def mark_causative(institute_id,
case_name,
variant_id,
partial_causative=False):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for("variant.variant",
institute_id=institute_id,
case_name=case_name,
variant_id=variant_id)
if request.form["action"] == "ADD":
if "partial_causative" in request.form:
omim_terms = request.form.getlist("omim_select")
hpo_terms = request.form.getlist("hpo_select")
store.mark_partial_causative(institute_obj, case_obj, user_obj,
link, variant_obj, omim_terms,
hpo_terms)
else:
store.mark_causative(institute_obj, case_obj, user_obj, link,
variant_obj)
elif request.form["action"] == "DELETE":
if partial_causative == "True":
store.unmark_partial_causative(institute_obj, case_obj, user_obj,
link, variant_obj)
else:
store.unmark_causative(institute_obj, case_obj, user_obj, link,
variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
return redirect(request.referrer)
def test_causatives(app, user_obj, institute_obj, case_obj):
# GIVEN an initialized app
# GIVEN a valid user and institute
# There should be no causative variants for test case:
assert "causatives" not in case_obj
var1_id = "4c7d5c70d955875504db72ef8e1abe77" # in POT1 gene
var2_id = "e24b65bf27feacec6a81c8e9e19bd5f1" # in TBX1 gene
var_ids = [var1_id, var2_id]
# for each variant
for var_id in var_ids:
# update case by marking variant as causative:
variant_obj = store.variant(document_id=var_id)
store.mark_causative(
institute=institute_obj,
case=case_obj,
user=user_obj,
link="causative_var_link/{}".format(variant_obj["_id"]),
variant=variant_obj,
)
updated_case = store.case_collection.find_one({"_id": case_obj["_id"]})
# The above variants should be registered as causatives in case object
assert updated_case["causatives"] == var_ids
# Call scout causatives view and check if the above causatives are displayed
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
assert resp.status_code == 200
# WHEN accessing the case page
resp = client.get(
url_for("overview.causatives",
institute_id=institute_obj["internal_id"]))
# THEN it should return a page
assert resp.status_code == 200
# with variant 1
assert var1_id in str(resp.data)
# and variant 2
assert var2_id in str(resp.data)
# Filter causatives by gene (POT1)
resp = client.get(
url_for(
"overview.causatives",
institute_id=institute_obj["internal_id"],
query="17284 | POT1 (DKFZp586D211, hPot1, POT1)",
))
# THEN it should return a page
assert resp.status_code == 200
# with variant 1
assert var1_id in str(resp.data)
# but NOT variant 2
assert var2_id not in str(resp.data)
def mark_causative(institute_id, case_name, variant_id):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.mark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unmark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
return redirect(case_url)
def mark_causative(institute_id, case_name, variant_id):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.mark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unmark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
return redirect(case_url)