def update_individual_hpo_terms(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
features = json.loads(request.body)
_create_patient_if_missing(project, individual)
patient_json = _get_patient_data(project, individual)
patient_json["features"] = features
patient_json_string = json.dumps(patient_json)
url = phenotips_patient_url(individual)
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=False)
make_phenotips_api_call('PUT', url, data=patient_json_string, auth_tuple=auth_tuple, expected_status_code=204)
phenotips_patient_id = patient_json['id']
phenotips_eid = patient_json.get('external_id')
individual.phenotips_data = json.dumps(patient_json)
individual.phenotips_patient_id = phenotips_patient_id
individual.phenotips_eid = phenotips_eid
individual.save()
return create_json_response({
individual.guid: {
'phenotipsData': patient_json,
'phenotipsPatientId': phenotips_patient_id,
'phenotipsEid': phenotips_eid
}
})
def _get_patient_data(project, individual):
"""Retrieves patient data from PhenoTips and returns a json obj.
Args:
project (Model): seqr Project - used to retrieve PhenoTips credentials
individual (Model): seqr Individual
Returns:
dict: json dictionary containing all PhenoTips information for this patient
Raises:
PhenotipsException: if unable to retrieve data from PhenoTips
"""
url = phenotips_patient_url(individual)
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id)
return make_phenotips_api_call('GET', url, auth_tuple=auth_tuple, verbose=False)