def individual(case_id, ind, key, value):
"""Update information on individual level in Scout"""
case_obj = store.case(case_id)
if not case_obj:
click.echo(f"Could not find case {case_id}")
return
individuals = {
ind_info["display_name"]: ind_info
for ind_info in case_obj["individuals"]
}
# If ind name is empty, print available individual names for this case to help the user to build the command
if ind is None:
click.echo(
f"Please specify individual name with '-n' option. Available individuals for this case:{list(individuals.keys())}"
)
return
if ind not in individuals:
click.echo(
f"Could not find individual '{ind}' in case individuals. Available individuals for this case: {list(individuals.keys())}"
)
return
# If key is null or non-valid, print a list of all the keys that can be updated using this function
if key is None or not key in UPDATE_KEYS:
click.echo(
f"Please specify a valid key to update. Valid keys:{ UPDATE_KEYS }"
)
return
if value is None:
click.echo(f"Please specify a file path for key {key}")
return
file_path = Path(value)
# If file is not found on the server, ask if user wants to update the key anyway
if file_path.exists() is False:
click.confirm(
"The provided path was not found on the server, update key anyway?",
abort=True,
)
# perform the update
for ind_obj in case_obj["individuals"]:
if ind_obj["display_name"] == ind:
ind_obj[key] = value
store.update_case(case_obj)
def _update_case(store, case_obj, user_obj, institute_obj, verb):
"""Update case with new sample data, and create an associated event"""
store.update_case(case_obj, keep_date=True)
link = url_for(
"cases.case",
institute_id=institute_obj["_id"],
case_name=case_obj["display_name"],
)
store.create_event(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=link,
category="case",
verb=verb,
subject=case_obj["display_name"],
)
def test_matchmaker_matches(app, institute_obj, case_obj, mme_submission,
user_obj, monkeypatch):
# Given a case object with a MME submission
case_obj["mme_submission"] = mme_submission
store.update_case(case_obj)
res = store.case_collection.find({"mme_submission": {"$exists": True}})
assert sum(1 for i in res) == 1
# Monkeypatch response with MME matches
def mock_matches(*args, **kwargs):
return {"institute": institute_obj, "case": case_obj, "matches": {}}
monkeypatch.setattr(controllers, "mme_matches", mock_matches)
# GIVEN an initialized app
# GIVEN a valid institute and a user with mme_submitter role
store.user_collection.update_one({"_id": user_obj["_id"]},
{"$set": {
"roles": ["mme_submitter"]
}})
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
# Given mock MME connection parameters
current_app.config["MME_URL"] = "http://fakey_mme_url:fakey_port"
current_app.config["MME_TOKEN"] = "test_token"
# WHEN accessing the case page
resp = client.get(
url_for(
"cases.matchmaker_matches",
institute_id=institute_obj["internal_id"],
case_name=case_obj["display_name"],
))
# Then a successful response should be generated
assert resp.status_code == 200
def test_matchmaker_match(app, institute_obj, case_obj, mme_submission,
user_obj, monkeypatch):
# Given a case object with a MME submission
case_obj["mme_submission"] = mme_submission
store.update_case(case_obj)
res = store.case_collection.find({"mme_submission": {"$exists": True}})
assert sum(1 for i in res) == 1
# Monkeypatch response with MME match
def mock_match(*args, **kwargs):
return [{"status_code": 200}]
monkeypatch.setattr(controllers, "mme_match", mock_match)
# GIVEN an initialized app
# GIVEN a valid institute and a user with mme_submitter role
store.user_collection.update_one({"_id": user_obj["_id"]},
{"$set": {
"roles": ["mme_submitter"]
}})
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
# Given mock MME connection parameters
current_app.config["MME_URL"] = "http://fakey_mme_url:fakey_port"
current_app.config["MME_TOKEN"] = "test_token"
# WHEN sending a POST request to match a patient
resp = client.post(
url_for(
"cases.matchmaker_match",
institute_id=institute_obj["internal_id"],
case_name=case_obj["display_name"],
target="mock_node_id",
))
# page redirects in the views anyway, so it will return a 302 code
assert resp.status_code == 302