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 clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = clinvar_export(store, institute_id, case_name, variant_id)
if request.method == "GET":
return data
# POST
form_dict = {}
# flatten up HPO and OMIM terms lists into string of keys separated by semicolon
for key, value in request.form.items():
if key.startswith("conditions@") or key.startswith("clin_features@"):
conditions = request.form.getlist(
key) # can be HPO or OMIM conditions
if conditions:
variant_id = key.split("@")[1]
cond_types = []
cond_values = []
for condition in conditions:
cond_types.append(
condition.split("_")[0]) # 'HPO' or 'OMIM'
cond_values.append(
condition.split("_")[1]) # HPO id or OMIM ID
if key.startswith(
"conditions@"
): # Filling in 'condition_id_type' and 'condition_id_value' in variant data
form_dict["@".join(["condition_id_type",
variant_id])] = ";".join(
cond_types) # Flattened list
form_dict["@".join(["condition_id_value",
variant_id])] = ";".join(
cond_values) # Flattened list
elif key.startswith(
"clin_features@"
): # Filling in 'clin_features' in casedata
form_dict["@".join(["clin_features",
variant_id])] = ";".join(
cond_values) # Flattened list
else:
form_dict[key] = value
# A tuple of submission objects (variants and casedata objects):
submission_objects = set_submission_objects(form_dict)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(institute_id)
updated_submission = store.add_to_submission(open_submission["_id"],
submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(
url_for("cases.clinvar_submissions", institute_id=institute_id))
def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(current_user.email, institute_id)
updated_submission = store.add_to_submission(open_submission['_id'], submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(current_user.email, institute_id)
updated_submission = store.add_to_submission(open_submission['_id'], submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
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"]
