async def get_ehr_by_id(conn, client_key, ehr_id):
client = await get_client(conn, client_key)
ehr_list = {}
if Permission(type=Permission.READ_PATIENT_DATA) in client.permissions:
# ehr_list_address = ehr_helper.make_ehr_list_address()
ehr_address = ehr_helper.make_ehr_address(ehr_id)
LOGGER.debug('has READ_PATIENT_DATA permission: ' + str(client_key))
# Get Consent
access = await get_data_processing_access(conn, client_key)
patient_list = {}
for address, pt in access.items():
LOGGER.debug('patient access: ' + str(pt))
patient = await get_patient(conn, pt.src_pkey)
patient_list[pt.src_pkey] = patient
#
ehr_resources = await messaging.get_state_by_address(conn, ehr_address)
for entity in ehr_resources.entries:
cl = EHRWithUser()
cl.ParseFromString(entity.data)
ehr_list[entity.address] = cl
LOGGER.debug('ehr: ' + str(cl))
# Apply Consent
for patient_address, pt in patient_list.items():
LOGGER.debug('patient: ' + str(pt))
for claim_address, e in ehr_list.items():
LOGGER.debug('ehr: ' + str(e))
if patient_address == e.client_pkey:
LOGGER.debug('match!')
pt_local = patient_list[patient_address]
e.name = pt_local.name
e.surname = pt_local.surname
ehr_list[claim_address] = e
if not ehr_list:
raise ApiForbidden("Cat not get EHR having '" + str(ehr_id) + "' id")
return list(ehr_list.values())[0]
elif Permission(type=Permission.READ_OWN_PATIENT_DATA) in client.permissions:
# ehr_list_ids_address = ehr_helper.make_ehr_list_by_patient_address(client_key)
LOGGER.debug('has READ_OWN_PATIENT_DATA permission: ' + str(client_key))
# ehr_list_ids = await messaging.get_state_by_address(conn, ehr_list_ids_address)
# for entity in ehr_list_ids.entries:
# ehr_id = entity.data.decode()
ehr_address = ehr_helper.make_ehr_address(ehr_id)
LOGGER.debug('get ehr: ' + str(ehr_address))
ehr_resources = await messaging.get_state_by_address(conn, ehr_address)
for entity in ehr_resources.entries:
LOGGER.debug('get ehr entity: ' + str(entity.address))
e = EHRWithUser()
e.ParseFromString(entity.data)
ehr_list[entity.address] = e
if not ehr_list:
raise ApiForbidden("Cat not get EHR having '" + str(ehr_id) + "' id")
return list(ehr_list.values())[0]
else:
LOGGER.debug('neither READ_PATIENT_DATA nor READ_OWN_PATIENT_DATA permissions')
raise ApiForbidden("Insufficient permission")
async def get_consent_request_list(conn, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.GET_REQUESTS_LIST) in client.permissions:
LOGGER.debug('has GET_REQUESTS_LIST permission: ' + str(client_key))
consent_request_list = await get_consent_request(conn, client_key)
return consent_request_list
raise ApiForbidden("Insufficient permission")
async def get_inform_consent_request_list(conn, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.READ_INFORM_CONSENT_REQUEST) in client.permissions and \
Permission(type=Permission.READ_SIGNED_INFORM_CONSENT) in client.permissions:
LOGGER.debug('has READ_INFORM_CONSENT_REQUEST and READ_SIGNED_INFORM_CONSENT permission: ' + str(client_key))
inform_consent_request_list = await get_inform_consent_request(conn, client_key)
return inform_consent_request_list
raise ApiForbidden("Insufficient permission")
async def revoke_investigator_access(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.REVOKE_INVESTIGATOR_ACCESS) in client.permissions:
LOGGER.debug('has permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def import_screening_data(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.IMPORT_TRIAL_DATA) in client.permissions:
LOGGER.debug('has IMPORT_TRIAL_DATA permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def decline_request(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.DECLINE_CONSENT) in client.permissions:
LOGGER.debug('has permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def add_ehr(conn, timeout, batches, dest_pkey, src_pkey):
client = await get_client(conn, dest_pkey)
if Permission(type=Permission.WRITE_PATIENT_DATA) in client.permissions:
LOGGER.debug('has WRITE_PATIENT_DATA permission: True')
# Has consent from patient
access = await has_data_processing_access(conn, dest_pkey, src_pkey)
if not access:
LOGGER.debug('no data processing access')
raise ApiForbidden("Insufficient permission")
#
await _send(conn, timeout, batches)
return
# LOGGER.debug('has permission: True')
# await _send(conn, timeout, batches)
# return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def sign_inform_document_consent(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.SIGN_INFORM_CONSENT) in client.permissions:
LOGGER.debug('has permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def update_investigator(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.UPDATE_TRIAL_DATA) in client.permissions:
LOGGER.debug('has UPDATE_TRIAL_DATA permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def revoke_data_processing(conn, timeout, batches, client_key):
client = await get_client(conn, client_key)
if Permission(type=Permission.REVOKE_READ_DATA_ACCESS) in client.permissions and \
Permission(type=Permission.REVOKE_WRITE_DATA_ACCESS) in client.permissions:
LOGGER.debug('has permission: True')
await _send(conn, timeout, batches)
return
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def get_pre_screening_data(conn, investigator_pkey, inc_excl_criteria):
client = await get_client(conn, investigator_pkey)
if Permission(type=Permission.READ_PATIENT_DATA) in client.permissions:
ehr_list = await get_shared_ehrs(conn, investigator_pkey)
ehr_screening_list = {}
for address, ehr in ehr_list.items():
if _match_incl_excl_criteria(ehr, inc_excl_criteria):
ehr_screening_list[address] = ehr
return ehr_screening_list
else:
LOGGER.debug('has permission: False')
raise ApiForbidden("Insufficient permission")
async def get_patients(ehr_conn, consent_conn, client_key):
client = await get_client(consent_conn, client_key)
patient_list = {}
if Permission(type=Permission.READ_PATIENT) in client.permissions:
LOGGER.debug('has READ_PATIENT permission: ' + str(client_key))
list_patient_address = ehr_helper.make_patient_list_address()
# Get Data Processing Access
data_processing_access = await get_data_processing_access(
consent_conn, client_key)
data_processing_access_list = {}
for address, pt in data_processing_access.items():
LOGGER.debug('data_processing_access: ' + str(pt))
patient = await get_patient(ehr_conn, pt.src_pkey)
data_processing_access_list[pt.src_pkey] = patient
# consent = await get_read_ehr_consent(conn, client_key)
# consent_list = {}
# for address, pt in consent.items():
# LOGGER.debug('consent: ' + str(pt))
# patient = await get_patient(conn, pt.src_pkey)
# consent_list[pt.src_pkey] = patient
#
patient_list_resources = await messaging.get_state_by_address(
ehr_conn, list_patient_address)
for entity in patient_list_resources.entries:
pat = Patient()
pat.ParseFromString(entity.data)
patient_list[entity.address] = pat
LOGGER.debug('patient: ' + str(pat))
# Apply Access
for patient_address, pt in patient_list.items():
LOGGER.debug('patient: ' + str(pt))
if Permission(
type=Permission.READ_OWN_PATIENT
) in client.permissions and pt.public_key == client_key:
pass
elif pt.public_key not in data_processing_access_list:
pat2 = Patient()
patient_list[patient_address] = pat2
return patient_list
elif Permission(type=Permission.READ_OWN_PATIENT) in client.permissions:
LOGGER.debug('has READ_OWN_PATIENT: ' + str(client_key))
# Get Data Processing Access
data_processing_access = await get_data_processing_access(
consent_conn, client_key)
data_processing_access_list = {}
for address, pt in data_processing_access.items():
LOGGER.debug('data_processing_access: ' + str(pt))
patient = await get_patient(ehr_conn, pt.src_pkey)
data_processing_access_list[pt.src_pkey] = patient
return data_processing_access_list
raise ApiForbidden("Insufficient permission")
async def get_hospitals(conn, client_key):
client = await get_client(conn, client_key)
hospital_list = {}
if Permission(type=Permission.READ_HOSPITAL) in client.permissions:
list_hospital_address = ehr_helper.make_hospital_list_address()
list_hospital_resources = await messaging.get_state_by_address(conn, list_hospital_address)
for entity in list_hospital_resources.entries:
hp = Hospital()
hp.ParseFromString(entity.data)
LOGGER.debug('hospital: ' + str(hp))
hospital_list[entity.address] = hp
return hospital_list
raise ApiForbidden("Insufficient permission")
async def get_consumers(conn, client_key):
client = await get_client(conn, client_key)
consumers_list = {}
if Permission(type=Permission.GET_CONSUMERS_LIST) in client.permissions:
list_consumer_address = data_helper.make_consumer_list_address()
list_consumer_resources = await messaging.get_state_by_address(
conn, list_consumer_address)
for entity in list_consumer_resources.entries:
cn = Consumer()
cn.ParseFromString(entity.data)
LOGGER.debug('consumer: ' + str(cn))
consumers_list[entity.address] = cn
return consumers_list
raise ApiForbidden("Insufficient permission")
async def get_academics(conn, client_key):
client = await get_client(conn, client_key)
academic_list = {}
if Permission(type=Permission.GET_ACADEMICS_LIST) in client.permissions:
LOGGER.debug('has GET_ACADEMICS_LIST permission: ' + str(client_key))
list_academic_address = data_helper.make_academic_list_address()
# Get Data Processing Access
# data_processing_access = await get_consent_by_consumer(consent_conn, client_key)
# data_processing_access_list = {}
# for address, pt in data_processing_access.items():
# LOGGER.debug('data_processing_access: ' + str(pt))
# patient = await get_patient(ehr_conn, pt.src_pkey)
# data_processing_access_list[pt.src_pkey] = patient
# consent = await get_read_ehr_consent(conn, client_key)
# consent_list = {}
# for address, pt in consent.items():
# LOGGER.debug('consent: ' + str(pt))
# patient = await get_patient(conn, pt.src_pkey)
# consent_list[pt.src_pkey] = patient
#
academic_list_resources = await messaging.get_state_by_address(
conn, list_academic_address)
for entity in academic_list_resources.entries:
ac = Academic()
ac.ParseFromString(entity.data)
academic_list[entity.address] = ac
LOGGER.debug('academic: ' + str(ac))
# Apply Access
# for patient_address, pt in academic_list.items():
# LOGGER.debug('patient: ' + str(pt))
# if Permission(type=Permission.READ_OWN_PATIENT) in client.permissions and pt.public_key == client_key:
# pass
# elif pt.public_key not in data_processing_access_list:
# pat2 = Patient()
# patient_list[patient_address] = pat2
return academic_list
# elif Permission(type=Permission.READ_OWN_PATIENT) in client.permissions:
# LOGGER.debug('has READ_OWN_PATIENT: ' + str(client_key))
# # Get Data Processing Access
# data_processing_access = await get_consent_by_consumer(consent_conn, client_key)
# data_processing_access_list = {}
# for address, pt in data_processing_access.items():
# LOGGER.debug('data_processing_access: ' + str(pt))
# patient = await get_patient(ehr_conn, pt.src_pkey)
# data_processing_access_list[pt.src_pkey] = patient
# return data_processing_access_list
raise ApiForbidden("Insufficient permission")
async def get_data_from_investigators(conn, client_key):
client = await get_client(conn, client_key)
data_list = {}
if Permission(type=Permission.READ_TRIAL_DATA) in client.permissions:
data_list_address = ehr_helper.make_investigator_data_list_address()
LOGGER.debug('has READ_DATA permission: ' + str(client_key))
data_list_resources = await messaging.get_state_by_address(conn, data_list_address)
for entity in data_list_resources.entries:
data = Data()
data.ParseFromString(entity.data)
data_list[entity.address] = data
LOGGER.debug('data: ' + str(data))
return data_list
else:
LOGGER.debug('no READ_DATA permissions')
raise ApiForbidden("Insufficient permission")
def _match_incl_excl_criteria(data, inc_excl_criteria):
for criteria, value in inc_excl_criteria.items():
LOGGER.debug('_match_incl_excl_criteria -> criteria: ' + criteria + '; value: ' + value + ';')
v = _get_int(value)
if criteria == "excl_height_less":
if _get_int(data.height) < v:
return False
elif criteria == "excl_height_more":
if _get_int(data.height) > v:
return False
elif criteria == "incl_height_less":
if _get_int(data.height) > v:
return False
elif criteria == "incl_height_more":
if _get_int(data.height) < v:
return False
else:
raise ApiForbidden("Invalid excl/incl criteria specified. "
"Only {excl_height_less,excl_height_more,incl_height_less,incl_height_more} allowed")
return True
async def get_investigators(conn, client_key):
client = await get_client(conn, client_key)
investigator_list = {}
if Permission(type=Permission.READ_INVESTIGATOR) in client.permissions:
list_investigator_address = ehr_helper.make_investigator_list_address()
list_investigator_resources = await messaging.get_state_by_address(conn, list_investigator_address)
for entity in list_investigator_resources.entries:
dp = Investigator()
dp.ParseFromString(entity.data)
LOGGER.debug('investigator: ' + str(dp))
investigator_list[entity.address] = dp
return investigator_list
elif Permission(type=Permission.READ_OWN_INVESTIGATOR) in client.permissions:
list_investigator_address = ehr_helper.make_investigator_address(client_key)
list_investigator_resources = await messaging.get_state_by_address(conn, list_investigator_address)
for entity in list_investigator_resources.entries:
dp = Investigator()
dp.ParseFromString(entity.data)
LOGGER.debug('investigator: ' + str(dp))
investigator_list[entity.address] = dp
return investigator_list
raise ApiForbidden("Insufficient permission")
def get_request_key_header(request):
if 'ClientKey' not in request.headers:
raise ApiForbidden('Client key not specified')
return request.headers['ClientKey']
async def get_data(conn, client_key):
client = await get_client(conn, client_key)
data_list = {}
if Permission(type=Permission.READ_DATA) in client.permissions:
LOGGER.debug('has READ_DATA permission: ' + str(client_key))
# Get Consumers with Consent
consumers_with_consent = await get_consent_by_consumer(
conn, client_key)
for address, cn in consumers_with_consent.items():
LOGGER.debug('consumer with consent: ' + str(cn))
data_id_list_address = data_helper.make_data_list_by_consumer_address(
cn.src_pkey)
data_id_list_resources = await messaging.get_state_by_address(
conn, data_id_list_address)
for entity in data_id_list_resources.entries:
data_id = entity.data.decode()
data_address = data_helper.make_data_address(data_id)
LOGGER.debug('get data: ' + str(data_address))
data_resources = await messaging.get_state_by_address(
conn, data_address)
for entity2 in data_resources.entries:
entity_data_decode = entity2.data.decode()
LOGGER.debug('entity_data_decode: ' +
str(entity_data_decode))
cde = ConsumerDataExt()
cde.ParseFromString(entity2.data)
LOGGER.debug('data: ' + str(cde))
data_list[entity2.address] = cde
# data_list_resources = await messaging.get_state_by_address(conn, data_list_address)
# for entity in data_list_resources.entries:
# cde = ConsumerDataExt()
# cde.ParseFromString(entity.data)
#
# data_list[entity.address] = cde
# LOGGER.debug('data: ' + str(cde))
# # Apply Consent
# for patient_address, pt in patient_list.items():
# LOGGER.debug('patient: ' + str(pt))
# for claim_address, e in ehr_list.items():
# LOGGER.debug('ehr: ' + str(e))
# if patient_address == e.client_pkey:
# LOGGER.debug('match!')
# pt_local = patient_list[patient_address]
# e.name = pt_local.name
# e.surname = pt_local.surname
# ehr_list[claim_address] = e
return data_list
elif Permission(type=Permission.READ_OWN_DATA) in client.permissions:
data_id_list_address = data_helper.make_data_list_by_consumer_address(
client_key)
LOGGER.debug('has READ_OWN_DATA permission: ' + str(client_key))
data_id_list_resources = await messaging.get_state_by_address(
conn, data_id_list_address)
for entity in data_id_list_resources.entries:
data_id = entity.data.decode()
data_address = data_helper.make_data_address(data_id)
LOGGER.debug('get data: ' + str(data_address))
data_resources = await messaging.get_state_by_address(
conn, data_address)
for entity2 in data_resources.entries:
entity_data_decode = entity2.data.decode()
LOGGER.debug('entity_data_decode: ' + str(entity_data_decode))
cde = ConsumerDataExt()
cde.ParseFromString(entity2.data)
LOGGER.debug('data: ' + str(cde))
data_list[entity2.address] = cde
return data_list
# elif Permission(type=Permission.READ_OWN_PATIENT_DATA) in client.permissions:
# ehr_list_ids_address = ehr_helper.make_ehr_list_by_patient_address(client_key)
# LOGGER.debug('has READ_OWN_PATIENT_DATA permission: ' + str(ehr_list_ids_address))
# ehr_list_ids = await messaging.get_state_by_address(ehr_conn, ehr_list_ids_address)
# for entity in ehr_list_ids.entries:
# ehr_id = entity.data.decode()
# ehr_address = ehr_helper.make_ehr_address(ehr_id)
# LOGGER.debug('get ehr: ' + str(ehr_address))
# ehr_resources = await messaging.get_state_by_address(ehr_conn, ehr_address)
# for entity2 in ehr_resources.entries:
# LOGGER.debug('get ehr entity2: ' + str(entity2.address))
# e = EHRWithUser()
# e.ParseFromString(entity2.data)
# ehr_list[entity2.address] = e
# return ehr_list
else:
LOGGER.debug('neither READ_DATA permissions')
raise ApiForbidden("Insufficient permission")
