def add():
"""Add patient to database"""
formatted_patient = controllers.check_request(current_app.db, request)
if isinstance(formatted_patient, int): # some error must have occurred during validation
return controllers.bad_request(formatted_patient)
match_external = False
if controllers.get_nodes(database=current_app.db):
match_external = True
# else import patient to database
modified, inserted, matching_obj= backend_add_patient(mongo_db=current_app.db, patient=formatted_patient,
match_external=match_external)
message = {}
if modified:
message['message'] = 'Patient was successfully updated.'
elif inserted:
message['message'] = 'Patient was successfully inserted into database.'
else:
message['message'] = 'Database content is unchanged.'
# if patient is matching any other patient on other nodes
# and match notifications are on
if current_app.config.get('MAIL_SERVER') and matching_obj and len(matching_obj.get('results')):
# send an email to patient's contact:
notify_match_external(match_obj=matching_obj, admin_email=current_app.config.get('MAIL_USERNAME'),
mail=current_app.mail, notify_complete=current_app.config.get('NOTIFY_COMPLETE'))
resp = jsonify(message)
resp.status_code = 200
return resp
def test_notify_match_external(match_objs, mock_sender, mock_mail):
match_obj = match_objs[0] #an external match object with results
assert match_obj['match_type'] == 'external'
# When calling the function that sends external match notifications
notify_complete = True # test notification of complete patient data by email
notify_match_external(match_obj, mock_sender, mock_mail, notify_complete)
# make sure send method was called
assert mock_mail._send_was_called
# and that mail object message was set correctly
assert mock_mail._message
def match_external(patient_id):
"""Trigger a patient matching on external nodes by providing a patient ID"""
resp = None
message = {}
if not authorize(current_app.db, request): # not authorized, return a 401 status code
message['message'] = STATUS_CODES[401]['message']
resp = jsonify(message)
resp.status_code = 401
return resp
LOG.info('Authorized clients is matching patient with ID {} against external nodes'.format(patient_id))
query_patient = controllers.patient(current_app.db, patient_id)
if not query_patient:
LOG.error('ERROR. Could not find any patient with ID {} in database'.format(patient_id))
message['message'] = "ERROR. Could not find any patient with ID {} in database".format(patient_id)
resp = jsonify(message)
resp.status_code = 200
return resp
node = request.args.get('node')
# if search should be performed on a specific node, make sure node is in database
if node and current_app.db['nodes'].find_one({'_id':node}) is None:
LOG.info('ERROR, theres no node with id "{}" in database'.format(request.args['node']))
message['message'] = 'ERROR. Could not find any connected node with id {} in database'.format(request.args['node'])
resp = jsonify(message)
resp.status_code = 200
return resp
matching_obj = controllers.match_external(current_app.db, query_patient, node)
if not matching_obj:
message['message'] = "Could not find any other node connected to this MatchMaker server"
resp = jsonify(message)
resp.status_code = 200
return resp
results = matching_obj.get('results')
# if patient is matching any other patient on other nodes
# and match notifications are on
if current_app.config.get('MAIL_SERVER') and matching_obj and len(results):
# send an email to patient's contact:
notify_match_external(match_obj=matching_obj, admin_email=current_app.config.get('MAIL_USERNAME'),
mail=current_app.mail, notify_complete=current_app.config.get('NOTIFY_COMPLETE'))
resp = jsonify({'results':results})
resp.status_code = 200
return resp
def asynch_match_response():
"""Receives and handles asynchronous match responses.
This implies that patientMatcher has already submitted a match request
to a server x and has received not results, but a query id in response.
Query id was previously saved into patientMatcher database.
This delayed response from server x contains match results and
the same query id and server x source key.
"""
LOG.info("Receiving an asynchronous request.")
data = controllers.check_async_request(current_app.db, request)
# returned data after check_async_request is a dictionary if request is valid
if isinstance(data,
int): # some error must have occurred during validation
return controllers.bad_request(data)
# create a match object from specifics you first sent to the node
async_match_obj = async_match(current_app.db, data)
if async_match_obj:
# save match object to database
LOG.info("saving match object to database")
current_app.db["matches"].insert_one(async_match_obj)
# Remove query_id from async responses, this is not used any more
current_app.db["async_responses"].delete_one(
{"query_id": data["query_id"]})
else:
message = "Error: could not create a valid match object from request data"
resp = jsonify({"message": message})
resp.status_code = 200
return resp
# notify matches if there are matching patients and app is configured to do so
if len(async_match_obj["results"]) > 0 and current_app.config.get(
"MAIL_SERVER"):
# send an email to patient's contact:
notify_match_external(
match_obj=async_match_obj,
admin_email=current_app.config.get("MAIL_USERNAME"),
mail=current_app.mail,
notify_complete=current_app.config.get("NOTIFY_COMPLETE"),
)
resp = jsonify({"message": "results received, many thanks!"})
resp.status_code = 200
return resp