def test_variant_controller_with_clnsig(app, institute_obj, case_obj):
## GIVEN a populated database with a variant
variant_obj = store.variant_collection.find_one({"clnsig": {"$exists": True}})
assert variant_obj
assert "clinsig_human" not in variant_obj
category = "snv"
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
institute_id = institute_obj["_id"]
case_name = case_obj["display_name"]
var_id = variant_obj["_id"]
## WHEN fetching the variant from the controller
data = variant(
store,
institute_id,
case_name,
variant_id=var_id,
add_case=True,
add_other=True,
get_overlapping=True,
variant_type=category,
)
## THEN assert the data is on correct format
assert "clinsig_human" in data["variant"]
assert data["variant"]["clinsig_human"] is not None
def test_variant_controller(app, institute_obj, case_obj, variant_obj):
## GIVEN a populated database with a variant
category = "snv"
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
institute_id = institute_obj["_id"]
case_name = case_obj["display_name"]
var_id = variant_obj["_id"]
## WHEN fetching the variant from the controller
data = variant(
store,
institute_id,
case_name,
variant_id=var_id,
add_case=True,
add_other=True,
get_overlapping=True,
variant_type=category,
)
## THEN assert the data is on correct format
assert "overlapping_vars" in data
def test_variant_controller_with_compounds(app, institute_obj, case_obj):
## GIVEN a populated database with a variant that have compounds
variant_obj = store.variant_collection.find_one({"compounds": {"$exists": True}})
assert variant_obj
assert isinstance(variant_obj["compounds"], list)
assert len(variant_obj["compounds"]) > 0
category = "snv"
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
institute_id = institute_obj["_id"]
case_name = case_obj["display_name"]
var_id = variant_obj["_id"]
## WHEN fetching the variant from the controller
data = variant(
store,
institute_id,
case_name,
variant_id=var_id,
add_case=True,
add_other=True,
get_overlapping=True,
add_compounds=True,
variant_type=category,
)
## THEN assert that the compounds are sorted
combined_score = None
prev_score = None
for compound in data["variant"]["compounds"]:
combined_score = compound["combined_score"]
if prev_score is None:
prev_score = combined_score
continue
assert combined_score <= prev_score
prev_score = combined_score
