def testGetSourceCodeSystem_withInvalidCodeSystem_returnsNone(self):
"""Test get_source_code_system when source_code_system is not present."""
year_value_descriptor = (
datatypes_pb2.Date.Precision.DESCRIPTOR.values_by_number[
datatypes_pb2.Date.Precision.YEAR])
self.assertIsNone(
annotation_utils.get_source_code_system(year_value_descriptor))
def get_system_for_code(code: message.Message) -> str:
"""Returns the code system associated with the provided Code."""
system_field = code.DESCRIPTOR.fields_by_name.get('system')
if system_field is not None:
return proto_utils.get_value_at_field(code, system_field)
fixed_coding_system = annotation_utils.get_fixed_coding_system(code)
if fixed_coding_system is not None:
# The entire profiled coding can only be from a single system. Use that.
return fixed_coding_system
# There is no single system for the whole coding. Look for the coding system
# annotation on the enum.
enum_field = code.DESCRIPTOR.fields_by_name.get('value')
if (enum_field is None
or enum_field.type != descriptor.FieldDescriptor.TYPE_ENUM):
raise fhir_errors.InvalidFhirError(
f'Invalid profiled Coding: {code.DESCRIPTOR.full_name}; missing system '
'information on string code.')
enum_value = proto_utils.get_value_at_field(code, enum_field)
enum_value_descriptor = enum_field.enum_type.values_by_number[enum_value]
if not annotation_utils.has_source_code_system(enum_value_descriptor):
raise fhir_errors.InvalidFhirError(
f'Invalid profiled Coding: {code.DESCRIPTOR.full_name}; missing system '
'information on enum code')
return cast(str,
annotation_utils.get_source_code_system(enum_value_descriptor))
def testGetSourceCodeSystem_withValidCodeSystem_returnsValue(self):
"""Test get_source_code_system when source_code_system is present."""
birth_sex_valueset = uscore_codes_pb2.BirthSexValueSet()
female_value_descriptor = (
birth_sex_valueset.Value.DESCRIPTOR.values_by_number[
birth_sex_valueset.Value.F])
self.assertEqual(
annotation_utils.get_source_code_system(female_value_descriptor),
'http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender')
male_value_descriptor = (birth_sex_valueset.Value.DESCRIPTOR.
values_by_number[birth_sex_valueset.Value.M])
self.assertEqual(
annotation_utils.get_source_code_system(male_value_descriptor),
'http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender')
unk_value_descriptor = (birth_sex_valueset.Value.DESCRIPTOR.
values_by_number[birth_sex_valueset.Value.UNK])
self.assertEqual(
annotation_utils.get_source_code_system(unk_value_descriptor),
'http://terminology.hl7.org/CodeSystem/v3-NullFlavor')