def _add_user_to_patient(username, patient_id, allow_edit=True):
"""Grant a PhenoTips user access to the given patient.
Args:
username (string): PhenoTips username to grant access to.
patient_id (string): PhenoTips internal patient id.
"""
headers = {"Content-Type": "application/x-www-form-urlencoded"}
data = {
'collaborator': 'XWiki.' + str(username),
'patient': patient_id,
'accessLevel': 'edit' if allow_edit else 'view',
'xaction': 'update',
'submit': 'Update'
}
url = '/bin/get/PhenoTips/PatientAccessRightsManagement?outputSyntax=plain'
make_phenotips_api_call(
'POST',
url,
http_headers=headers,
data=data,
auth_tuple=(settings.PHENOTIPS_ADMIN_UNAME,
settings.PHENOTIPS_ADMIN_PWD),
expected_status_code=204,
parse_json_resonse=False,
)
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 _create_patient_if_missing(project, individual):
"""Create a new PhenoTips patient record with the given patient id.
Args:
project (Model): seqr Project - used to retrieve PhenoTips credentials
individual (Model): seqr Individual
Returns:
True if patient created
Raises:
PhenotipsException: if unable to create patient record
"""
if phenotips_patient_exists(individual):
return False
url = '/rest/patients'
headers = {"Content-Type": "application/json"}
data = json.dumps({'external_id': individual.guid})
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id)
response_items = make_phenotips_api_call('POST', url, auth_tuple=auth_tuple, http_headers=headers, data=data, expected_status_code=201, parse_json_resonse=False)
patient_id = response_items['Location'].split('/')[-1]
logger.info("Created PhenoTips record with patient id {patient_id} and external id {external_id}".format(patient_id=patient_id, external_id=individual.guid))
username_read_only, _ = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=True)
_add_user_to_patient(username_read_only, patient_id, allow_edit=False)
logger.info("Added PhenoTips user {username} to {patient_id}".format(username=username_read_only, patient_id=patient_id))
individual.phenotips_patient_id = patient_id
individual.phenotips_eid = individual.guid
individual.save()
return True
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)