def parse_location(shell, input_wstl_arg, file_ext=None, load_contents=True):
r"""Parses the argument and returns a Location protobuf message.
Input arguments with the following prefixes are supported:
* json://{\"hello\": \"world\"} - using python dict and list notation to
define a json object or list.
* file://<file_path> - path to file on local file system.
* gs://<gcs_path> - path to file on Google Cloud Storage.
* py://<name_of_python_variable> - name of python variable instantiated within
session. Note that a python list will be parsed as a single JSON Array and a
single Location protobuf message is created. If list entries should be parsed
separately, use pylist instead.
* pylist://<name_of_python_variable> - name of python list variable
instantiated within session. Each entry in the list will be parsed as a
separate Location protobuf message.
Args:
shell: ipython interactive shell.
input_wstl_arg: wstl magic command input argument.
file_ext: list of valid file extensions. Either `_constants.JSON_FILE_EXT`
or `WSTL_FILE_EXT`.
load_contents: flag indicating whether to load contents from disk instead of
storing a path.
Returns:
A Location protobuf message.
Raises:
ValueError: An unknown location prefix or the python variable can not be
encoded into json.
"""
(inputs, gcs_paths) = _parser.parse_object(
shell, input_wstl_arg, file_ext=file_ext, load_contents=load_contents)
if input_wstl_arg.startswith(_constants.JSON_ARG_PREFIX) or \
input_wstl_arg.startswith(_constants.PYTHON_ARG_PREFIX) or \
input_wstl_arg.startswith(_constants.PYTHON_LIST_ARG_PREFIX) or \
input_wstl_arg.startswith(_constants.FILE_ARG_PREFIX):
if not load_contents:
return [
wstlservice_pb2.Location(local_path=inline_json)
for inline_json in inputs
]
else:
return [
wstlservice_pb2.Location(inline_json=inline_json)
for inline_json in inputs
]
elif input_wstl_arg.startswith(_constants.GS_ARG_PREFIX):
return [
wstlservice_pb2.Location(gcs_location=gcs_path)
for gcs_path in gcs_paths
]
else:
raise ValueError("Missing {} supported prefix".format(",".join([
_constants.JSON_ARG_PREFIX, _constants.GS_ARG_PREFIX,
_constants.PYTHON_ARG_PREFIX, _constants.PYTHON_LIST_ARG_PREFIX
])))
def test_fhir_validate_magic_gcs(self, mock_bucket, mock_client, mock_stub,
mock_channel):
class FakeChannel:
def __init__(self, channel):
self.channel = channel
def __enter__(self):
return self.channel
def __exit__(self, exc_type, exc_val, exc_tb):
self.channel._close()
return False
class FakeService:
def __init__(self, res):
self.resp = res
def FhirValidate(self, req):
del req
raise grpc.RpcError(code_pb2.UNIMPLEMENTED,
"GCS source not implemented yet")
class Item(object):
def __init__(self, bucket, name):
self.bucket = bucket
self.name = name
class FakeBucket(object):
def __init__(self, bucket_name):
self.name = bucket_name
mock_channel.return_value = FakeChannel(self._channel)
bucket = FakeBucket("fake_bucket")
items = [Item(bucket, "file.wstl")]
mock_bucket.list_blobs.return_value = items
mock_client.return_value.get_bucket.return_value = mock_bucket
ip = self.shell.get_ipython()
failure = ip.magics_manager.register(wstl.WSTLMagics)
self.assertIsNone(failure)
with mock.patch.object(FakeService, "FhirValidate") as mock_method:
mock_stub.return_value = FakeService(None)
mock_method.side_effect = grpc.RpcError
result = ip.run_line_magic(
"fhir_validate", "--version=stu3 --input=gs://fake_bucket/file.wstl")
self.assertIsInstance(result, grpc.RpcError)
req_gs = wstlservice_pb2.ValidationRequest(
fhir_version=wstlservice_pb2.ValidationRequest.FhirVersion.STU3,
input=[
wstlservice_pb2.Location(
gcs_location="gs://fake_bucket/file.wstl")
])
mock_method.assert_called_once_with(req_gs)
def test_fhir_validate_magic_ipython(self, mock_stub, mock_channel):
class FakeChannel:
def __init__(self, channel):
self.channel = channel
def __enter__(self):
return self.channel
def __exit__(self, exc_type, exc_val, exc_tb):
self.channel._close()
return False
class FakeService:
def __init__(self, res):
self.resp = res
def FhirValidate(self, req):
del req
return self.resp
mock_channel.return_value = FakeChannel(self._channel)
ip = self.shell.get_ipython()
failure = ip.magics_manager.register(wstl.WSTLMagics)
self.assertIsNone(failure)
st1 = "{'id':'example','resourceType':'Device','udi':{'carrierHRF':'test'}}"
st2 = "{'id':'example','resourceType':'3','udi':{'carrierHRF':'test'}}"
stList = [st1, st1]
ip.push("st1")
ip.push("st2")
ip.push("stList")
lines = [
"--version=stu3 --input=py://st1", "--version=stu3 --input=py://st2",
"--version=stu3 --input=py://stList",
"--version=stu3 --input=pylist://stList"
]
results = []
resps = [
wstlservice_pb2.ValidationResponse(status=[
status_pb2.Status(code=code_pb2.OK, message="Validation Success")
]),
wstlservice_pb2.ValidationResponse(status=[
status_pb2.Status(
code=code_pb2.INVALID_ARGUMENT, message="invalid FHIR resource")
]),
wstlservice_pb2.ValidationResponse(status=[
status_pb2.Status(
code=code_pb2.INVALID_ARGUMENT, message="invalid FHIR resource")
]),
wstlservice_pb2.ValidationResponse(status=[
status_pb2.Status(code=code_pb2.OK, message="Validation Success")
]),
]
reqs = [
wstlservice_pb2.ValidationRequest(
fhir_version=wstlservice_pb2.ValidationRequest.FhirVersion.STU3,
input=[
wstlservice_pb2.Location(
inline_json="{'id':'example','resourceType':" +
"'Device','udi':{'carrierHRF':'test'}}")
]),
wstlservice_pb2.ValidationRequest(
fhir_version=wstlservice_pb2.ValidationRequest.FhirVersion.STU3,
input=[
wstlservice_pb2.Location(
inline_json="{'id':'example','resourceType':" +
"'3','udi':{'carrierHRF':'test'}}")
]),
wstlservice_pb2.ValidationRequest(
fhir_version=wstlservice_pb2.ValidationRequest.FhirVersion.STU3,
input=[
wstlservice_pb2.Location(
inline_json="[\"{'id':'example','resourceType':" +
"'Device','udi':{'carrierHRF':'test'}}\", " +
"\"{'id':'example','resourceType':" +
"'Device','udi':{'carrierHRF':'test'}}\"]")
]),
wstlservice_pb2.ValidationRequest(
fhir_version=wstlservice_pb2.ValidationRequest.FhirVersion.STU3,
input=[
wstlservice_pb2.Location(
inline_json="{'id':'example','resourceType':" +
"'Device','udi':{'carrierHRF':'test'}}"),
wstlservice_pb2.Location(
inline_json="{'id':'example','resourceType':" +
"'Device','udi':{'carrierHRF':'test'}}"),
]),
]
for i in range(len(lines)):
mock_service = mock.create_autospec(FakeService)
mock_service.FhirValidate.return_value = resps[i]
mock_stub.return_value = mock_service
result = ip.run_line_magic("fhir_validate", lines[i])
results.append(result)
mock_service.FhirValidate.assert_called_once_with(reqs[i])
wants = [
"{'status': [{'message': 'Validation Success'}]}",
"{'status': [{'code': 3, 'message': 'invalid FHIR resource'}]}",
"{'status': [{'code': 3, 'message': 'invalid FHIR resource'}]}",
"{'status': [{'message': 'Validation Success'}]}",
]
for j in range(len(wants)):
result = results[j]
want = JSON(wants[j])
self.assertEqual(
result.data,
want.data,
msg="JSON.data mismatch on input {}".format(lines[j]))
self.assertEqual(
result.url,
want.url,
msg="JSON.url mismatch on input {}".format(lines[j]))
self.assertEqual(
result.filename,
want.filename,
msg="JSON.filename mismatch on input {}".format(lines[j]))
# Delete created variables to suppress the unused-variable linter warning.
del st1
del st2
del stList
