def backend_add_patient(mongo_db, patient, match_external=False):
"""
Insert or update a patient in patientMatcher database
Args:
mongo_db(pymongo.database.Database)
patient(dict) : a MME patient entity
Returns:
inserted_id(str) : the ID of the inserted patient or None if patient couldn't be saved
"""
modified = None
upserted = None
matching_obj = None
try:
result = mongo_db['patients'].replace_one({'_id': patient['_id']}, patient , upsert=True)
modified = result.modified_count
upserted = result.upserted_id
except Exception as err:
LOG.fatal("Error while inserting a patient into database: {}".format(err))
# this will happen only if patient is added via POST request,
# and if there is a change in patients' collections (new patient or updated patient)
# Matching is not triggered by inserting demo data into database
if match_external and (modified or upserted):
matching_obj = external_matcher(mongo_db, patient)
#save matching object to database
mongo_db['matches'].insert_one(matching_obj)
return modified, upserted, matching_obj
def test_external_matching(database, test_node, gpx4_patients, monkeypatch):
"""Testing the function that trigger patient matching across connected nodes"""
patient = gpx4_patients[0]
# insert test node object in database
database['nodes'].insert_one(test_node)
# insert patient object in database
inserted_ids = backend_add_patient(mongo_db=database,
patient=patient,
match_external=False)
assert inserted_ids
class MockResponse(object):
def __init__(self):
self.status_code = 200
def json(self):
resp = {
"disclaimer": "This is a test disclaimer",
"results": gpx4_patients
}
return resp
def mock_response(*args, **kwargs):
return MockResponse()
monkeypatch.setattr(requests, 'request', mock_response)
ext_m_result = external_matcher(database, patient, test_node['_id'])
assert isinstance(ext_m_result, dict)
assert ext_m_result['data']['patient']['id'] == patient['id']
assert ext_m_result['has_matches'] == True
assert ext_m_result['match_type'] == 'external'
def match_external(database, query_patient, node=None):
"""Trigger an external patient matching for a given patient object"""
# trigger the matching and save the matching id to variable
matching_obj = external_matcher(database, query_patient, node)
# save matching object to database only if there are results or error messages
if matching_obj and (matching_obj.get("has_matches") or matching_obj.get("errors")):
database["matches"].insert_one(matching_obj)
return matching_obj