def get_value_for_annotation_extension(
message_or_descriptor: proto_utils.MessageOrDescriptorBase,
extension_field: descriptor.FieldDescriptor) -> Optional[Any]:
"""Returns the value associated with the annotation extension field.
Args:
message_or_descriptor: A protobuf DescriptorProto, Message, or
DescriptorBase to examine.
extension_field: A FieldDescriptor describing the annotation whose value to
retrieve.
Returns:
The value associated with extension_field, if one exists. Otherwise returns
None.
Raises:
ValueError: Unable to retrieve Options for type: <type>.
"""
options = get_options(message_or_descriptor)
if proto_utils.field_is_repeated(extension_field):
return options.Extensions[extension_field]
if options.HasExtension(extension_field):
return options.Extensions[extension_field]
return None
def _print_message_field(self, field_name: str,
field: descriptor.FieldDescriptor, value: Any):
"""Prints singular and repeated fields from a message."""
self.generator.add_field(field_name)
if proto_utils.field_is_repeated(field):
self._print_list(cast(List[Any], value), self._print)
else:
self._print(cast(message.Message, value))
def _print_primitive_field(self, field_name: str,
field: descriptor.FieldDescriptor,
value: Any) -> None:
"""Prints the primitive field.
Args:
field_name: The name of the field.
field: The FielDescriptor whose contents to print.
value: The value present at field to print.
"""
if proto_utils.field_is_repeated(field):
string_values = []
elements = []
extensions_found = False
nonnull_values_found = False
for primitive in value:
wrapper = self.primitive_handler.primitive_wrapper_from_primitive(
primitive)
string_values.append(wrapper.json_value())
elements.append(wrapper.get_element())
nonnull_values_found = nonnull_values_found or wrapper.has_value(
)
extensions_found = extensions_found or wrapper.has_element()
# print string primitive representations
if nonnull_values_found:
self.generator.add_field(field_name)
self._print_list(string_values, self.generator.push)
# print Element representations
if extensions_found:
if nonnull_values_found:
self.generator.push(',')
self.generator.add_newline()
self.generator.add_field(f'_{field_name}')
self._print_list(elements, self._print)
else: # Singular field
# TODO: Detect ReferenceId using an annotation
if (self.json_format == _FhirJsonFormat.ANALYTIC
and field.message_type.name == 'ReferenceId'):
str_value = proto_utils.get_value_at_field(value, 'value')
self.generator.add_field(field_name, f'"{str_value}"')
else: # Wrap and print primitive value and (optionally), its element
wrapper = self.primitive_handler.primitive_wrapper_from_primitive(
value)
if wrapper.has_value():
self.generator.add_field(field_name, wrapper.json_value())
if wrapper.has_element(
) and self.json_format == _FhirJsonFormat.PURE:
if wrapper.has_value():
self.generator.push(',')
self.generator.add_newline()
self.generator.add_field(f'_{field_name}')
self._print(wrapper.get_element())
def add_message_to_extension(msg: message.Message,
extension: message.Message) -> None:
"""Adds the contents of msg to extension.
Args:
msg: A FHIR profile of Extension, whose contents should be added to the
generic extension.
extension: The generic Extension to populate.
"""
if not fhir_types.is_profile_of_extension(msg):
raise ValueError(f'Message: {msg.DESCRIPTOR.full_name} is not a valid '
'FHIR Extension profile.')
if not fhir_types.is_extension(extension):
raise ValueError(
f'Extension: {extension.DESCRIPTOR.full_name} is not a '
'valid FHIR Extension.')
cast(Any,
extension).url.value = annotation_utils.get_structure_definition_url(
msg.DESCRIPTOR)
# Copy over the id field if present
if proto_utils.field_is_set(msg, 'id'):
proto_utils.copy_common_field(msg, extension, 'id')
# Copy the vlaue fields from message into the extension
value_fields = [
field for field in msg.DESCRIPTOR.fields
if field.name not in NON_VALUE_FIELDS
]
if not value_fields:
raise ValueError(
f'Extension has no value fields: {msg.DESCRIPTOR.name}.')
# Add fields to the extension. If there is a single value field, a simple
# value assignment will suffice. Otherwise, we need to loop over all fields
# and add them as child extensions
if (len(value_fields) == 1
and not proto_utils.field_is_repeated(value_fields[0])):
value_field = value_fields[0]
_verify_field_is_proto_message_type(value_field)
if proto_utils.field_is_set(msg, value_field):
value = proto_utils.get_value_at_field(msg, value_field)
_add_value_to_extension(
value, extension,
annotation_utils.is_choice_type_field(value_field))
else:
# TODO: Invalid FHIR; throw an error here?
pass
else: # Add child extensions...
_add_fields_to_extension(msg, extension)
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)