def test_create_multiple_individuals(_admin_client):
individual = Individual()
test_external_id = "for_test_Sample"
individual.external_id = test_external_id
individual.sex = "M"
individual.genes = "DRAM2"
individual.observed_features = "HP:0000001"
individual2 = Individual()
test_external_id2 = "for_test_Sample2"
individual2.external_id = test_external_id2
individual2.sex = "F"
response = _admin_client.post(
"/individual", json=[individual.as_dict(), individual2.as_dict()], content_type="application/json"
)
assert response.status_code == 200
with session_scope() as db_session:
observed_individual = db_session.query(Individual).filter(Individual.external_id == test_external_id).first()
assert observed_individual is not None, "Empty newly created individual"
assert observed_individual.sex.name == individual.sex
observed_individual2 = db_session.query(Individual).filter(Individual.external_id == test_external_id2).first()
assert observed_individual2 is not None, "Empty newly created individual"
assert observed_individual2.sex.name == individual2.sex
# cleans the database
_clean_test_individuals(_admin_client, db_session, test_external_id)
_clean_test_individuals(_admin_client, db_session, test_external_id2)
def test_create_individual_existing_individual_fails(_admin_client):
individual = Individual()
test_external_id = "for_test_Sample"
individual.external_id = test_external_id
individual.sex = "M"
individual.genes = "DRAM2,TTLL5"
individual.observed_features = "HP:0000001,HP:0000618"
response = _admin_client.post("/individual", json=[individual.as_dict()], content_type="application/json")
assert response.status_code == 200
with session_scope() as db_session:
observed_individual = db_session.query(Individual).filter(Individual.external_id == test_external_id).first()
assert observed_individual is not None, "Empty newly created individual"
# try to create the same individual again
response = _admin_client.post("/individual", json=[individual.as_dict()], content_type="application/json")
assert response.status_code == 400
# cleans the database
_clean_test_individuals(_admin_client, db_session, test_external_id)
def test_create_individual_with_admin_user(_admin_client, sample, sex):
individual = Individual()
test_external_id = sample
individual.external_id = test_external_id
response = _admin_client.post("/individual", json=[individual.as_dict()], content_type="application/json")
assert response.status_code == 400
assert response.json == {"error": "Null individual", "success": False}, "Sex cannot be null"
individual.sex = sex
individual.consanguinity = "unknown"
individual.genes = "DRAM2"
individual.observed_features = "HP:0000001"
response = _admin_client.post("/individual", json=[Individual().as_dict()], content_type="application/json")
assert response.status_code == 400
assert response.json == {"error": "Null individual", "success": False}, "Empty individual"
response = _admin_client.post("/individual", json={}, content_type="application/json")
assert response.status_code == 400
assert response.json == {"error": "Empty payload or wrong formatting", "success": False}
response = _admin_client.post("/individual", json="not_dict_nor_list", content_type="application/json")
assert response.status_code == 400
assert response.json == {"error": "Payload of unexpected type: <class 'str'>", "success": False}
response = _admin_client.post("/individual", json=[individual.as_dict()], content_type="application/json")
assert response.status_code == 200
with session_scope() as db_session:
observed_individual = db_session.query(Individual).filter(Individual.external_id == test_external_id).first()
phenopolis_id = observed_individual.phenopolis_id
assert observed_individual is not None, "Empty newly created individual"
assert observed_individual.external_id == test_external_id
assert observed_individual.sex.name == individual.sex
assert observed_individual.consanguinity == individual.consanguinity
response = _admin_client.post(
f"/update_patient_data/{phenopolis_id}",
data="genes[]=TTLL5",
content_type="application/x-www-form-urlencoded",
)
assert response.status_code == 200, "Test empty features"
# cleans the database
_clean_test_individuals(_admin_client, db_session, test_external_id)