def test_metrics(mock_app, database, test_client, demo_data_path, match_objs):
"""Testing viewing the list of patients on server for authorized users"""
# load demo data of 50 test patients
inserted_ids = load_demo(demo_data_path, database)
assert len(inserted_ids) == 50 # 50 test cases should be loaded
# load mock matches into database
database.matches.insert_many(match_objs)
results = database.matches.find()
assert len(list(results)) == 3
# send a get request without being authorized
response = mock_app.test_client().get("metrics")
assert response.status_code == 200
data = json.loads(response.data)
assert data["disclaimer"] # disclaimer should be returned
metrics = data["metrics"]
assert metrics["numberOfCases"] == 50
assert metrics["numberOfSubmitters"] > 0
assert metrics["numberOfGenes"] > metrics["numberOfUniqueGenes"]
assert metrics["numberOfVariants"] > metrics["numberOfUniqueVariants"]
assert metrics["numberOfFeatures"] > metrics["numberOfUniqueFeatures"]
assert metrics["numberOfCasesWithDiagnosis"] > 0
assert metrics[
"numberOfUniqueGenesMatched"] == 0 # no gene was provided in match_obj results
assert metrics["numberOfRequestsReceived"] == 2 # Sent 2 requests
assert metrics[
"numberOfPotentialMatchesSent"] == 1 # Just one has returned results
def demodata(ensembl_genes):
"""Adds a set of 50 demo patients to database"""
click.echo('Adding 50 test patients to database..')
click.echo('ENSEMBL GENES IS {}'.format(ensembl_genes))
inserted_ids = load_demo(path_to_json_data=path_to_benchmark_patients, mongo_db=current_app.db,
convert_to_ensembl=ensembl_genes)
click.echo('inserted {} patients into db'.format(len(inserted_ids)))
def test_load_demo_patients(demo_data_path, database):
"""Testing if loading of 50 test patients in database is working as it should"""
# demo data file should be present in the expected directory
assert os.path.isfile(demo_data_path)
# load demo data to mock database using function located under utils/load
inserted_ids = load_demo(demo_data_path, database)
assert len(inserted_ids) == 50 # 50 test cases should be loaded
# make sure that trying to re-insert the same patients will not work
re_inserted_ids = load_demo(demo_data_path, database)
assert len(re_inserted_ids) == 0
# try to call load_demo with an invalid patient file:
inserted_ids = load_demo('this_is_a_fakey_json_file.json', database)
assert len(inserted_ids) == 0
def test_patients(demo_data_path, database):
"""Tests the function that retrieves patient objects"""
# load demo data in mock database
inserted_ids = load_demo(demo_data_path, database)
assert type(inserted_ids) == list
assert len(inserted_ids) == 50 # 50 test cases are loaded
# get all 50 patients available in database
all_patients = list(patients(database=database))
assert len(all_patients) == 50
# test collecting just a few patients:
selected_patients = list(patients(database=database, ids=inserted_ids[:3]))
assert len(inserted_ids[:3]) == 3
assert len(selected_patients) == 3
def test_metrics(mock_app, database, test_client, demo_data_path, match_objs):
"""Testing viewing the list of patients on server for authorized users"""
# send a get request without being authorized
response = mock_app.test_client().get('metrics')
assert response.status_code == 401
# add an authorized client to database
ok_token = test_client['auth_token']
add_node(mongo_db=mock_app.db, obj=test_client, is_client=True)
# make sure that database contains at least one client with auth_token == test_client['auth_token']
clients = mock_app.db['clients'].find({'auth_token': ok_token}).count()
assert clients > 0
# load demo data of 50 test patients
inserted_ids = load_demo(demo_data_path, database)
assert len(inserted_ids) == 50 # 50 test cases should be loaded
# load mock matches into database
database.matches.insert_many(match_objs)
assert database.matches.find().count() == 3
# if a valid token is provided the server should return metrics with patient data and matching results
auth_response = mock_app.test_client().get('metrics',
headers=auth_headers(ok_token))
assert auth_response.status_code == 200
data = json.loads(auth_response.data)
assert data['disclaimer'] # disclaimer should be returned
metrics = data['metrics']
assert metrics['numberOfCases'] == 50
assert metrics['numberOfSubmitters'] > 0
assert metrics['numberOfGenes'] > metrics['numberOfUniqueGenes']
assert metrics['numberOfVariants'] > metrics['numberOfUniqueVariants']
assert metrics['numberOfFeatures'] > metrics['numberOfUniqueFeatures']
assert metrics['numberOfCasesWithDiagnosis'] > 0
assert metrics[
'numberOfUniqueGenesMatched'] == 0 # no gene was provided in match_obj results
assert metrics['numberOfRequestsReceived'] == 2 # Sent 2 requests
assert metrics[
'numberOfPotentialMatchesSent'] == 1 # Just one has returned results
