poojavenkatram commented on a change in pull request #13137: URL: https://github.com/apache/beam/pull/13137#discussion_r509433845
########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,95 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.TupleTag; + +public class DicomIO { + + /** + * Read dicom study metadata from a PCollection of resource webpath. + * + * @return the read Review comment: DICOM study metadata? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,95 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.TupleTag; + +public class DicomIO { + + /** Review comment: Why not move this comment into the Class to show that the class does...this method is only returning an Object of the class.. ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,95 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.TupleTag; + +public class DicomIO { Review comment: Right on the top of this page I would add some information on what this connector is and what it is doing. Somthing like this is used to connect Google Cloud Healthcare DICOM API with links to the API, how to configure pubsub, etc. to make it easy for a customer of the connector to get some context. ########## File path: sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIOTest.java ########## @@ -0,0 +1,52 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import static java.nio.charset.StandardCharsets.UTF_8; + +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.values.PCollection; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class DicomIOTest { + @Rule public final transient TestPipeline pipeline = TestPipeline.create(); + + @Test + public void test_Dicom_failedMetadataRead() { Review comment: How about a test for the success case? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,95 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.TupleTag; + +public class DicomIO { + + /** + * Read dicom study metadata from a PCollection of resource webpath. Review comment: Read the DICOM study metadata from the resource path obtained from PubSub ? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java ########## @@ -196,6 +197,64 @@ public Empty deleteFhirStore(String name) throws IOException { return client.projects().locations().datasets().fhirStores().delete(name).execute(); } + @Override + public String retrieveDicomStudyMetadata(String dicomWebPath) throws IOException { + String[] webPathSplit; + webPathSplit = dicomWebPath.split("/dicomWeb/"); + String dicomStorePath = webPathSplit[0]; + + String[] searchParameters; + searchParameters = webPathSplit[1].split("/"); + String studyId = searchParameters[1]; + // String seriesId = searchParameters[3]; + // String instanceId = searchParameters[5]; Review comment: nit: remove ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,95 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.TupleTag; + +public class DicomIO { + + /** + * Read dicom study metadata from a PCollection of resource webpath. + * + * @return the read + * @see ReadDicomStudyMetadata + */ + public static ReadDicomStudyMetadata retrieveStudyMetadata() { + return new ReadDicomStudyMetadata(); + } + + /** The type ReadDicomStudyMetadata. */ + public static class ReadDicomStudyMetadata + extends PTransform<PCollection<PubsubMessage>, PCollection<String>> { + + public ReadDicomStudyMetadata() {} + + public static final TupleTag<String> OUT = new TupleTag<String>() {}; + + /** + * DoFn to fetch the metadata of a study from a Dicom store based on it's location and study id. + */ + static class FetchStudyMetadataFn extends DoFn<PubsubMessage, String> { + + private HealthcareApiClient dicomStore; + + /** + * Instantiate the healthcare client. + * + * @throws IOException + */ + @Setup + public void instantiateHealthcareClient() throws IOException { + this.dicomStore = new HttpHealthcareApiClient(); + } + + /** + * Process The Pub/Sub message. + * + * @param context The input containing the pub/sub message + */ + @ProcessElement + public void processElement(ProcessContext context) { + PubsubMessage msg = context.element(); + byte[] msgPayload = msg.getPayload(); + try { + String dicomWebPath = new String(msgPayload, "UTF-8"); + String responseData = dicomStore.retrieveDicomStudyMetadata(dicomWebPath); + context.output(responseData); + } catch (Exception e) { + // IO exception, unsupported encoding exception + System.out.println(e); + if (e.getClass() == IOException.class) { + } else if (e.getClass() == UnsupportedEncodingException.class) { + } else { + } + } Review comment: this seems incomplete? ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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