def split_if_relative_reference(reference: message.Message):
"""Splits relative references into their components.
For example, a reference with the uri set to "Patient/ABCD" will be changed
into a reference with the patientId set to "ABCD".
Args:
reference: The FHIR reference to potentially split.
"""
_validate_reference(reference)
uri_field = reference.DESCRIPTOR.fields_by_name.get('uri')
if not proto_utils.field_is_set(reference, uri_field):
return # No URI to split
uri = proto_utils.get_value_at_field(reference, uri_field)
# We're permissive about various full URL schemes. If we're able to find a
# match, the URI is valid as-is.
url_match = re.fullmatch(_URL_REFERENCE_PATTERN, uri.value)
if url_match is not None:
return # URI is valid
internal_match = re.fullmatch(_INTERNAL_REFERENCE_PATTERN, uri.value)
if internal_match is not None:
# Note that we make the reference_id off of the reference before adding it,
# since adding the reference_id would destroy the uri field, as they are
# both in the same oneof. This allows us to copy fields from uri to
# reference_id without making an extra copy.
reference_id_field = get_reference_id_field_for_resource(
reference, internal_match.group('resource_type'))
reference_id = proto_utils.create_message_from_descriptor(
reference_id_field.message_type)
populate_typed_reference_id(reference_id,
internal_match.group('resource_id'),
internal_match.group('version'))
proto_utils.copy_common_field(uri, reference_id, 'id')
proto_utils.copy_common_field(uri, reference_id, 'extension')
proto_utils.set_value_at_field(reference, reference_id_field,
reference_id)
return
fragment_match = re.fullmatch(_FRAGMENT_REFERENCE_PATTERN, uri.value)
if fragment_match is not None:
# Note that we make the fragment off of the reference before adding it,
# since adding the fragment would destroy the uri field, as they are both in
# the same oneof. This allows us to copy fields from uri to fragment without
# making an extra copy.
fragment_field = reference.DESCRIPTOR.fields_by_name['fragment']
fragment = proto_utils.create_message_from_descriptor(
fragment_field.message_type)
value_field = fragment.DESCRIPTOR.fields_by_name['value']
proto_utils.set_value_at_field(fragment, value_field, uri.value[1:])
proto_utils.copy_common_field(uri, fragment, 'id')
proto_utils.copy_common_field(uri, fragment, 'extension')
proto_utils.set_value_at_field(reference, fragment_field, fragment)
return
raise ValueError(f'String {uri.value!r} cannot be parsed as a reference.')
def _parse_field_value(self, field: descriptor.FieldDescriptor,
json_value: Any) -> message.Message:
"""Returns a new Message described by the FieldDescriptor and json_value.
Args:
field: The FieldDescriptor of the Message instance to create.
json_value: The JSON value representation to merge into the newly created
Message.
Returns:
A new Message as described by the provided FieldDescriptor merged with the
contents of json_value.
"""
if field.type != descriptor.FieldDescriptor.TYPE_MESSAGE:
raise ValueError('Error in FHIR proto definition, field: '
f'{field.full_name} is not a message.')
if field.message_type.full_name == any_pb2.Any.DESCRIPTOR.full_name:
contained = self.primitive_handler.new_contained_resource()
self._merge_contained_resource(json_value, contained)
any_message = any_pb2.Any()
any_message.Pack(contained)
return any_message
else:
target = proto_utils.create_message_from_descriptor(
field.message_type)
self.merge_value(json_value, target)
return target
def test_no_value_behaviour_valid(self):
for primitive_data in self.primitive_data_list:
file_name = primitive_data.name
field_type = primitive_data.field_type
# Xhtml cannot have extentions. It is always consdered to have a value.
# So we are not testing it here.
if file_name == 'Xhtml':
continue
# It's ok to have no value if there's at least another extension present
# (More than one extension).
primitive_with_no_value = field_type()
self._set_primitive_has_no_value_extension(
primitive_with_no_value)
# Add arbitrary extension.
extensions_field = primitive_with_no_value.DESCRIPTOR.fields_by_name[
'extension']
extension = proto_utils.create_message_from_descriptor(
extensions_field.message_type)
cast(Any, extension).url.value = 'abcd'
cast(Any, extension).value.boolean.value = True
proto_utils.append_value_at_field(primitive_with_no_value,
'extension', extension)
_ = self.json_format.print_fhir_to_json_string(
primitive_with_no_value)
def testCreateMessageFromDescriptor_withArguments_returnsMessage(self):
"""Tests that the correct class is instantiated with kwargs."""
patient_name = datatypes_pb2.HumanName(
text=datatypes_pb2.String(value="Foo"),
family=datatypes_pb2.String(value="Bar"))
expected_patient = patient_pb2.Patient(name=[patient_name])
actual_patient = proto_utils.create_message_from_descriptor(
patient_pb2.Patient.DESCRIPTOR, name=[patient_name])
self.assertEqual(expected_patient, actual_patient)
def create_primitive_has_no_value(
desc: descriptor.Descriptor) -> message.Message:
"""Returns a PrimitiveHasNoValue extension provided a descriptor."""
primitive_has_no_value = proto_utils.create_message_from_descriptor(desc)
# Silencing the type checkers as pytype doesn't fully support structural
# subtyping yet.
# See: https://mypy.readthedocs.io/en/stable/casts.html#casts-and-type-assertions.
# Soon: https://www.python.org/dev/peps/pep-0544/.
cast(Any, primitive_has_no_value).url.value = PRIMITIVE_HAS_NO_VALUE_URL
cast(Any, primitive_has_no_value).value.boolean.value = True
return primitive_has_no_value
def test_no_value_behaviour_valid(self, field_type: Type[message.Message]):
# It's ok to have no value if there's another extension present
# (Two extensions in total).
primitive_with_no_value = field_type()
self._set_primitive_has_no_value_extension(primitive_with_no_value)
# Add arbitrary extension.
extensions_field = primitive_with_no_value.DESCRIPTOR.fields_by_name[
'extension']
extension = proto_utils.create_message_from_descriptor(
extensions_field.message_type)
cast(Any, extension).url.value = 'abcd'
cast(Any, extension).value.boolean.value = True
proto_utils.append_value_at_field(primitive_with_no_value, 'extension',
extension)
_ = json_format.print_fhir_to_json_string(primitive_with_no_value)
def get_element(self) -> Optional[message.Message]:
"""Returns the raw Element underlying the wrapped primitive.
Note that conversion-only extensions are removed prior to returning.
"""
if not (proto_utils.field_is_set(self.wrapped, 'id') or
proto_utils.field_is_set(self.wrapped, 'extension')):
return None # Early-exit if we can't populate an Element
element = proto_utils.create_message_from_descriptor(
self.wrapped.DESCRIPTOR)
if proto_utils.field_is_set(self.wrapped, 'id'):
proto_utils.copy_common_field(self.wrapped, element, 'id')
extensions_list = cast(List[Any],
extensions.get_fhir_extensions(self.wrapped))
for extension in extensions_list:
if extension.url.value not in extensions.CONVERSION_ONLY_EXTENSION_URLS:
proto_utils.append_value_at_field(element, 'extension', extension)
return element
def testCreateMessageFromDescriptor_returnsMessage(self):
"""Tests that the correct class is returned for a message."""
self.assertEqual(
proto_utils.create_message_from_descriptor(
patient_pb2.Patient.DESCRIPTOR), patient_pb2.Patient())
def split_if_relative_reference(reference: message.Message):
"""If possible, parses a `Reference` `uri` into more structured fields.
This is only possible for two forms of reference uris:
* Relative references of the form $TYPE/$ID, e.g., "Patient/1234"
In this case, this will be parsed to a proto of the form:
{patient_id: {value: "1234"}}
* Fragments of the form "#$FRAGMENT", e.g., "#vs1". In this case, this would
be parsed into a proto of the form:
{fragment: {value: "vs1"} }
If the reference URI matches one of these schemas, the `uri` field will be
cleared, and the appropriate structured fields set. Otherwise, the reference
will be unchanged.
Args:
reference: The FHIR reference to potentially split.
Raises:
ValueError: If the message is not a valid FHIR Reference proto.
"""
_validate_reference(reference)
uri_field = reference.DESCRIPTOR.fields_by_name.get('uri')
if not proto_utils.field_is_set(reference, uri_field):
return # No URI to split
uri = proto_utils.get_value_at_field(reference, uri_field)
internal_match = re.fullmatch(_INTERNAL_REFERENCE_PATTERN, uri.value)
if internal_match is not None:
# Note that we make the reference_id off of the reference before adding it,
# since adding the reference_id would destroy the uri field, as they are
# both in the same oneof. This allows us to copy fields from uri to
# reference_id without making an extra copy.
reference_id_field = get_reference_id_field_for_resource(
reference, internal_match.group('resource_type'))
reference_id = proto_utils.create_message_from_descriptor(
reference_id_field.message_type)
populate_typed_reference_id(reference_id,
internal_match.group('resource_id'),
internal_match.group('version'))
proto_utils.copy_common_field(uri, reference_id, 'id')
proto_utils.copy_common_field(uri, reference_id, 'extension')
proto_utils.set_value_at_field(reference, reference_id_field, reference_id)
return
fragment_match = re.fullmatch(_FRAGMENT_REFERENCE_PATTERN, uri.value)
if fragment_match is not None:
# Note that we make the fragment off of the reference before adding it,
# since adding the fragment would destroy the uri field, as they are both in
# the same oneof. This allows us to copy fields from uri to fragment without
# making an extra copy.
fragment_field = reference.DESCRIPTOR.fields_by_name['fragment']
fragment = proto_utils.create_message_from_descriptor(
fragment_field.message_type)
value_field = fragment.DESCRIPTOR.fields_by_name['value']
proto_utils.set_value_at_field(fragment, value_field, uri.value[1:])
proto_utils.copy_common_field(uri, fragment, 'id')
proto_utils.copy_common_field(uri, fragment, 'extension')
proto_utils.set_value_at_field(reference, fragment_field, fragment)
return