def test_3_get_sample_ids(self):
"""Test getting sample ids given flowcell and sample_prj"""
sample_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
sample_ids = sample_con.get_sample_ids(fc_id=self.examples["flowcell"])
print "Number of samples before subsetting: " + str(len(sample_ids))
sample_ids = sample_con.get_sample_ids(fc_id=self.examples["flowcell"], sample_prj=self.examples["project"])
print "Number of samples after subsetting: " + str(len(sample_ids))
def test_get_sample_ids(self):
"""Test getting sample ids given flowcell and sample_prj"""
sample_con = SampleRunMetricsConnection(dbname="samples-test", username=self.user, password=self.pw, url=self.url)
sample_ids = sample_con.get_sample_ids(fc_id=self.examples["flowcell"])
LOG.info("Number of samples before subsetting: " + str(len(sample_ids)))
self.assertEqual(len(sample_ids), 5)
sample_ids = sample_con.get_sample_ids(fc_id=self.examples["flowcell"], sample_prj=self.examples["project"])
LOG.info( "Number of samples after subsetting: " + str(len(sample_ids)))
self.assertEqual(len(sample_ids), 2)
def test_get_sample_ids(self):
"""Test getting sample ids given flowcell and sample_prj"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
sample_ids = sample_con.get_sample_ids(fc_id=self.examples["flowcell"])
LOG.info("Number of samples before subsetting: " +
str(len(sample_ids)))
self.assertEqual(len(sample_ids), 5)
sample_ids = sample_con.get_sample_ids(
fc_id=self.examples["flowcell"],
sample_prj=self.examples["project"])
LOG.info("Number of samples after subsetting: " + str(len(sample_ids)))
self.assertEqual(len(sample_ids), 2)
def test_get_project_sample_ids(self):
"""Test getting project sample ids"""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
sample_ids = sample_con.get_sample_ids(sample_prj=self.examples["project"])
sample_names = [sample_con.db.get(x)["name"] for x in sample_ids]
self.assertEqual(
set(sample_names),
set(["1_120924_AC003CCCXX_TGACCA", "2_120924_AC003CCCXX_ACAGTG", "1_121015_BB002BBBXX_TGACCA"]),
)
def test_get_project_sample_ids(self):
"""Test getting project sample ids"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
sample_ids = sample_con.get_sample_ids(
sample_prj=self.examples["project"])
sample_names = [sample_con.db.get(x)["name"] for x in sample_ids]
self.assertEqual(
set(sample_names),
set([
'1_120924_AC003CCCXX_TGACCA', '2_120924_AC003CCCXX_ACAGTG',
'1_121015_BB002BBBXX_TGACCA'
]))
