def get_element(self) -> Optional[message.Message]:
"""Return Element of the primitive. Xhtml cannot have extensions."""
if not proto_utils.field_is_set(self.wrapped, 'id'):
return None
element = type(self.wrapped)()
proto_utils.copy_common_field(self.wrapped, element, 'id')
return element
def testCopyCommonField_notPresentInBothMessages_raisesException(self):
"""Tests copy_common_field with an invalid descriptor raises."""
first_patient = patient_pb2.Patient(
active=datatypes_pb2.Boolean(value=True))
second_patient = patient_pb2.Patient(
active=datatypes_pb2.Boolean(value=False))
with self.assertRaises(ValueError) as ve:
proto_utils.copy_common_field(first_patient, second_patient, "value")
self.assertIsInstance(ve.exception, ValueError)
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 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 testCopyCommonField_differentMessageTypes_succeeds(self):
"""Tests that copy_common_field succeeds on a single Message field."""
string_value = datatypes_pb2.String(id=datatypes_pb2.String(value="foo"))
boolean_value = datatypes_pb2.Boolean(id=datatypes_pb2.String(value="bar"))
# Before copy
self.assertEqual(string_value.id.value, "foo")
self.assertEqual(boolean_value.id.value, "bar")
proto_utils.copy_common_field(string_value, boolean_value, "id")
# After copy
self.assertEqual(string_value.id.value, "foo")
self.assertEqual(boolean_value.id.value, "foo")
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 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 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 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 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
