def main(argv):
if len(argv) != 2:
raise app.UsageError('Should have exactly one argument for workspace')
workspace = argv[1]
with open(workspace + '/ndjson/Patient.fhir.ndjson', 'r',
encoding='utf-8') as f:
# Read first 200 patient records.
for i in range(0, 200):
ndjson_line = f.readline()
# For 5% of records, insert a spelling error in Patient.gender, which is
# bound to a value from
# https://www.hl7.org/fhir/valueset-administrative-gender.html
# See: http://hl7.org/fhir/patient.html
if random.random() < .05:
ndjson_line = re.sub(r'"gender":"((fe)?)(male)"',
'"gender":\"\\2mael\"', ndjson_line)
try:
patient_proto = json_format.json_fhir_string_to_proto(
ndjson_line, patient_pb2.Patient)
except ValueError as e:
print(f'Failed parsing record {i}: {e}')
def _parse_proto_from_file(uri: str, zip_file_path: str, path: str,
resource_type: str) -> Optional[_T]:
"""Parses a protocol buffer from the resource at the given path.
Args:
uri: The URI of the resource to parse.
zip_file_path: The file path to the zip file containing resource
definitions.
path: The path within the zip file to the resource file to parse.
resource_type: The type of the resource contained at `path`.
Returns:
The protocol buffer for the resource or `None` if it can not be found.
"""
with zipfile.ZipFile(zip_file_path, mode='r') as f:
raw_json = f.read(path).decode('utf-8')
if resource_type in _PROTO_CLASSES_FOR_TYPES:
return json_format.json_fhir_string_to_proto(
raw_json, _PROTO_CLASSES_FOR_TYPES[resource_type])
elif resource_type == 'Bundle':
json_value = _find_resource_in_bundle(
uri, json_format.load_json(raw_json))
if json_value is None:
return None
else:
return json_format.json_fhir_object_to_proto(
json_value,
_PROTO_CLASSES_FOR_TYPES[json_value['resourceType']])
else:
logging.warning(
'Unhandled JSON entry: %s for unexpected resource type %s.',
path, resource_type)
return None
def test_invalid_json(self, file_name: str,
field_type: Type[message.Message]):
test_suite = self.get_test_suite(file_name)
if not test_suite.invalid_json:
self.fail('Must have at least one invalid json example!')
for invalid_json in test_suite.invalid_json:
# Some of the invalid examples may cause non InvalidFhirError errors,
# which is acceptable.
with self.assertRaises(Exception):
_ = json_format.json_fhir_string_to_proto(
invalid_json, field_type)
def test_valid_pairs(self, file_name: str, field_name: str,
field_type: Type[message.Message]):
test_suite = self.get_test_suite(file_name)
for pair in test_suite.valid_pairs:
expected_proto = proto_utils.get_value_at_field(
pair.proto, field_name)
expected_json = pair.json_string
actual_json = json_format.print_fhir_to_json_string(expected_proto)
actual_proto = json_format.json_fhir_string_to_proto(
actual_json, field_type, default_timezone='Australia/Sydney')
self.assertEqual(expected_json, actual_json)
self.assertProtoEqual(expected_proto, actual_proto)
def main(argv):
if len(argv) != 2:
raise app.UsageError('Should have exactly one argument for workspace')
workspace = argv[1]
with open(workspace + '/ndjson/Patient.fhir.ndjson', 'r',
encoding='utf-8') as f:
patients = []
# Read first 200 patient records.
for i in range(0, 200):
ndjson_line = f.readline()
try:
patient_proto = json_format.json_fhir_string_to_proto(
ndjson_line, patient_pb2.Patient)
patients.append(patient_proto)
except ValueError as e:
print(f'Failed parsing record {i}: {e}')
for i, patient in enumerate(patients):
# Insert a validation error into 5% of the records.
# Patient.communication is an optional BackboneElement field, but if one
# is added, it *MUST* contain a populated Patient.communication.language
# field.
# See: http://hl7.org/fhir/patient.html
communication = patient.communication.add()
communication.preferred.value = True
# Add the required language field to 95% of records
if random.random() < .95:
language = communication.language.coding.add()
language.system.value = 'http://hl7.org/fhir/valueset-all-languages.html'
language.code.value = 'fr'
try:
resource_validation.validate_resource(patient)
except fhir_errors.InvalidFhirError as e:
print(f'Failed validating record {i}: {e}')
import json
from pathlib import Path
from google.fhir.r4 import json_format
from proto.google.fhir.proto.r4.core.resources.bundle_and_contained_resource_pb2 import ( # noqa: E501
Bundle,
)
LPR = Path("25dc5040-5875-8486-a49c-ed4789b7c88c.json")
lpr_json = LPR.read_text()
original_lpr = json.loads(lpr_json)
bundle = json_format.json_fhir_string_to_proto(lpr_json, Bundle)
new_lpr_json = json_format.pretty_print_fhir_to_json_string(bundle)
new_lpr = json.loads(new_lpr_json)
print(new_lpr_json)
