def test_dicom_search_instances(self):
# Search and compare the metadata of a persistent DICOM store.
# Both refine and comprehensive search will be tested.
input_dict_all = {}
input_dict_all['project_id'] = self.project
input_dict_all['region'] = REGION
input_dict_all['dataset_id'] = DATA_SET_ID
input_dict_all['dicom_store_id'] = PERSISTENT_DICOM_STORE_NAME
input_dict_all['search_type'] = "instances"
input_dict_refine = {}
input_dict_refine['project_id'] = self.project
input_dict_refine['region'] = REGION
input_dict_refine['dataset_id'] = DATA_SET_ID
input_dict_refine['dicom_store_id'] = PERSISTENT_DICOM_STORE_NAME
input_dict_refine['search_type'] = "instances"
input_dict_refine['params'] = {
'StudyInstanceUID': 'study_000000001',
'limit': 500,
'offset': 0
}
expected_dict_all = {}
expected_dict_all['result'] = self.expected_output_all_metadata
expected_dict_all['status'] = 200
expected_dict_all['input'] = input_dict_all
expected_dict_all['success'] = True
expected_dict_refine = {}
expected_dict_refine['result'] = self.expected_output_refined_metadata
expected_dict_refine['status'] = 200
expected_dict_refine['input'] = input_dict_refine
expected_dict_refine['success'] = True
with self.test_pipeline as p:
results_all = (p
| 'create all dict' >> beam.Create([input_dict_all])
| 'search all' >> DicomSearch())
results_refine = (
p
| 'create refine dict' >> beam.Create([input_dict_refine])
| 'search refine' >> DicomSearch())
assert_that(results_all,
equal_to([expected_dict_all]),
label='all search assert')
assert_that(results_refine,
equal_to([expected_dict_refine]),
label='refine search assert')
def test_param_dict_passing(self, FakeClient):
input_dict = {}
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
input_dict['search_type'] = "instances"
input_dict['params'] = {'PatientName': 'Brian'}
expected_dict = {}
expected_dict['result'] = [{
'PatientName': 'Brian',
'Age': 20,
'TestResult': 'Positive'
}]
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
fc = FakeHttpClient()
FakeClient.return_value = fc
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_dict]))
def test_dicom_store_instance(self):
# Store DICOM files to a empty DICOM store from a GCS bucket,
# then check if the store metadata match.
input_dict = {}
input_dict['project_id'] = self.project
input_dict['region'] = REGION
input_dict['dataset_id'] = DATA_SET_ID
input_dict['dicom_store_id'] = self.temp_dicom_store
input_dict['search_type'] = "instances"
expected_dict = {}
expected_dict['result'] = self.expected_output_metadata
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
with TestPipeline() as p:
gcs_path = DICOM_FILES_PATH + "/*"
results = (p
| fileio.MatchFiles(gcs_path)
| fileio.ReadMatches()
| UploadToDicomStore(input_dict, 'fileio')
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True] * NUM_INSTANCE))
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_dict]))
def test_missing_parameters(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
expected_invalid_dict = {}
expected_invalid_dict['result'] = []
expected_invalid_dict['status'] = 'Must have dataset_id in the dict.'
expected_invalid_dict['input'] = input_dict
expected_invalid_dict['success'] = False
fc = FakeHttpClient()
FakeClient.return_value = fc
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_invalid_dict]))
def test_dicom_search(self):
# Search and compare the metadata of a persistent DICOM store.
input_dict = {}
input_dict['project_id'] = self.project
input_dict['region'] = REGION
input_dict['dataset_id'] = DATA_SET_ID
input_dict['dicom_store_id'] = PERSISTENT_DICOM_STORE_NAME
input_dict['search_type'] = "instances"
expected_dict = {}
expected_dict['result'] = self.expected_output_metadata
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_dict]))
def test_client_search_notfound(self, FakeClient):
input_dict = {}
# search instances in a not exist store
input_dict['project_id'] = "wrong_project"
input_dict['region'] = "wrong_region"
input_dict['dataset_id'] = "wrong_dataset_id"
input_dict['dicom_store_id'] = "wrong_dicom_store_id"
input_dict['search_type'] = "instances"
expected_invalid_dict = {}
expected_invalid_dict['result'] = []
expected_invalid_dict['status'] = 204
expected_invalid_dict['input'] = input_dict
expected_invalid_dict['success'] = False
fc = FakeHttpClient()
FakeClient.return_value = fc
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_invalid_dict]))
def test_wrong_input_type(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
input_dict['search_type'] = "not exist type"
expected_invalid_dict = {}
expected_invalid_dict['result'] = []
expected_invalid_dict[
'status'] = 'Search type can only be "studies", "instances" or "series"'
expected_invalid_dict['input'] = input_dict
expected_invalid_dict['success'] = False
fc = FakeHttpClient()
FakeClient.return_value = fc
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_invalid_dict]))
def test_Qido_search_small_buffer_flush(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
input_dict['search_type'] = "instances"
fc = FakeHttpClient()
FakeClient.return_value = fc
expected_dict = {}
expected_dict['result'] = fc.dicom_metadata
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
with TestPipeline() as p:
results = (p | beam.Create([input_dict] * 5) | DicomSearch(buffer_size=1))
assert_that(results, equal_to([expected_dict] * 5))