def setUpModule():
"""Create test databases in local server"""
if not has_couchdb:
return
server = couchdb.Server()
## Create databases
for x in DATABASES:
if not server.__contains__(x):
LOG.info("Creating database {}".format(x))
server.create(x)
## Create views for flowcells and samples
for dbname in DATABASES:
dblab = dbname.replace("-test", "")
db = server[dbname]
for k, v in VIEWS[dblab].items():
for title, view in v.items():
viewdef = ViewDefinition(k, title, view)
viewdef.sync(db)
## Create and upload project summary
with open(os.path.join(filedir, "data", "config",
"project_summary.yaml")) as fh:
prj_sum = yaml.load(fh)
db = server["samples-test"]
p_con = ProjectSummaryConnection(dbname="projects-test",
username="******",
password="******")
for p in prj_sum:
prj = ProjectSummaryDocument(**p)
p_con.save(prj, key="project_name")
def setUpModule():
"""Create test databases in local server"""
if not has_couchdb:
return
server = couchdb.Server()
## Create databases
for x in DATABASES:
if not server.__contains__(x):
LOG.info("Creating database {}".format(x))
server.create(x)
## Create views for flowcells and samples
for dbname in DATABASES:
dblab = dbname.replace("-test", "")
db = server[dbname]
for k, v in VIEWS[dblab].items():
for title, view in v.items():
viewdef = ViewDefinition(k, title, view)
viewdef.sync(db)
## Create and upload project summary
with open(os.path.join(filedir, "data", "config", "project_summary.yaml")) as fh:
prj_sum = yaml.load(fh)
db = server["samples-test"]
p_con = ProjectSummaryConnection(dbname="projects-test", username="******", password="******")
for p in prj_sum:
prj = ProjectSummaryDocument(**p)
p_con.save(prj, key="project_name")
class TestDbConnection(unittest.TestCase):
def setUp(self):
self.user = "******"
self.pw = "pw"
self.url = "localhost"
self.examples = {
"sample": "1_120924_AC003CCCXX_TGACCA",
"flowcell": "AC003CCCXX",
"project": "J.Doe_00_01"
}
self.p_con = ProjectSummaryConnection(dbname="projects-test",
username=self.user,
password=self.pw,
url=self.url)
def test_connection(self):
"""Test database connection"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
self.assertEqual(sample_con.url_string,
"http://{}:5984".format(self.url))
def test_get_flowcell(self):
"""Test getting a flowcell for a given sample"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
fc = sample_con.get_entry(self.examples["sample"], "flowcell")
self.assertEqual(str(fc), self.examples["flowcell"])
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_samples(self):
"""Test getting samples given flowcell and sample_prj."""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"])
LOG.info("Selecting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 5)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"],
sample_prj=self.examples["project"])
LOG.info("Selecting on flowcell, subsetting on project: " +
str(len(samples)))
self.assertEqual(len(samples), 2)
samples = sample_con.get_samples(sample_prj=self.examples["project"])
LOG.info("Selecting on project: " + str(len(samples)))
self.assertEqual(len(samples), 3)
samples = sample_con.get_samples(sample_prj=self.examples["project"],
fc_id=self.examples["flowcell"])
LOG.info("Selecting on project, subsetting on flowcell: " +
str(len(samples)))
self.assertEqual(len(samples), 2)
def test_get_samples_wrong_info(self):
"""Test getting samples when either flowcell or project id information is wrong"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
samples = sample_con.get_samples(sample_prj="bogusproject",
fc_id=self.examples["flowcell"])
LOG.info("Selecting on bogus project, subsetting on flowcell: " +
str(len(samples)))
self.assertEqual(len(samples), 0)
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_latest_library_prep(self):
"""Test getting latest library prep"""
prj = self.p_con.get_entry("J.Doe_00_01")
prj['samples']['P001_102']['library_prep']['B'] = {
'sample_run_metrics': {
'2_120924_AC003CCCXX_TTGGAA': None
}
}
self.p_con.save(prj)
preps = self.p_con.get_latest_library_prep(
project_name=self.examples["project"])
srm = [x for l in preps.values() for x in l]
# Make sure A prep not in list
self.assertNotIn('2_120924_AC003CCCXX_ACAGTG', srm)
# Make sure B prep in list
self.assertIn('2_120924_AC003CCCXX_TTGGAA', srm)
# Reset data
prj = self.p_con.get_entry("J.Doe_00_01")
del prj['samples']['P001_102']['library_prep']['B']
self.p_con.save(prj)
def test_get_barcode_lane_statistics(self):
"""Test getting barcode lane statistics from flowcell database"""
fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test",
username="******",
password="******")
# Try getting wrong sample name, should return None
data = fc_con.get_barcode_lane_statistics("J.Doe_00_01",
"P001_101_index6",
"120924_AC003CCCXX", "1")
self.assertEqual(data, (None, None))
data = fc_con.get_barcode_lane_statistics("J.Doe_00_01",
"P001_101_index3",
"120924_AC003CCCXX", "1")
self.assertEqual(data, (u'35.22', u'90.05'))
class TestDbConnection(unittest.TestCase):
def setUp(self):
self.user = "******"
self.pw = "pw"
self.url = "localhost"
self.examples = {"sample": "1_120924_AC003CCCXX_TGACCA", "flowcell": "AC003CCCXX", "project": "J.Doe_00_01"}
self.p_con = ProjectSummaryConnection(
dbname="projects-test", username=self.user, password=self.pw, url=self.url
)
def test_connection(self):
"""Test database connection"""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
self.assertEqual(sample_con.url_string, "http://{}:5984".format(self.url))
def test_get_flowcell(self):
"""Test getting a flowcell for a given sample"""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
fc = sample_con.get_entry(self.examples["sample"], "flowcell")
self.assertEqual(str(fc), self.examples["flowcell"])
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), 4)
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_samples(self):
"""Test getting samples given flowcell and sample_prj."""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"])
LOG.info("Selecting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 4)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"], sample_prj=self.examples["project"])
LOG.info("Selecting on flowcell, subsetting on project: " + str(len(samples)))
self.assertEqual(len(samples), 2)
samples = sample_con.get_samples(sample_prj=self.examples["project"])
LOG.info("Selecting on project: " + str(len(samples)))
self.assertEqual(len(samples), 3)
samples = sample_con.get_samples(sample_prj=self.examples["project"], fc_id=self.examples["flowcell"])
LOG.info("Selecting on project, subsetting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 2)
def test_get_samples_wrong_info(self):
"""Test getting samples when either flowcell or project id information is wrong"""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
samples = sample_con.get_samples(sample_prj="bogusproject", fc_id=self.examples["flowcell"])
LOG.info("Selecting on bogus project, subsetting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 0)
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_latest_library_prep(self):
"""Test getting latest library prep"""
prj = self.p_con.get_entry("J.Doe_00_01")
prj["samples"]["P001_102"]["library_prep"]["B"] = {"sample_run_metrics": {"2_120924_AC003CCCXX_TTGGAA": None}}
self.p_con.save(prj)
preps = self.p_con.get_latest_library_prep(project_name=self.examples["project"])
srm = [x for l in preps.values() for x in l]
# Make sure A prep not in list
self.assertNotIn("2_120924_AC003CCCXX_ACAGTG", srm)
# Make sure B prep in list
self.assertIn("2_120924_AC003CCCXX_TTGGAA", srm)
# Reset data
prj = self.p_con.get_entry("J.Doe_00_01")
del prj["samples"]["P001_102"]["library_prep"]["B"]
self.p_con.save(prj)
class TestDbConnection(unittest.TestCase):
def setUp(self):
self.user = "******"
self.pw = "pw"
self.url = "localhost"
self.examples = {"sample":"1_120924_AC003CCCXX_TGACCA",
"flowcell":"AC003CCCXX",
"project":"J.Doe_00_01"}
self.p_con = ProjectSummaryConnection(dbname="projects-test", username=self.user, password=self.pw, url=self.url)
def test_connection(self):
"""Test database connection"""
sample_con = SampleRunMetricsConnection(dbname="samples-test", username=self.user, password=self.pw, url=self.url)
self.assertEqual(sample_con.url_string, "http://{}:5984".format(self.url))
def test_get_flowcell(self):
"""Test getting a flowcell for a given sample"""
sample_con = SampleRunMetricsConnection(dbname="samples-test", username=self.user, password=self.pw, url=self.url)
fc = sample_con.get_entry(self.examples["sample"], "flowcell")
self.assertEqual(str(fc), self.examples["flowcell"])
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_samples(self):
"""Test getting samples given flowcell and sample_prj."""
sample_con = SampleRunMetricsConnection(dbname="samples-test", username=self.user, password=self.pw, url=self.url)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"])
LOG.info("Selecting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 5)
samples = sample_con.get_samples(fc_id=self.examples["flowcell"], sample_prj=self.examples["project"])
LOG.info("Selecting on flowcell, subsetting on project: " + str(len(samples)))
self.assertEqual(len(samples), 2)
samples = sample_con.get_samples(sample_prj=self.examples["project"])
LOG.info("Selecting on project: " + str(len(samples)))
self.assertEqual(len(samples), 3)
samples = sample_con.get_samples(sample_prj=self.examples["project"], fc_id=self.examples["flowcell"])
LOG.info("Selecting on project, subsetting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 2)
def test_get_samples_wrong_info(self):
"""Test getting samples when either flowcell or project id information is wrong"""
sample_con = SampleRunMetricsConnection(dbname="samples-test", username=self.user, password=self.pw, url=self.url)
samples = sample_con.get_samples(sample_prj="bogusproject", fc_id=self.examples["flowcell"])
LOG.info("Selecting on bogus project, subsetting on flowcell: " + str(len(samples)))
self.assertEqual(len(samples), 0)
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_latest_library_prep(self):
"""Test getting latest library prep"""
prj = self.p_con.get_entry("J.Doe_00_01")
prj['samples']['P001_102']['library_prep']['B'] = {'sample_run_metrics': {'2_120924_AC003CCCXX_TTGGAA': None}}
self.p_con.save(prj)
preps = self.p_con.get_latest_library_prep(project_name=self.examples["project"])
srm = [x for l in preps.values() for x in l]
# Make sure A prep not in list
self.assertNotIn('2_120924_AC003CCCXX_ACAGTG', srm)
# Make sure B prep in list
self.assertIn('2_120924_AC003CCCXX_TTGGAA', srm)
# Reset data
prj = self.p_con.get_entry("J.Doe_00_01")
del prj['samples']['P001_102']['library_prep']['B']
self.p_con.save(prj)
def test_get_barcode_lane_statistics(self):
"""Test getting barcode lane statistics from flowcell database"""
fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="******", password="******")
# Try getting wrong sample name, should return None
data = fc_con.get_barcode_lane_statistics("J.Doe_00_01", "P001_101_index6", "120924_AC003CCCXX", "1")
self.assertEqual(data, (None, None))
data = fc_con.get_barcode_lane_statistics("J.Doe_00_01", "P001_101_index3", "120924_AC003CCCXX", "1")
self.assertEqual(data, (u'35.22', u'90.05'))
