def _validate_field(msg: message.Message, field: descriptor.FieldDescriptor,
field_name: str,
primitive_handler_: primitive_handler.PrimitiveHandler):
"""Validates that required fields are set, and performs basic temporal checks.
Args:
msg: The Message that the field belongs to.
field: The FieldDescriptor of the field to examine.
field_name: The name of the field.
primitive_handler_: Responsible for returning PrimitiveWrappers.
Raises:
fhir_errors.InvalidFhirError: In the event that a required field is not set
or if temporal requirements are not met.
"""
if annotation_utils.field_is_required(
field) and not proto_utils.field_is_set(msg, field):
raise fhir_errors.InvalidFhirError(
f'Required field `{field.full_name}` is missing.')
if annotation_utils.is_reference(field.message_type):
_validate_reference_field(msg, field)
return
if field.type == descriptor.FieldDescriptor.TYPE_MESSAGE:
# Returns the first value only for a singular field
for i in range(proto_utils.field_content_length(msg, field)):
submessage = proto_utils.get_value_at_field_index(msg, field, i)
_validate_fhir_constraints(submessage, field_name,
primitive_handler_)
# Run extra validation for some types, until FHIRPath validation covers
# these as well
if fhir_types.is_period(submessage):
_validate_period(submessage, field_name)
def testAppendValueAtField_repeatedCompositeValue_appendsValue(self):
"""Test append_value_at_field with a repeated composite type."""
patient = patient_pb2.Patient()
patient_names = [
datatypes_pb2.HumanName(text=datatypes_pb2.String(value="Foo")),
datatypes_pb2.HumanName(text=datatypes_pb2.String(value="Bar")),
datatypes_pb2.HumanName(text=datatypes_pb2.String(value="Bats")),
]
self.assertEqual(proto_utils.field_content_length(patient, "name"), 0)
for name in patient_names:
proto_utils.append_value_at_field(patient, "name", name)
self.assertEqual(proto_utils.field_content_length(patient, "name"), 3)
self.assertEqual(patient.name[:], patient_names)
def _validate_reference_field(parent: message.Message,
field: descriptor.FieldDescriptor):
"""Ensure that the provided reference field is valid.
Args:
parent: The containing Message.
field: The reference field descriptor.
Raises:
fhir_errors.InvalidFhirError: In the event of an empty reference (no
extensions, no identifier, no display).
"""
oneof = field.message_type.oneofs[0]
# Singular fields have a length of 1
for i in range(proto_utils.field_content_length(parent, field)):
reference = proto_utils.get_value_at_field_index(parent, field, i)
reference_field_name = reference.WhichOneof(oneof.name)
if reference_field_name is None:
if not (reference.extension or reference.HasField('identifier')
or reference.HasField('display')):
raise fhir_errors.InvalidFhirError(
f'`{reference.DESCRIPTOR.name}` is an empty reference.')
# There's no reference field, but there is other data. This is valid.
return
field_options = field.GetOptions()
if not field_options.Extensions[annotations_pb2.valid_reference_type]:
# The reference field does not have restrictions, so any value is fine.
return
if reference.HasField('uri') or reference.HasField('fragment'):
# Uri and Fragment references are untyped.
return
# There are no reference annotations for DSTU2; skip validation
if annotation_utils.get_fhir_version(
reference) == annotations_pb2.FhirVersion.DSTU2:
return
reference_field = reference.DESCRIPTOR.fields_by_name[
reference_field_name]
if annotation_utils.is_typed_reference_field(reference_field):
# Ensure that the reference type is listed as "valid"
reference_type = reference_field.GetOptions().Extensions[
annotations_pb2.referenced_fhir_type]
is_allowed = False
for valid_type in field_options.Extensions[
annotations_pb2.valid_reference_type]:
if valid_type == reference_type or valid_type == 'Resource':
is_allowed = True
break
if not is_allowed:
raise fhir_errors.InvalidFhirError(
f'Message `{parent.DESCRIPTOR.full_name}` contains an invalid '
f'reference type: `{reference_type}` set at: '
f'`{reference_field_name}`.')
def _add_fields_to_extension(msg: message.Message, extension: message.Message):
"""Adds the fields from message to extension."""
for field in msg.DESCRIPTOR.fields:
_verify_field_is_proto_message_type(field)
# Add submessages to nested extensions; singular fields have a length of 1
for i in range(proto_utils.field_content_length(msg, field)):
child_extension = proto_utils.set_in_parent_or_add(
extension, 'extension')
cast(Any,
child_extension).url.value = get_inlined_extension_url(field)
value = proto_utils.get_value_at_field_index(msg, field, i)
_add_value_to_extension(
value, child_extension,
annotation_utils.is_choice_type_field(field))
def testFieldContentLength_withNonExistentField_returnsZero(self):
"""Test field_content_length functionality on non-existent field input."""
default_patient = patient_pb2.Patient() # Leave active unset
self.assertEqual(
proto_utils.field_content_length(default_patient, "active"), 0)
def testFieldContentLength_withSingularField_returnsSingleCount(self): """Test field_content_length functionality on singular field input.""" patient = patient_pb2.Patient(active=datatypes_pb2.Boolean(value=True)) self.assertEqual(proto_utils.field_content_length(patient, "active"), 1)
def testFieldContentLength_withRepeatedField_returnsContentLength(self): """Test field_content_length functionality on repeated field input.""" patient = self._create_patient_with_names(["A", "B", "C"]) self.assertEqual(proto_utils.field_content_length(patient, "name"), 3)
def _merge_field(self, json_value: Any, field: descriptor.FieldDescriptor,
parent: message.Message):
"""Merges the json_value into the provided field of the parent Message.
Args:
json_value: The JSON value to set.
field: The FieldDescriptor of the field to set in parent.
parent: The parent Message to set the value on.
Raises:
ValueError: In the event that a non-primitive field has already been set.
ValueError: In the event that a oneof field has already been set.
"""
# If the field is non-primitive, ensure that it hasn't been set yet. Note
# that we allow primitive types to be set already, because FHIR represents
# extensions to primitives as separate, subsequent JSON elements, with the
# field prepended by an underscore
if (not annotation_utils.is_primitive_type(field.message_type)
and proto_utils.field_is_set(parent, field)):
raise ValueError('Target field {} is already set.'.format(
field.full_name))
# Consider it an error if a oneof field is already set.
#
# Exception: When a primitive in a choice type has a value and an extension,
# it will get set twice, once by the value (e.g. valueString) and once by an
# extension (e.g., _valueString)
if field.containing_oneof is not None:
oneof_field = parent.DESCRIPTOR.oneofs_by_name[
field.containing_oneof.name]
if (annotation_utils.is_primitive_type(field.message_type)
and oneof_field.full_name == field.full_name):
raise ValueError(
'Cannot set field {} since oneof field {} is already set.'.
format(field.full_name, oneof_field.full_name))
# Ensure that repeated fields get proper list assignment
existing_field_size = proto_utils.field_content_length(parent, field)
if proto_utils.field_is_repeated(field):
if not isinstance(json_value, list):
raise ValueError(
f'Attempted to merge a repeated field, {field.name}, a json_value '
f'with type {type(json_value)} instead of a list.')
if existing_field_size != 0 and existing_field_size != len(
json_value):
raise ValueError(
'Repeated primitive list length does not match extension list for '
'field: {field.full_name!r}.')
# Set the JSON values, taking care to clear the PRIMITIVE_HAS_NO_VALUE_URL
# if we've already visited the field before.
json_value = (json_value if proto_utils.field_is_repeated(field) else
[json_value])
for (i, value) in enumerate(json_value):
parsed_value = self._parse_field_value(field, value)
if existing_field_size > 0:
field_value = proto_utils.get_value_at_field_index(
parent, field, i)
field_value.MergeFrom(parsed_value)
extensions.clear_fhir_extensions_with_url(
field_value, extensions.PRIMITIVE_HAS_NO_VALUE_URL)
else:
field_value = proto_utils.set_in_parent_or_add(parent, field)
field_value.MergeFrom(parsed_value)
def add_extension_to_message(extension: message.Message, msg: message.Message):
"""Recursively parses extension and adds to message.
Args:
extension: The FHIR extension to serialize and add.
msg: The message to add the extension onto
Raises:
InvalidFhirError: In the event that a value is set on the extension, but the
corresponding message field to copy it to is repeated (extension values are
singular only).
"""
desc = msg.DESCRIPTOR
fields_by_url = {
get_inlined_extension_url(field): field
for field in desc.fields if field.name != 'id'
}
# Copy the id field if present
id_field = desc.fields_by_name.get('id')
if proto_utils.field_is_set(extension, id_field):
proto_utils.set_value_at_field(msg, id_field, cast(Any, extension).id)
# Handle simple extensions (only one value present)
if proto_utils.field_is_set(extension, 'value'):
if len(fields_by_url) != 1:
raise fhir_errors.InvalidFhirError(
f'Expected a single field, found {len(fields_by_url)}; '
f'{desc.full_name} is an invalid extension type.')
field = list(fields_by_url.items())[0][1]
if proto_utils.field_is_repeated(field):
raise fhir_errors.InvalidFhirError(
f'Expected {field.full_name} to be a singular field. '
f'{desc.full_name} is an invalid extension type.')
_add_extension_value_to_message(extension, msg, field)
return
# Else, iterate through all child extensions...
child_extensions = proto_utils.get_value_at_field(extension, 'extension')
for child_extension in child_extensions:
field = fields_by_url.get(child_extension.url.value)
if field is None:
raise ValueError(f'Message of type: {desc.full_name} has no field '
f'with name: {child_extension.url.value}.')
# Simple value type on child_extension...
if proto_utils.field_is_set(child_extension, 'value'):
_add_extension_value_to_message(child_extension, msg, field)
continue
# Recurse for nested composite messages...
if not proto_utils.field_is_repeated(field):
if proto_utils.field_is_set(msg, field):
raise ValueError(
f'Field: {field.full_name} is already set on message: '
f'{desc.full_name}.')
if proto_utils.field_content_length(child_extension,
'extension') > 1:
raise ValueError(
f'Cardinality mismatch between field: {field.full_name} and '
f'extension: {desc.full_name}.')
child_message = proto_utils.set_in_parent_or_add(msg, field)
add_extension_to_message(child_extension, child_message)
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)
