def test_clinvar_submissions(app, institute_obj, clinvar_variant,
clinvar_casedata):
""""Test the web page containing the clinvar submissions for an institute"""
# GIVEN an institute with a clinvar submission
store.create_submission(institute_obj["_id"])
open_submission = store.get_open_clinvar_submission(institute_obj["_id"])
submission_with_data = store.add_to_submission(
open_submission["_id"], ([clinvar_variant], [clinvar_casedata]))
assert submission_with_data
# GIVEN an initialized app and a valid user and institute
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 visiting the clinvar submission page (get request)
resp = client.get(
url_for(
"overview.clinvar_submissions",
institute_id=institute_obj["internal_id"],
))
# a successful response should be returned
assert resp.status_code == 200
assert str(submission_with_data["_id"]) in str(resp.data)
def test_rename_clinvar_samples(app, institute_obj, clinvar_variant,
clinvar_casedata):
"""Test the form button triggering the renaming of samples for a clinvar submission"""
# GIVEN an institute with a clinvar submission
store.create_submission(institute_obj["_id"])
open_submission = store.get_open_clinvar_submission(institute_obj["_id"])
submission_with_data = store.add_to_submission(
open_submission["_id"], ([clinvar_variant], [clinvar_casedata]))
assert submission_with_data["_id"]
# GIVEN an initialized app and a valid user
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
case_id = clinvar_casedata["case_id"]
old_name = clinvar_casedata["individual_id"]
form_data = dict(new_name="new_sample_name", )
referer = url_for("overview.clinvar_submissions",
institute_id=institute_obj["internal_id"])
# WHEN the sample name is edited from the submission page (POST request)
resp = client.post(
url_for(
f"overview.clinvar_rename_casedata",
submission=submission_with_data["_id"],
case=case_id,
old_name=old_name,
),
data=form_data,
headers={"referer": referer},
)
# a successful response should be redirect to the submssions page
assert resp.status_code == 302
# And the sample name should have been updated in the database
updated_casedata = store.clinvar_collection.find_one(
{"_id": clinvar_casedata["_id"]})
assert updated_casedata["individual_id"] != clinvar_casedata[
"individual_id"]