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_delete_individual_for_user(_nondemo_client):
# creates an individual
individual = Individual()
test_external_id = "for_test_Sample"
individual.external_id = test_external_id
individual.sex = "M"
response = _nondemo_client.post("/individual", json=[individual.as_dict()], content_type="application/json")
assert response.status_code == 200
# confirms existence of new individual
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"
# deletes individual
response = _nondemo_client.delete(
f"/individual/{observed_individual.phenopolis_id}", content_type="application/json"
)
assert response.status_code == 200
# confirms it does not exist
observed_individual = db_session.query(Individual).filter(Individual.external_id == test_external_id).first()
assert observed_individual is None, "Deletion was not successful"
# try to delete non-existent individual
response = _nondemo_client.delete("/individual/PH00000000", content_type="application/json")
assert response.status_code == 404
# try to delete a non-authorised patient for a given user
response = _nondemo_client.delete("/individual/PH00008258", content_type="application/json")
assert response.status_code == 404, "PH00008258 exists but access not authorised"
def _update_individual(consanguinity, gender: Sex, genes, hpos: List[tuple],
individual: Individual):
"""
Updates tables:
phenopolis.individual: col(gender)
phenopolis.individual_feature: col(feature_id) # hpo_ids
phenopolis.individual_gene: col(gene_id) # maps hgnc_symbol -> gene.identifier
given hgnc_symbol MUST exactly match hgnc_symbols in ensembl.gene table otherwise returns []
"""
individual.sex = gender
individual.consanguinity = consanguinity
hpo_ids = [h[0] for h in hpos]
with get_db() as conn:
with conn.cursor() as cur:
cur.execute(
"""
delete from phenopolis.individual_feature where individual_id = %(id)s
and "type" = any('{observed,simplified}');
insert into phenopolis.individual_feature (individual_id, feature_id, type) select %(id)s as individual_id,
unnest(%(hpo_ids)s::int[]) as feature_id, 'observed' as type;
insert into phenopolis.individual_feature (individual_id, feature_id, type) select %(id)s as individual_id,
unnest(%(hpo_ids)s::int[]) as feature_id, 'simplified' as type;
delete from phenopolis.individual_gene where individual_id = %(id)s;
insert into phenopolis.individual_gene (individual_id, gene_id) select %(id)s as individual_id,
identifier from ensembl.gene where hgnc_symbol = any(%(genes)s::text[]) and assembly = %(hga)s;
""",
{
"id": individual.id,
"hpo_ids": hpo_ids,
"genes": genes,
"hga": HG_ASSEMBLY
},
)
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)