def test_create_kits(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
with self.assertRaisesRegex(KeyError, "does not exist"):
admin_repo.create_kits(5, 3, '', ['foo', 'bar'])
non_tmi = admin_repo.create_kits(5, 3, '',
['Project - /J/xL_|Eãt'])
self.assertEqual([
'created',
], list(non_tmi.keys()))
self.assertEqual(len(non_tmi['created']), 5)
for obj in non_tmi['created']:
self.assertEqual(len(obj['sample_barcodes']), 3)
self.assertEqual({'kit_id', 'kit_uuid', 'sample_barcodes'},
set(obj))
# should not be present in the ag tables
non_tmi_kits = [k['kit_id'] for k in non_tmi['created']]
with t.cursor() as cur:
cur.execute(
"SELECT supplied_kit_id "
"FROM ag.ag_kit "
"WHERE supplied_kit_id IN %s", (tuple(non_tmi_kits), ))
observed = cur.fetchall()
self.assertEqual(len(observed), 0)
tmi = admin_repo.create_kits(4, 2, 'foo', ['American Gut Project'])
self.assertEqual([
'created',
], list(tmi.keys()))
self.assertEqual(len(tmi['created']), 4)
for obj in tmi['created']:
self.assertEqual(len(obj['sample_barcodes']), 2)
self.assertEqual({'kit_id', 'kit_uuid', 'sample_barcodes'},
set(obj))
self.assertTrue(obj['kit_id'].startswith('foo_'))
# should be present in the ag tables
tmi_kits = [k['kit_id'] for k in tmi['created']]
with t.cursor() as cur:
cur.execute(
"SELECT supplied_kit_id "
"FROM ag.ag_kit "
"WHERE supplied_kit_id IN %s", (tuple(tmi_kits), ))
observed = cur.fetchall()
self.assertEqual(len(observed), 4)
def create_kits(body, token_info):
validate_admin_access(token_info)
number_of_kits = body['number_of_kits']
number_of_samples = body['number_of_samples']
kit_prefix = body.get('kit_id_prefix', None)
projects = body['projects']
with Transaction() as t:
admin_repo = AdminRepo(t)
try:
kits = admin_repo.create_kits(number_of_kits, number_of_samples,
kit_prefix, projects)
except KeyError:
return jsonify(code=422, message="Unable to create kits"), 422
else:
t.commit()
return jsonify(kits), 201
def test_create_kits_success_not_microsetta(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
non_tmi = admin_repo.create_kits(5, 3, '',
[33])
self.assertEqual(['created', ], list(non_tmi.keys()))
self.assertEqual(len(non_tmi['created']), 5)
for obj in non_tmi['created']:
self.assertEqual(len(obj['sample_barcodes']), 3)
self.assertEqual({'kit_id', 'kit_uuid', 'sample_barcodes'},
set(obj))
# should not be present in the ag tables
non_tmi_kits = [k['kit_id'] for k in non_tmi['created']]
with t.cursor() as cur:
cur.execute("SELECT supplied_kit_id "
"FROM ag.ag_kit "
"WHERE supplied_kit_id IN %s",
(tuple(non_tmi_kits),))
observed = cur.fetchall()
self.assertEqual(len(observed), 0)
def test_create_kits_success_is_microsetta(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
tmi = admin_repo.create_kits(4, 2, 'foo',
[1])
self.assertEqual(['created', ], list(tmi.keys()))
self.assertEqual(len(tmi['created']), 4)
for obj in tmi['created']:
self.assertEqual(len(obj['sample_barcodes']), 2)
self.assertEqual({'kit_id', 'kit_uuid', 'sample_barcodes'},
set(obj))
self.assertTrue(obj['kit_id'].startswith('foo_'))
# should be present in the ag tables
tmi_kits = [k['kit_id'] for k in tmi['created']]
with t.cursor() as cur:
cur.execute("SELECT supplied_kit_id "
"FROM ag.ag_kit "
"WHERE supplied_kit_id IN %s",
(tuple(tmi_kits),))
observed = cur.fetchall()
self.assertEqual(len(observed), 4)
def test_create_kits_fail_nonexistent_project(self):
with Transaction() as t:
admin_repo = AdminRepo(t)
with self.assertRaisesRegex(KeyError, "does not exist"):
admin_repo.create_kits(5, 3, '', [10000, 10001])
