poojavenkatram commented on a change in pull request #13137: URL: https://github.com/apache/beam/pull/13137#discussion_r510404106
########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud Review comment: add a link to the Dicom API here.. ########## File path: sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIOTest.java ########## @@ -0,0 +1,53 @@ +/* + * 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.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() { + PubsubMessage badMessage = createPubSubMessage("foo"); + + DicomIO.ReadDicomStudyMetadata.Result retrievedData; + retrievedData = + pipeline.apply(Create.of(badMessage)).apply(new DicomIO.ReadDicomStudyMetadata()); + + PAssert.that(retrievedData.getReadResponse()).empty(); Review comment: you can also check for the error in the result now? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can + * learn how to configure PubSub messages to be published when an instance is stored in a data store + * by following: https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector will output + * a {@link ReadDicomStudyMetadata.Result} which will contain metadata of a study encoded in json + * string + */ +public class DicomIO { + + /** The type ReadDicomStudyMetadata. */ + public static class ReadDicomStudyMetadata + extends PTransform<PCollection<PubsubMessage>, DicomIO.ReadDicomStudyMetadata.Result> { + + public ReadDicomStudyMetadata() {} + + public static final TupleTag<String> OUT = new TupleTag<String>() {}; + public static final TupleTag<String> DEAD_LETTER = new TupleTag<String>() {}; + + public static class Result implements POutput, PInput { + private PCollection<String> readResponse; + + private PCollection<String> failedReads; + /** The Pct. */ Review comment: please be more descriptive in the comment ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can + * learn how to configure PubSub messages to be published when an instance is stored in a data store + * by following: https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector will output + * a {@link ReadDicomStudyMetadata.Result} which will contain metadata of a study encoded in json + * string + */ +public class DicomIO { + + /** The type ReadDicomStudyMetadata. */ + public static class ReadDicomStudyMetadata + extends PTransform<PCollection<PubsubMessage>, DicomIO.ReadDicomStudyMetadata.Result> { + + public ReadDicomStudyMetadata() {} + + public static final TupleTag<String> OUT = new TupleTag<String>() {}; Review comment: why not give these both better names like "Response" and "Error"? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. Review comment: nit: read from the Google Cloud Healthcare DICOM API. ? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can + * learn how to configure PubSub messages to be published when an instance is stored in a data store + * by following: https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector will output + * a {@link ReadDicomStudyMetadata.Result} which will contain metadata of a study encoded in json Review comment: study encoded as a json string? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can + * learn how to configure PubSub messages to be published when an instance is stored in a data store + * by following: https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector will output + * a {@link ReadDicomStudyMetadata.Result} which will contain metadata of a study encoded in json + * string + */ +public class DicomIO { + + /** The type ReadDicomStudyMetadata. */ Review comment: You can move the Description you gave for ReadStudyMetadata above here because we might add other methods to the same connector in the future.. ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a Review comment: DICOM study metadata can be read? ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can Review comment: nit: contain the path to the study. ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java ########## @@ -0,0 +1,172 @@ +/* + * 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.util.Collection; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +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.PCollectionTuple; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.sdk.values.TupleTagList; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap; + +/** + * The DicomIO connectors allows Beam pipelines to read from the Dicom API from Google Cloud + * Healthcare. + * + * <p>Study-level metadata can be read using {@link ReadDicomStudyMetadata}. It is expecting a + * PubSub message as input, where the message's body will contain the location of the Study. You can + * learn how to configure PubSub messages to be published when an instance is stored in a data store Review comment: when a DICOM instance is stored by following.. ---------------------------------------------------------------- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. For queries about this service, please contact Infrastructure at: [email protected]
