def error_response(scope: Scope, errors) -> Response:
default = MIME_FHIR_VERSION_MAP[DEFAULT_FHIR_VERSION]
klass = lookup_fhir_class("OperationOutcome", fhir_release=default)
issues = list()
for error in errors:
issue = {
"severity":
"fatal",
"code":
"value",
"details": {
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/operation-outcome",
"code": "MSG_BAD_FORMAT",
"display": error["msg"],
}]
},
"diagnostics":
f"Request loc: {error['loc']}, Original Value: {error['original']}",
}
issues.append(issue)
outcome = klass(**{
"id": str(scope["FHIR_REQUEST_ID"]),
"issue": issues
})
return FHIRHttpJsonResponse(outcome,
status_code=422,
fhir_version=default,
locked=True)
def make_outcome(request: Request, exc: RequestValidationError):
"""
https://terminology.hl7.org/2.0.0/CodeSystem-operation-outcome.html
:param exc:
:param status_code:
:return:
"""
klass = lookup_fhir_class(
"OperationOutcome", fhir_release=request.scope["FHIR_VERSION"]
)
issues = list()
for error in exc.errors():
issue = {
"severity": "error",
"code": exc.code,
"details": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/operation-outcome",
"code": exc.system_code,
"display": exc.body,
}
]
},
"diagnostics": f"loc: {error['loc']}, message: {error['msg']}",
}
issues.append(issue)
outcome = klass(**{"id": str(request.scope["FHIR_REQUEST_ID"]), "issue": issues})
return outcome
def test_fhirpath_list_type_info():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Patient.json"), "r") as fp:
data = fp.read()
obj = lookup_fhir_class("Patient", FHIR_VERSION.R4).parse_raw(data)
fpath = fhirpath.FHIRPath(obj)
assert isinstance(fpath.address.get_type(), fhirpath.ListTypeInfo)
assert fpath.address.get_type().elementType == "FHIR.Address"
assert isinstance(
fhirpath.FHIRPath.__storage__[fpath.address.get_type().elementType],
fhirpath.ClassInfo,
)
with pytest.raises(ValueError) as exc_info:
fhirpath.FHIRPath(["mu", "mn"])
assert "root fhirpath cannot be initialized" in exc_info.value.args[0]
obj.address = None
fpath = fhirpath.FHIRPath(obj)
assert isinstance(fpath.address.get_type(), fhirpath.ListTypeInfo)
obj.address = []
fpath = fhirpath.FHIRPath(obj)
assert isinstance(fpath.address.get_type(), fhirpath.ListTypeInfo)
assert isinstance(fpath.extension.get_type(), fhirpath.ListTypeInfo)
assert fpath.extension() is None
def test_fhirpath_tuple_type_info():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Patient.json"), "r") as fp:
data = fp.read()
obj = lookup_fhir_class("Patient", FHIR_VERSION.R4).parse_raw(data)
fpath = fhirpath.FHIRPath(obj)
assert isinstance(fpath.contact[0].get_type(), fhirpath.TupleTypeInfo)
assert len(fpath.contact[0].get_type().get_elements()) == 10
def test_existence_5_1_1_empty():
""" """
obj = lookup_fhir_class("Patient", FHIR_VERSION.R4).parse_file(
FHIR_EXAMPLE_RESOURCES / "Patient.json")
f_path = fhirpath.FHIRPath(obj)
assert f_path.name.empty() is False
assert f_path.name.count() == 2
assert f_path.extension.empty() is True
assert f_path.extension.count() == 0
async def fhir_resource_from_request(request: Request, resource_type: str) -> BaseModel:
"""
:param request:
:param resource_type:
:return:
"""
raw = await request.body()
klass = lookup_fhir_class(resource_type, request.scope["FHIR_VERSION"])
obj = klass.parse_raw(raw)
return obj
def test_bundle_response_as_dict(self):
""" """
self.load_contents()
context = self.get_context("Task", True)
result = zcatalog_fhir_search(context,
bundle_response=True,
bundle_as_dict=True)
self.assertIsInstance(result, dict)
try:
bundle = lookup_fhir_class("Bundle",
FHIR_VERSION.STU3).parse_obj(result)
self.assertEqual(len(bundle.entry), len(result["entry"]))
except Exception:
raise AssertionError("Code should not come here.")
def test_fhirpath_class_type_info():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Patient.json"), "r") as fp:
data = fp.read()
obj = lookup_fhir_class("Patient", FHIR_VERSION.R4).parse_raw(data)
fpath = fhirpath.FHIRPath(obj)
assert isinstance(fpath.get_type(), fhirpath.ClassInfo)
# Patient has 26 elements
assert len(fpath.get_type().element) == 26
assert fpath.get_type().name == "Patient"
assert fpath.get_type().baseType == "FHIR.DomainResource"
# Test Element from Base
assert fpath.meta.get_type().name == "Meta"
def test_fhir_field_value_pickling():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Organization.json"), "r") as fp:
fhir_json = json.load(fp)
model = implementer(IFhirResource)(lookup_fhir_class(
fhir_json["resourceType"]))
fhir_resource = model(fhir_json)
fhir_resource_value = FhirFieldValue(obj=fhir_resource)
serialized = pickle.dumps(fhir_resource_value)
deserialized = pickle.loads(serialized)
assert len(deserialized.stringify()) == len(
fhir_resource_value.stringify())
def test_fhirpath_simple_type_info():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Patient.json"), "r") as fp:
data = fp.read()
obj = lookup_fhir_class("Patient", FHIR_VERSION.R4).parse_raw(data)
fpath = fhirpath.FHIRPath(obj)
assert fpath.gender.get_type().name == "code"
assert fpath.gender.get_type().baseType == "FHIR.Primitive"
assert fpath.active.get_type().name == "boolean"
assert fpath.identifier[0].type.text.get_type().name == "string"
obj.gender = None
obj.active = None
fpath = fhirpath.FHIRPath(obj)
assert fpath.gender.get_type().name == "code"
assert fpath.active.get_type().name == "boolean"
async def test_fhir_field_value_serializer(dummy_request):
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Organization.json"), "r") as fp:
fhir_json = json.load(fp)
model = implementer(IFhirResource)(lookup_fhir_class(
fhir_json["resourceType"]))
fhir_resource = model(fhir_json)
value = FhirFieldValue(obj=fhir_resource)
serialized = query_adapter(value, IValueToJson)
assert serialized == value.as_json()
serialized = query_adapter(FhirFieldValue(), IValueToJson)
assert serialized is None
def _from_dict(self, dict_value):
""" """
self._pre_value_validate(dict_value)
klass = self._resource_class
if klass is None:
# relay on json value for resource type
klass = implementer(IFhirResource)(
lookup_fhir_class(dict_value["resourceType"])
)
# check constraint
if klass.resource_type != dict_value.get("resourceType"):
raise ConstraintNotSatisfied(
"Fhir Resource mismatched with provided resource type!\n"
"`{0}` resource type is permitted but got `{1}`".format(
klass.resource_type, dict_value.get("resourceType")
),
field_name=self.getName(),
)
value = FhirFieldValue(obj=klass(dict_value))
return value
def _init(
self, resource_class, resource_interface, resource_type, fhir_release, **kw
):
""" """
if "default" in kw:
if (
isinstance(kw["default"], (str, dict)) or kw["default"] is None
) is False:
msg = (
"Only dict or string or None is accepted as "
"default value but got {0}".format(type(kw["default"]))
)
raise Invalid(msg)
field_attributes = get_fields(IFhirField)
attribute = field_attributes["resource_class"].bind(self)
if resource_class is None:
attribute.validate(resource_class)
attribute_val = None
else:
attribute_val = attribute.from_unicode(resource_class)
attribute.set(self, attribute_val)
attribute = field_attributes["resource_interface"].bind(self)
if resource_interface is None:
attribute.validate(resource_interface)
attribute_val = None
else:
attribute_val = attribute.from_unicode(resource_interface)
attribute.set(self, attribute_val)
attribute = field_attributes["resource_type"].bind(self)
if resource_type is None:
attribute.validate(resource_type)
attribute_val = None
else:
attribute_val = attribute.from_unicode(resource_type)
attribute.set(self, attribute_val)
attribute = field_attributes["fhir_release"].bind(self)
if fhir_release is None:
attribute.validate(fhir_release)
attribute_val = None
else:
attribute_val = attribute.from_unicode(fhir_release)
# just for ensure correct value
FHIR_VERSION[attribute_val]
attribute.set(self, attribute_val)
if self.resource_type and self.resource_class is not None:
raise Invalid(
"Either `resource_class` or `resource_type` value is acceptable! "
"you cannot provide both!"
)
if self.resource_class:
try:
klass = import_string(self.resource_class)
self.ensure_fhir_abstract(klass)
except ImportError:
msg = (
"Invalid FHIR Resource class `{0}`! "
"Please check the module or class name."
).format(self.resource_class)
return reraise(Invalid, msg)
if not IFhirResource.implementedBy(klass):
raise Invalid(
"{0!r} must be valid resource class from fhir.resources".format(
klass
)
)
self._resource_class = klass
if self.resource_type:
try:
self._resource_class = implementer(IFhirResource)(
lookup_fhir_class(self.resource_type)
)
except ImportError:
msg = "{0} is not valid fhir resource type!".format(self.resource_type)
return reraise(Invalid, msg)
if self.resource_interface:
try:
klass = implementer(IFhirResource)(
import_string(self.resource_interface)
)
except ImportError:
msg = (
"Invalid FHIR Resource Interface`{0}`! "
"Please check the module or class name."
).format(self.resource_interface)
return reraise(Invalid, msg)
if not IInterface.providedBy(klass):
raise WrongType("An interface is required", klass, self.__name__)
if klass is not IFhirResource and not issubclass(klass, IFhirResource):
msg = "`{0!r}` must be derived from {1}".format(
klass,
IFhirResource.__module__ + "." + IFhirResource.__class__.__name__,
)
raise Invalid(msg)
self._resource_interface_class = klass
def test_fhir_field_value():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Organization.json"), "r") as f:
fhir_json = json.load(f)
model = implementer(IFhirResource)(lookup_fhir_class(
fhir_json["resourceType"]))
fhir_resource = model(fhir_json)
fhir_resource_value = FhirFieldValue(obj=fhir_resource)
# __bool__ should be True
assert bool(fhir_resource_value) is True
assert IFhirResource.providedBy(
fhir_resource_value.foreground_origin()) is True
assert isinstance(fhir_resource_value.stringify(), str) is True
# Test Patch
patch_data = {"hello": 123}
try:
fhir_resource_value.patch(patch_data)
raise AssertionError(
"Code should not come here! because wrong type data is provided for patch!"
)
except WrongType:
pass
patch_data = [{
"path": "/text/fake path",
"value": "patched!",
"Invalid Option": "replace"
}]
# Test getting original error from json patcher
try:
fhir_resource_value.patch(patch_data)
raise AssertionError(
"Code should not come here! because wrong patch data is"
" provided for patch and invalid format as well!")
except Invalid as exc:
assert "does not contain 'op' member" in str(exc)
patch_data = [{
"path": "/text/status",
"value": "patched!",
"op": "replace"
}]
fhir_resource_value.patch(patch_data)
assert "patched!" == fhir_resource_value.text.status
# Make sure string is transformable to fhir resource
json_str = fhir_resource_value.stringify()
json_dict = parse_json_str(json_str)
try:
model(json_dict).as_json()
except Exception:
raise AssertionError("Code should not come here!")
# Test self representation
assert fhir_resource_value.__class__.__module__ in repr(
fhir_resource_value)
empty_resource = FhirFieldValue()
# __bool__ should be False
assert bool(empty_resource) is False
assert empty_resource.foreground_origin() is None
# assert (fhir_resource_value == empty_resource) is False
# assert (empty_resource == fhir_resource_value) is False
# assert (empty_resource != fhir_resource_value) is True
# Test Patch with empty value
try:
empty_resource.patch(patch_data)
raise AssertionError(
"Code should not come here! because empty resource cannot be patched!"
)
except Invalid:
pass
# Let's try to modify
fhir_resource_value.identifier[0].use = "no-official"
# test if it impact
assert fhir_resource_value.as_json(
)["identifier"][0]["use"] == "no-official"
# Let's try to set value on empty value
try:
empty_resource.id = "my value"
raise AssertionError(
"Code should not come here! because no fhir resource!")
except AttributeError:
pass
assert "NoneType" in repr(empty_resource)
assert "" == str(empty_resource)
# Validation Test:: more explict???
try:
FhirFieldValue(obj=dict(hello="Ketty"))
raise AssertionError(
"Code should not come here, because should raise validation error!"
)
except (WrongType, Invalid):
pass
@implementer(IFhirResource)
class TestBrokenInterfaceObject(object):
def __init__(self):
pass
broken_obj = TestBrokenInterfaceObject()
try:
fhir_resource_value._validate_object(broken_obj)
raise AssertionError(
"Code should not come here! because of validation error")
except Invalid as exc:
assert " attribute was not provided" in str(exc)
def test_field_validate():
""" """
with open(str(FHIR_EXAMPLE_RESOURCES / "Organization.json"), "r") as f:
json_dict = json.load(f)
organization = implementer(IFhirResource)(
lookup_fhir_class("Organization"))(json_dict)
fhir_resource_value = FhirFieldValue(obj=organization)
fhir_field = FhirField(title="Organization resource", fhir_release="R4")
try:
fhir_field._validate(fhir_resource_value)
except Invalid as exc:
raise AssertionError("Code should not come here!\n{0!s}".format(exc))
# Test wrong type value!
try:
fhir_field._validate(dict(hello="wrong"))
raise AssertionError(
"Code should not come here! wrong data type is provide")
except WrongType as exc:
assert "fhirpath_guillotina.field.FhirFieldValue" in str(exc)
type_, address_ = fhir_resource_value.type, fhir_resource_value.address
fhir_resource_value.type = 390
fhir_resource_value.address = "i am wrong type"
try:
fhir_field._validate(fhir_resource_value)
raise AssertionError(
"Code should not come here! wrong element data type is provided")
except Invalid as exc:
assert "invalid element inside fhir model object" in str(exc)
# Restore
fhir_resource_value.type = type_
fhir_resource_value.address = address_
# Test model constraint
fhir_field = FhirField(
title="Organization resource",
resource_class="tests.fixtures.MyTaskResource",
fhir_release="R4",
)
try:
fhir_field._validate(fhir_resource_value)
raise AssertionError("Code should not come here! model mismatched!")
except WrongContainedType as exc:
assert "Wrong fhir resource value" in str(exc)
# Test resource type constraint!
fhir_field = FhirField(title="Organization resource",
resource_type="Task",
fhir_release="R4")
try:
fhir_field._validate(fhir_resource_value)
raise AssertionError("Code should not come here! model mismatched!")
except ConstraintNotSatisfied as exc:
assert "Resource type must be `Task`" in str(exc)
# Wrong interface attributes
fhir_field = FhirField(
title="Organization resource",
resource_interface="tests.fixtures.IWrongInterface",
fhir_release="R4",
)
try:
fhir_field._validate(fhir_resource_value)
raise AssertionError(
"Code should not come here! interface and object mismatched!")
except Invalid as exc:
assert "has failed to implement interface" in str(exc)