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Posted to github@beam.apache.org by GitBox <gi...@apache.org> on 2020/08/06 17:20:58 UTC
[GitHub] [beam] pabloem commented on a change in pull request #12473: [BEAM-10601] DICOM API Beam IO connector e2e test
pabloem commented on a change in pull request #12473:
URL: https://github.com/apache/beam/pull/12473#discussion_r466559724
##########
File path: sdks/python/apache_beam/io/gcp/dicomio_integration_test.py
##########
@@ -0,0 +1,215 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""
+Integration test for Google Cloud DICOM IO connector.
+"""
+# pytype: skip-file
+
+from __future__ import absolute_import
+
+import random
+import string
+import unittest
+
+from nose.plugins.attrib import attr
+
+import apache_beam as beam
+from apache_beam.io import fileio
+from apache_beam.testing.test_pipeline import TestPipeline
+from apache_beam.testing.util import assert_that
+from apache_beam.testing.util import equal_to
+
+# pylint: disable=wrong-import-order, wrong-import-position
+try:
+ from apache_beam.io.gcp.dicomio import DicomSearch
+ from apache_beam.io.gcp.dicomio import UploadToDicomStore
+ from google.auth import default
+ from google.auth.transport import requests
+except ImportError:
+ DicomSearch = None
+# pylint: enable=wrong-import-order, wrong-import-position
+
+REGION = 'us-central1'
+DATA_SET_ID = 'apache-beam-integration-testing'
+HEALTHCARE_BASE_URL = 'https://healthcare.googleapis.com/v1'
+GCS_BASE_URL = 'https://storage.googleapis.com/storage/v1'
+PERSISTENT_DICOM_STORE_NAME = "dicom_it_persistent_store"
+TEMP_BUCKET_NAME = 'temp-storage-for-dicom-io-tests'
Review comment:
please make sure that this bucket has lifecycle policies to ensure any left over files will be erased automatically (or feel free to use any of the other `temp-storage-*` in Beam which do have lifecycle policies
##########
File path: sdks/python/apache_beam/io/gcp/dicomio_integration_test.py
##########
@@ -0,0 +1,215 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""
+Integration test for Google Cloud DICOM IO connector.
Review comment:
Can you please add detailed documentation on how the test works? for example, are there any instances of Dicom stores expected to be running? What files are used for the test? (I see it all gets created, so that's great. just please document all of that here).
##########
File path: sdks/python/apache_beam/io/gcp/dicomio_integration_test.py
##########
@@ -0,0 +1,215 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""
+Integration test for Google Cloud DICOM IO connector.
+"""
+# pytype: skip-file
+
+from __future__ import absolute_import
+
+import random
+import string
+import unittest
+
+from nose.plugins.attrib import attr
+
+import apache_beam as beam
+from apache_beam.io import fileio
+from apache_beam.testing.test_pipeline import TestPipeline
+from apache_beam.testing.util import assert_that
+from apache_beam.testing.util import equal_to
+
+# pylint: disable=wrong-import-order, wrong-import-position
+try:
+ from apache_beam.io.gcp.dicomio import DicomSearch
+ from apache_beam.io.gcp.dicomio import UploadToDicomStore
+ from google.auth import default
+ from google.auth.transport import requests
+except ImportError:
+ DicomSearch = None
+# pylint: enable=wrong-import-order, wrong-import-position
+
+REGION = 'us-central1'
+DATA_SET_ID = 'apache-beam-integration-testing'
+HEALTHCARE_BASE_URL = 'https://healthcare.googleapis.com/v1'
+GCS_BASE_URL = 'https://storage.googleapis.com/storage/v1'
+PERSISTENT_DICOM_STORE_NAME = "dicom_it_persistent_store"
+TEMP_BUCKET_NAME = 'temp-storage-for-dicom-io-tests'
+TEMP_FILES_PATH = 'gs://' + TEMP_BUCKET_NAME
+META_DATA_ALL_NAME = 'Dicom_io_it_test_data.json'
+META_DATA_REFINED_NAME = 'Dicom_io_it_test_refined_data.json'
+NUM_INSTANCE = 18
+RAND_LEN = 15
+
+
+def random_string_generator(length):
+ letters_and_digits = string.ascii_letters + string.digits
+ result = ''.join((random.choice(letters_and_digits) for i in range(length)))
+ return result
+
+
+def create_dicom_store(project_id, dataset_id, region, dicom_store_id):
+ # Create a an empty DICOM store
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+ api_endpoint = "{}/projects/{}/locations/{}".format(
+ HEALTHCARE_BASE_URL, project_id, region)
+
+ # base of dicomweb path.
+ dicomweb_path = "{}/datasets/{}/dicomStores".format(api_endpoint, dataset_id)
+
+ response = session.post(
+ dicomweb_path, params={"dicomStoreId": dicom_store_id})
+ response.raise_for_status()
+ return response.status_code
+
+
+def delete_dicom_store(project_id, dataset_id, region, dicom_store_id):
+ # Delete an existing DICOM store
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+ api_endpoint = "{}/projects/{}/locations/{}".format(
+ HEALTHCARE_BASE_URL, project_id, region)
+
+ # base of dicomweb path.
+ dicomweb_path = "{}/datasets/{}/dicomStores/{}".format(
+ api_endpoint, dataset_id, dicom_store_id)
+
+ response = session.delete(dicomweb_path)
+ response.raise_for_status()
+ return response.status_code
+
+
+def get_gcs_file_http(file_name):
+ # Get gcs file from REST Api
+ api_endpoint = "{}/b/{}/o/{}?alt=media".format(
+ GCS_BASE_URL, TEMP_BUCKET_NAME, file_name)
+
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+
+ response = session.get(api_endpoint)
+ response.raise_for_status()
+ return response.json()
+
+
+@unittest.skipIf(DicomSearch is None, 'GCP dependencies are not installed')
+class DICOMIoIntegrationTest(unittest.TestCase):
+ def setUp(self):
+ self.test_pipeline = TestPipeline(is_integration_test=True)
+ self.project = self.test_pipeline.get_option('project')
+ self.expected_output_all_metadata = get_gcs_file_http(META_DATA_ALL_NAME)
+ self.expected_output_refined_metadata = get_gcs_file_http(
+ META_DATA_REFINED_NAME)
+
+ # create a temp Dicom store based on the time stamp
+ self.temp_dicom_store = "DICOM_store_" + random_string_generator(RAND_LEN)
+ create_dicom_store(self.project, DATA_SET_ID, REGION, self.temp_dicom_store)
+
+ def tearDown(self):
+ # clean up the temp Dicom store
+ delete_dicom_store(self.project, DATA_SET_ID, REGION, self.temp_dicom_store)
+
+ @attr('IT')
+ def test_dicom_search_all_instances(self):
Review comment:
as you realized, each test takes 5 minutes to run. With that in mind, would it be possible to consolidate the all_instance and refined_instance searches into a single test case?
Something roughly like this:
```
with p:
refined = p | searchrefined
all = p | searchall
assert_that(exp_ref, refined)
assert_that(exp_all, all, "allmatch")
```
##########
File path: sdks/python/apache_beam/io/gcp/dicomio_integration_test.py
##########
@@ -0,0 +1,215 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""
+Integration test for Google Cloud DICOM IO connector.
+"""
+# pytype: skip-file
+
+from __future__ import absolute_import
+
+import random
+import string
+import unittest
+
+from nose.plugins.attrib import attr
+
+import apache_beam as beam
+from apache_beam.io import fileio
+from apache_beam.testing.test_pipeline import TestPipeline
+from apache_beam.testing.util import assert_that
+from apache_beam.testing.util import equal_to
+
+# pylint: disable=wrong-import-order, wrong-import-position
+try:
+ from apache_beam.io.gcp.dicomio import DicomSearch
+ from apache_beam.io.gcp.dicomio import UploadToDicomStore
+ from google.auth import default
+ from google.auth.transport import requests
+except ImportError:
+ DicomSearch = None
+# pylint: enable=wrong-import-order, wrong-import-position
+
+REGION = 'us-central1'
+DATA_SET_ID = 'apache-beam-integration-testing'
+HEALTHCARE_BASE_URL = 'https://healthcare.googleapis.com/v1'
+GCS_BASE_URL = 'https://storage.googleapis.com/storage/v1'
+PERSISTENT_DICOM_STORE_NAME = "dicom_it_persistent_store"
+TEMP_BUCKET_NAME = 'temp-storage-for-dicom-io-tests'
+TEMP_FILES_PATH = 'gs://' + TEMP_BUCKET_NAME
+META_DATA_ALL_NAME = 'Dicom_io_it_test_data.json'
+META_DATA_REFINED_NAME = 'Dicom_io_it_test_refined_data.json'
+NUM_INSTANCE = 18
+RAND_LEN = 15
+
+
+def random_string_generator(length):
+ letters_and_digits = string.ascii_letters + string.digits
+ result = ''.join((random.choice(letters_and_digits) for i in range(length)))
+ return result
+
+
+def create_dicom_store(project_id, dataset_id, region, dicom_store_id):
+ # Create a an empty DICOM store
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+ api_endpoint = "{}/projects/{}/locations/{}".format(
+ HEALTHCARE_BASE_URL, project_id, region)
+
+ # base of dicomweb path.
+ dicomweb_path = "{}/datasets/{}/dicomStores".format(api_endpoint, dataset_id)
+
+ response = session.post(
+ dicomweb_path, params={"dicomStoreId": dicom_store_id})
+ response.raise_for_status()
+ return response.status_code
+
+
+def delete_dicom_store(project_id, dataset_id, region, dicom_store_id):
+ # Delete an existing DICOM store
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+ api_endpoint = "{}/projects/{}/locations/{}".format(
+ HEALTHCARE_BASE_URL, project_id, region)
+
+ # base of dicomweb path.
+ dicomweb_path = "{}/datasets/{}/dicomStores/{}".format(
+ api_endpoint, dataset_id, dicom_store_id)
+
+ response = session.delete(dicomweb_path)
+ response.raise_for_status()
+ return response.status_code
+
+
+def get_gcs_file_http(file_name):
+ # Get gcs file from REST Api
+ api_endpoint = "{}/b/{}/o/{}?alt=media".format(
+ GCS_BASE_URL, TEMP_BUCKET_NAME, file_name)
+
+ credential, _ = default()
+ session = requests.AuthorizedSession(credential)
+
+ response = session.get(api_endpoint)
+ response.raise_for_status()
+ return response.json()
+
+
+@unittest.skipIf(DicomSearch is None, 'GCP dependencies are not installed')
+class DICOMIoIntegrationTest(unittest.TestCase):
+ def setUp(self):
+ self.test_pipeline = TestPipeline(is_integration_test=True)
+ self.project = self.test_pipeline.get_option('project')
+ self.expected_output_all_metadata = get_gcs_file_http(META_DATA_ALL_NAME)
+ self.expected_output_refined_metadata = get_gcs_file_http(
+ META_DATA_REFINED_NAME)
+
+ # create a temp Dicom store based on the time stamp
+ self.temp_dicom_store = "DICOM_store_" + random_string_generator(RAND_LEN)
+ create_dicom_store(self.project, DATA_SET_ID, REGION, self.temp_dicom_store)
+
+ def tearDown(self):
+ # clean up the temp Dicom store
+ delete_dicom_store(self.project, DATA_SET_ID, REGION, self.temp_dicom_store)
+
+ @attr('IT')
+ def test_dicom_search_all_instances(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_all_metadata
+ expected_dict['status'] = 200
+ expected_dict['input'] = input_dict
+ expected_dict['success'] = True
+
+ with self.test_pipeline as p:
+ results = (p | beam.Create([input_dict]) | DicomSearch())
+ assert_that(results, equal_to([expected_dict]), label='all search assert')
+
+ @attr('IT')
+ def test_dicom_search_refined_instances(self):
+ # Refine 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"
+ input_dict['params'] = {
+ 'StudyInstanceUID': 'study_000000001', 'limit': 500, 'offset': 0
+ }
+
+ expected_dict = {}
+ expected_dict['result'] = self.expected_output_refined_metadata
+ expected_dict['status'] = 200
+ expected_dict['input'] = input_dict
+ expected_dict['success'] = True
+
+ with self.test_pipeline as p:
+ results = (p | beam.Create([input_dict]) | DicomSearch())
+ assert_that(
+ results, equal_to([expected_dict]), label='refine search assert')
+
+ @attr('IT')
+ def test_dicom_store_instance_from_gcs(self):
+ # Store DICOM files to a empty DICOM store from a GCS bucket,
+ # then check if the store metadata match.
+ input_dict_store = {}
+ input_dict_store['project_id'] = self.project
+ input_dict_store['region'] = REGION
+ input_dict_store['dataset_id'] = DATA_SET_ID
+ input_dict_store['dicom_store_id'] = self.temp_dicom_store
+
+ expected_output = [True] * NUM_INSTANCE
+
+ with self.test_pipeline as p:
+ gcs_path = TEMP_FILES_PATH + "/dicom_files/*"
+ results = (
+ p
+ | fileio.MatchFiles(gcs_path)
+ | fileio.ReadMatches()
+ | UploadToDicomStore(input_dict_store, 'fileio')
+ | beam.Map(lambda x: x['success']))
+ assert_that(
+ results, equal_to(expected_output), label='store first assert')
+
+ input_dict_search = {}
+ input_dict_search['project_id'] = self.project
+ input_dict_search['region'] = REGION
+ input_dict_search['dataset_id'] = DATA_SET_ID
+ input_dict_search['dicom_store_id'] = self.temp_dicom_store
+ input_dict_search['search_type'] = "instances"
+
+ expected_dict = {}
+ expected_dict['result'] = self.expected_output_all_metadata
+ expected_dict['status'] = 200
+ expected_dict['input'] = input_dict_search
+ expected_dict['success'] = True
+
Review comment:
in this test case you're running two pipelines. This will therefore take 10 minutes to run. Perhaps it's worth making this the single test case that tests upload and search (or perhaps remove the search pipeline from this case to avoid the super long runtime?)
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