def check_request(database, request):
"""Check if request is valid, if it is return MME formatted patient
Otherwise return error code.
"""
check_result = None
# check that request is using a valid auth token
if not authorize(database, request):
LOG.info("Request is not authorized")
return 401
try: # make sure request has valid json data
request_json = request.get_json(force=True)
except Exception as err:
LOG.info("Json data in request is not valid:{}".format(err))
return 400
try: # validate json data against MME API
validate_api(json_obj=request_json, is_request=True)
except Exception as err:
LOG.info("Patient data does not conform to API:{}".format(err))
return 422
formatted_patient = mme_patient(json_patient=request_json['patient'],
convert_to_ensembl = True)
return formatted_patient
def nodes():
"""Get a list of all nodes connected to this MME server"""
resp = None
if not authorize(current_app.db, request):
message = STATUS_CODES[401]['message']
resp = jsonify(message)
resp.status_code = 401
return resp
LOG.info('Authorized client requests list of connected nodes..')
results = controllers.get_nodes(database=current_app.db)
resp = jsonify(results)
resp.status_code = 200
return resp
def delete(patient_id):
#check if request is authorized
resp = None
if not authorize(current_app.db, request): # not authorized, return a 401 status code
message = STATUS_CODES[401]['message']
resp = jsonify(message)
resp.status_code = 401
return resp
LOG.info('Authorized client is removing patient with id {}'.format(patient_id))
message = controllers.delete_patient(current_app.db, patient_id)
resp = jsonify(message)
resp.status_code = 200
return resp
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 heartbeat():
"""Get the server specs"""
resp = None
if authorize(current_app.db, request):
LOG.info('Authorized client requests heartbeat..')
LOG.info('current_app is {}'.format(current_app))
disclaimer = current_app.config.get('DISCLAIMER')
result = controllers.heartbeat(disclaimer)
resp = jsonify(result)
resp.status_code = 200
else: # not authorized, return a 401 status code
return controllers.bad_request(401)
return resp
def metrics():
"""Get database metrics"""
resp = None
if authorize(current_app.db, request):
LOG.info('Authorized client requests metrics..')
results = controllers.metrics(database=current_app.db)
resp = jsonify({
'metrics': results,
'disclaimer': current_app.config.get('DISCLAIMER')
})
resp.status_code = 200
else: # not authorized, return a 401 status code
return controllers.bad_request(401)
return resp
def matches(patient_id):
"""Get all matches (external and internal) for a patient ID"""
LOG.info('getting all matches for patient {}'.format(patient_id))
resp = None
message = {}
if not authorize(current_app.db, request): # not authorized, return a 401 status code
message = STATUS_CODES[401]['message']
resp = jsonify(message)
resp.status_code = 401
return resp
# return only matches with at least one result
results = patient_matches(current_app.db, patient_id)
if results:
message = json.loads(json_util.dumps({'matches' : results}))
else:
message['message'] = "Could not find any matches in database for patient ID {}".format(patient_id)
resp = jsonify(message)
resp.status_code = 200
return resp
