def testAreSameMessageType_withDifferentMessageType_returnsFalse(self):
"""Test are_same_message_type with two different message types."""
patient = patient_pb2.Patient()
uscore_patient_profile = uscore_pb2.USCorePatientProfile()
self.assertFalse(
proto_utils.are_same_message_type(patient.DESCRIPTOR,
uscore_patient_profile.DESCRIPTOR))
self.assertFalse(
proto_utils.are_same_message_type(patient_pb2.Patient.DESCRIPTOR,
uscore_patient_profile.DESCRIPTOR))
def testAreSameMessageType_withSameMessageType_returnsTrue(self):
"""Test are_same_message_type with the same message types."""
patient_a = patient_pb2.Patient()
patient_b = patient_pb2.Patient()
self.assertTrue(
proto_utils.are_same_message_type(patient_a.DESCRIPTOR,
patient_b.DESCRIPTOR))
self.assertTrue(
proto_utils.are_same_message_type(patient_pb2.Patient.DESCRIPTOR,
patient_pb2.Patient.DESCRIPTOR))
def testGetMessageClassFromDescriptor_returnsMessageClass(self):
"""Tests that the correct class is returned for a message."""
actual = proto_utils.get_message_class_from_descriptor(
patient_pb2.Patient.DESCRIPTOR)
self.assertTrue(
proto_utils.are_same_message_type(actual.DESCRIPTOR,
patient_pb2.Patient.DESCRIPTOR))
def __init__(self, wrapped: message.Message, context: Context):
"""Converts wrapped into an instance of context.code_cls and wraps."""
if not proto_utils.are_same_message_type(wrapped.DESCRIPTOR,
context.code_cls.DESCRIPTOR):
tmp = context.code_cls()
codes.copy_code(wrapped, tmp)
wrapped = tmp
super(CodeWrapper, self).__init__(wrapped, context)
def merge_into(self, target: message.Message) -> None:
"""Merges the underlying wrapped primitive into target."""
if not proto_utils.are_same_message_type(self.wrapped.DESCRIPTOR,
target.DESCRIPTOR):
raise ValueError(f'Type mismatch in merge_into. Attempted to merge '
f'{self.wrapped.DESCRIPTOR.full_name} into '
f'{target.DESCRIPTOR.full_name}.')
target.MergeFrom(self.wrapped)
def copy_coding(source: message.Message, target: message.Message):
"""Copies all fields from source to target "Coding" messages.
Args:
source: The FHIR coding instance to copy from.
target: The FHIR coding instance to copy to.
Raises:
InvalidFhirError: In the event that source or target is not a type/profile
of Coding.
"""
if not fhir_types.is_type_or_profile_of_coding(source.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Source: {source.DESCRIPTOR.full_name} '
'is not a type or profile of Coding.')
if not fhir_types.is_type_or_profile_of_coding(target.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Target: {target.DESCRIPTOR.full_name} '
'is not a type or profile of Coding.')
if proto_utils.are_same_message_type(source.DESCRIPTOR, target.DESCRIPTOR):
target.CopyFrom(source)
return
# Copy fields present in both profiled and unprofiled codings.
proto_utils.copy_common_field(source, target, 'id')
proto_utils.copy_common_field(source, target, 'extension')
proto_utils.copy_common_field(source, target, 'version')
proto_utils.copy_common_field(source, target, 'display')
proto_utils.copy_common_field(source, target, 'user_selected')
# Copy the "code" field from source to target
source_code = proto_utils.get_value_at_field(source, 'code')
copy_code(source_code, proto_utils.set_in_parent_or_add(target, 'code'))
target_system_field = target.DESCRIPTOR.fields_by_name.get('system')
# TODO: This will fail if there is a target system field,
# *and* a source system field, since in this case the source code will not
# contain the system information, the containing Coding would. In general,
# it's not quite right to get the system from Code, since unprofiled codes
# don't contain system information. In practice, this isn't a problem,
# because the only kind of profiled Codings we currently support are
# Codings with typed Codes (which contain source information) but this is
# not neccessary according to FHIR spec.
if target_system_field is not None:
source_system_str = get_system_for_code(source_code)
target_system_uri = proto_utils.set_in_parent_or_add(
target, target_system_field)
proto_utils.set_value_at_field(target_system_uri, 'value',
source_system_str)
def copy_coding(source: message.Message, target: message.Message):
"""Copies all fields from source to target "Coding" messages.
Args:
source: The FHIR coding instance to copy from.
target: The FHIR coding instance to copy to.
Raises:
InvalidFhirError: In the event that source or target is not a type/profile
of Coding.
"""
if not fhir_types.is_type_or_profile_of_coding(source.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Source: {source.DESCRIPTOR.full_name} '
'is not a type or profile of Coding.')
if not fhir_types.is_type_or_profile_of_coding(target.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Target: {target.DESCRIPTOR.full_name} '
'is not a type or profile of Coding.')
if proto_utils.are_same_message_type(source.DESCRIPTOR, target.DESCRIPTOR):
target.CopyFrom(source)
return
# Copy fields present in both profiled and unprofiled codings.
proto_utils.copy_common_field(source, target, 'id')
proto_utils.copy_common_field(source, target, 'extension')
proto_utils.copy_common_field(source, target, 'version')
proto_utils.copy_common_field(source, target, 'display')
proto_utils.copy_common_field(source, target, 'user_selected')
# Copy the "code" field from source to target
source_code = proto_utils.get_value_at_field(source, 'code')
copy_code(source_code, proto_utils.set_in_parent_or_add(target, 'code'))
target_system_field = target.DESCRIPTOR.fields_by_name.get('system')
if target_system_field is not None:
source_system_str = get_system_for_code(source_code)
target_system_uri = proto_utils.set_in_parent_or_add(
target, target_system_field)
proto_utils.set_value_at_field(target_system_uri, 'value',
source_system_str)
def copy_code(source: message.Message, target: message.Message):
"""Adds all fields from source to target.
Args:
source: The FHIR Code instance to copy from.
target: The target FHIR Code instance to copy to.
"""
if not fhir_types.is_type_or_profile_of_code(source.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Source: {source.DESCRIPTOR.full_name} '
'is not type or profile of Code.')
if not fhir_types.is_type_or_profile_of_code(target.DESCRIPTOR):
raise fhir_errors.InvalidFhirError(
f'Target: {target.DESCRIPTOR.full_name} '
'is not type or profile of Code.')
if proto_utils.are_same_message_type(source.DESCRIPTOR, target.DESCRIPTOR):
target.CopyFrom(source)
return
source_value_field = source.DESCRIPTOR.fields_by_name.get('value')
target_value_field = target.DESCRIPTOR.fields_by_name.get('value')
if source_value_field is None or target_value_field is None:
raise fhir_errors.InvalidFhirError(
'Unable to copy code from '
f'{source.DESCRIPTOR.full_name} '
f'to {target.DESCRIPTOR.full_name}.')
proto_utils.copy_common_field(source, target, 'id')
proto_utils.copy_common_field(source, target, 'extension')
# Handle specialized codes
if (source_value_field.type not in _CODE_TYPES
or target_value_field.type not in _CODE_TYPES):
raise ValueError(
f'Unable to copy from {source.DESCRIPTOR.full_name} '
f'to {target.DESCRIPTOR.full_name}. Must have a field '
'of TYPE_ENUM or TYPE_STRING.')
source_value = proto_utils.get_value_at_field(source, source_value_field)
if source_value_field.type == target_value_field.type:
# Perform a simple assignment if value_field types are equivalent
proto_utils.set_value_at_field(target, target_value_field,
source_value)
else:
# Otherwise, we need to transform the value prior to assignment...
if source_value_field.type == descriptor.FieldDescriptor.TYPE_STRING:
source_enum_value = code_string_to_enum_value_descriptor(
source_value, target_value_field.enum_type)
proto_utils.set_value_at_field(target, target_value_field,
source_enum_value.number)
elif source_value_field.type == descriptor.FieldDescriptor.TYPE_ENUM:
source_string_value = enum_value_descriptor_to_code_string(
source_value_field.enum_type.values_by_number[source_value])
proto_utils.set_value_at_field(target, target_value_field,
source_string_value)
else: # Should never hit
raise ValueError('Unexpected generic value field type: '
f'{source_value_field.type}. Must be a field of '
'TYPE_ENUM or TYPE_STRING in order to copy.')
def _add_extension_value_to_message(extension: message.Message,
msg: message.Message,
message_field: descriptor.FieldDescriptor):
"""Serialize the provided extension and add it to the message.
Args:
extension: The FHIR extension to serialize.
msg: The message to add the serialized extension to.
message_field: The field on the message to set.
Raises:
InvalidFhirError: In the event that the field to be set is not a singular
message type, or if the provided extension is not singular (has nested
extensions).
"""
if message_field.type != descriptor.FieldDescriptor.TYPE_MESSAGE:
raise fhir_errors.InvalidFhirError(
f'{msg.DESCRIPTOR.full_name} is not a FHIR extension type.')
extension_field = extension.DESCRIPTOR.fields_by_name['extension']
if proto_utils.field_content_length(extension, extension_field) > 0:
raise fhir_errors.InvalidFhirError(
'No child extensions should be set on '
f'{extension.DESCRIPTOR.full_name}.')
value_field = _get_populated_extension_value_field(extension)
# If a choice type, need to assign the extension value to the correct field.
if annotation_utils.is_choice_type_field(message_field):
choice_message = proto_utils.get_value_at_field(msg, message_field)
choice_descriptor = choice_message.DESCRIPTOR
for choice_field in choice_descriptor.fields:
if (value_field.message_type.full_name ==
choice_field.message_type.full_name):
_add_extension_value_to_message(extension, choice_message,
choice_field)
return
raise ValueError(
f'No field on Choice Type {choice_descriptor.full_name} '
f'for extension {extension.DESCRIPTOR.full_name}.')
# If the target message is a bound Code type, we need to convert the generic
# Code field from the extension into the target typed Code.
if annotation_utils.has_fhir_valueset_url(message_field.message_type):
typed_code = proto_utils.set_in_parent_or_add(msg, message_field)
codes.copy_code(cast(Any, extension).value.code, typed_code)
return
# If the target message is bound to a Coding type, we must convert the generic
# Coding field from the extension into the target typed Coding.
if fhir_types.is_type_or_profile_of_coding(message_field.message_type):
typed_coding = proto_utils.set_in_parent_or_add(msg, message_field)
codes.copy_coding(cast(Any, extension).value.coding, typed_coding)
return
# Value types must match
if not proto_utils.are_same_message_type(value_field.message_type,
message_field.message_type):
raise ValueError(
'Missing expected value of type '
f'{message_field.message_type.full_name} in extension '
f'{extension.DESCRIPTOR.full_name}.')
value = proto_utils.get_value_at_field(
cast(Any, extension).value, value_field)
if proto_utils.field_is_repeated(message_field):
proto_utils.append_value_at_field(msg, message_field, value)
else:
proto_utils.set_value_at_field(msg, message_field, value)
def get_primitive_wrapper_cls_for_primitive_cls(
self, primitive_cls: Type[message.Message]
) -> Type[_primitive_wrappers.PrimitiveWrapper]:
if fhir_types.is_type_or_profile_of_code(primitive_cls.DESCRIPTOR):
return _primitive_wrappers.CodeWrapper
elif proto_utils.are_same_message_type(
primitive_cls.DESCRIPTOR, self.base64_binary_cls.DESCRIPTOR):
return _base64_binary.Base64BinaryWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.boolean_cls.DESCRIPTOR):
return _primitive_wrappers.BooleanWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.date_cls.DESCRIPTOR):
return _date.DateWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.canonical_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.date_time_cls.DESCRIPTOR):
return _date_time.DateTimeWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.decimal_cls.DESCRIPTOR):
return _decimal.DecimalWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.id_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.instant_cls.DESCRIPTOR):
return _instant.InstantWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.integer_cls.DESCRIPTOR):
return _primitive_wrappers.IntegerLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.markdown_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.oid_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(
primitive_cls.DESCRIPTOR, self.positive_int_cls.DESCRIPTOR):
return _primitive_wrappers.IntegerLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.string_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.time_cls.DESCRIPTOR):
return _time.TimeWrapper
elif proto_utils.are_same_message_type(
primitive_cls.DESCRIPTOR, self.unsigned_int_cls.DESCRIPTOR):
return _primitive_wrappers.IntegerLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.uri_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.url_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.uuid_cls.DESCRIPTOR):
return _primitive_wrappers.StringLikePrimitiveWrapper
elif proto_utils.are_same_message_type(primitive_cls.DESCRIPTOR,
self.xhtml_cls.DESCRIPTOR):
return _primitive_wrappers.XhtmlWrapper
raise ValueError(
f'Unexpected R4 FHIR primitive: {primitive_cls.DESCRIPTOR.full_name!r} '
f'for handler: {type(self)}.')
