def _filter_order_fields(self, resource, pid):
fhir_resource = SimpleFhirR4Reader(resource)
summary = ParticipantSummaryDao().get(pid)
if not summary:
raise BadRequest('No summary for particpant id: {}'.format(pid))
code_dict = summary.asdict()
format_json_code(code_dict, self.code_dao, 'genderIdentityId')
format_json_code(code_dict, self.code_dao, 'stateId')
# MayoLink api has strong opinions on what should be sent and the order of elements. Dont touch.
order = {
'order': {
'collected':
fhir_resource.authoredOn,
'account':
'',
'number':
fhir_resource.extension.get(
url=VIBRENT_BARCODE_URL).valueString,
'patient': {
'medical_record_number': str(summary.biobankId),
'first_name': '*',
'last_name': str(summary.biobankId),
'middle_name': '',
'birth_date': '3/3/1933',
'gender': code_dict['genderIdentity'],
'address1': summary.streetAddress,
'address2': summary.streetAddress2,
'city': summary.city,
'state': code_dict['state'],
'postal_code': str(summary.zipCode),
'phone': str(summary.phoneNumber),
'account_number': None,
'race': summary.race,
'ethnic_group': None
},
'physician': {
'name': None,
'phone': None,
'npi': None
},
'report_notes':
fhir_resource.extension.get(url=VIBRENT_ORDER_URL).valueString,
'tests': {
'test': {
'code': '1SAL2',
'name': 'PMI Saliva, FDA Kit',
'comments': None
}
},
'comments':
'Salivary Kit Order, direct from participant'
}
}
return order
def _filter_order_fields(self, resource, pid):
fhir_resource = SimpleFhirR4Reader(resource)
summary = ParticipantSummaryDao().get(pid)
if not summary:
raise BadRequest('No summary for participant id: {}'.format(pid))
code_dict = summary.asdict()
format_json_code(code_dict, self.code_dao, 'genderIdentityId')
format_json_code(code_dict, self.code_dao, 'stateId')
if 'genderIdentity' in code_dict and code_dict['genderIdentity']:
if code_dict['genderIdentity'] == 'GenderIdentity_Woman':
gender_val = 'F'
elif code_dict['genderIdentity'] == 'GenderIdentity_Man':
gender_val = 'M'
else:
gender_val = 'U'
else:
gender_val = 'U'
order_id = int(fhir_resource.basedOn[0].identifier.value)
with self.session() as session:
result = session.query(BiobankDVOrder.barcode).filter(
BiobankDVOrder.order_id == order_id).first()
barcode = None if not result else result if isinstance(
result, str) else result.barcode
# MayoLink api has strong opinions on what should be sent and the order of elements. Dont touch.
order = {
'order': {
'collected': fhir_resource.occurrenceDateTime,
'account': '',
'number': barcode,
'patient': {
'medical_record_number':
str(to_client_biobank_id(summary.biobankId)),
'first_name':
'*',
'last_name':
str(to_client_biobank_id(summary.biobankId)),
'middle_name':
'',
'birth_date':
'3/3/1933',
'gender':
gender_val,
'address1':
summary.streetAddress,
'address2':
summary.streetAddress2,
'city':
summary.city,
'state':
code_dict['state'],
'postal_code':
str(summary.zipCode),
'phone':
str(summary.phoneNumber),
'account_number':
None,
'race':
summary.race,
'ethnic_group':
None
},
'physician': {
'name': 'None', # must be a string value, not None.
'phone': None,
'npi': None
},
'report_notes':
fhir_resource.extension.get(url=DV_ORDER_URL).valueString,
'tests': {
'test': {
'code': '1SAL2',
'name': 'PMI Saliva, FDA Kit',
'comments': None
}
},
'comments': 'Salivary Kit Order, direct from participant'
}
}
return order