
registered_accessions = self.db.register_samples(1, self.sample_bcs)
self.assertEqual(registered_accessions, [1, 2, 3])
# Registering the samples again should raise an error
self.assertRaises(ValueError, self.db.register_samples, 1,
self.sample_bcs)
def test_query_barcoded_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_barcoded_sample_accessions(1, self.sample_bcs),
[1, 2, 3])
def test_query_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(self.db.query_sample_accessions(1), [1, 2, 3])
def test_remove_samples(self):
self.db.register_samples(1, self.sample_bcs)
self.db.remove_samples([1, 2, 3])
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_register_and_remove_annotations(self):
sample_accessions = self.db.register_samples(1, self.sample_bcs)
for acc in sample_accessions:
ann = [(acc, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.db.remove_annotations(sample_accessions)
for acc in sample_accessions:
self.assertEqual(self.db.query_sample_annotations(acc), {})
def test_register_and_query_annotations(self):
self.db.register_samples(1, [("Sample1", "GGCCTT")])
ann = [(1, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.assertEqual(self.db.query_sample_annotations(1), self.annotations)
def test_collect_standard_annotations(self):
a = [
(1, "SampleType", "a"),
(1, "HostSpecies", "b"),
(2, "SubjectID", "c"),
]
obs = CoreDb._collect_standard_annotations(a)
self.assertEqual(obs, {1: ["a", None, "b"], 2: [None, "c", None]})
