msbukal commented on code in PR #17741: URL: https://github.com/apache/beam/pull/17741#discussion_r881954049
########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirBundleWithMetadata.java: ########## @@ -0,0 +1,73 @@ +/* + * 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 com.google.auto.value.AutoValue; +import java.util.Objects; +import javax.annotation.Nullable; +import org.apache.beam.sdk.coders.DefaultCoder; + +/** + * FhirBundleWithMetadata represents a FHIR bundle, with it's metadata (eg. source ID like HL7 Review Comment: I think we should change the name from "FhirBundleWithMetadata" to something more generic, since now ExecuteBundle MUST accepts this as input. How about "FhirBundleParameter", similar to the input to search (FhirSearchParameter). ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirBundleWithMetadata.java: ########## @@ -0,0 +1,73 @@ +/* + * 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 com.google.auto.value.AutoValue; +import java.util.Objects; +import javax.annotation.Nullable; +import org.apache.beam.sdk.coders.DefaultCoder; + +/** + * FhirBundleWithMetadata represents a FHIR bundle, with it's metadata (eg. source ID like HL7 + * message path) in JSON format to be executed on any FHIR store. * + */ +@DefaultCoder(FhirBundleWithMetadataCoder.class) +@AutoValue +public abstract class FhirBundleWithMetadata { + + static Builder builder() { + return new AutoValue_FhirBundleWithMetadata.Builder(); + } + + /** + * String representing the source of the Bundle to be written. Used to pass source data through + * the ExecuteBundles PTransform. + */ + public abstract String getMetadata(); Review Comment: Remove occurrences of "source" -> "metadata", since it doesn't have to be the source. ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirBundleWithMetadata.java: ########## @@ -0,0 +1,73 @@ +/* + * 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 com.google.auto.value.AutoValue; +import java.util.Objects; +import javax.annotation.Nullable; +import org.apache.beam.sdk.coders.DefaultCoder; + +/** + * FhirBundleWithMetadata represents a FHIR bundle, with it's metadata (eg. source ID like HL7 + * message path) in JSON format to be executed on any FHIR store. * + */ +@DefaultCoder(FhirBundleWithMetadataCoder.class) +@AutoValue +public abstract class FhirBundleWithMetadata { + + static Builder builder() { + return new AutoValue_FhirBundleWithMetadata.Builder(); + } + + /** + * String representing the source of the Bundle to be written. Used to pass source data through + * the ExecuteBundles PTransform. + */ + public abstract String getMetadata(); + + /** FHIR R4 bundle resource object as a string. */ + public abstract String getBundle(); + + /** HTTP response from the FHIR store after attempting to write the Bundle method. */ + public abstract String getResponse(); Review Comment: It seems confusing to include the "response" field in the input to an ExecuteBundle request. Especially since the only 2 constructors are "bundle only" or "bundle, metadata, and response". How would you create a bundle with metadata as input? I think the solution here should be to make the response of the ExecuteBundle DoFn it's own "FhirBundleResponse" class, which can contain a FhirBundleWithMetadata/FhirBundleParameter inside it (or just the two fields, this might be easier regarding serialization, either is fine) as the "source". ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirBundleWithMetadata.java: ########## @@ -0,0 +1,73 @@ +/* + * 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 com.google.auto.value.AutoValue; +import java.util.Objects; +import javax.annotation.Nullable; +import org.apache.beam.sdk.coders.DefaultCoder; + +/** + * FhirBundleWithMetadata represents a FHIR bundle, with it's metadata (eg. source ID like HL7 + * message path) in JSON format to be executed on any FHIR store. * Review Comment: Comment nits: * it's -> its * any FHIR store -> a FHIR store (specifying any can be confusing, it's the specific FHIR store that a user passes in) * change the example from "HL7v2 message path" to something more generic, eg. the Pubsub Notification ID (since most executes come from reads), don't need to bring up another modality. * mention the metadata seperately: emphasize the main purpose first: `FhirBundleWithMetadata represents a FHIR bundle in JSON format to be executed on a FHIR store` then mention that the passed in metadata will be returned in the response, and can be used for tracking metadata such as, for example, the source. ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java: ########## @@ -1496,16 +1517,22 @@ private void parseResponse(ProcessContext context, String inputBody, HttpBody re } else { fail++; context.output( - Write.FAILED_BODY, + FAILED_BUNDLES, HealthcareIOError.of( - inputBody, HealthcareHttpException.of(statusCode, entry.toString()))); + context.element(), HealthcareHttpException.of(statusCode, entry.toString()))); } } EXECUTE_BUNDLE_RESOURCE_SUCCESS.inc(success); EXECUTE_BUNDLE_RESOURCE_ERRORS.inc(fail); } else if (bundleType.equals(BUNDLE_RESPONSE_TYPE_TRANSACTION)) { EXECUTE_BUNDLE_RESOURCE_SUCCESS.inc(entries.size()); - context.output(Write.SUCCESSFUL_BODY, bundle.toString()); + context.output( Review Comment: In the BATCH case above (line 1516) we output to Write.SUCCESSFUL_BODY, which the PTransform no longer returns, since the output tags are only: `.withOutputTags(SUCCESSFUL_BUNDLES, TupleTagList.of(FAILED_BUNDLES)));` This means that nothing will be returned in the batch case. If you run the integration tests (can comment `Run Java PostCommit`) it'll fail. Please fix. ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/GetStringHealthcareIOErrorFn.java: ########## @@ -0,0 +1,40 @@ +/* + * 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 org.apache.beam.sdk.transforms.DoFn; + +/** + * ParDo function that transforms a HealthcareIOError for a FhirBundleWithMetadata to an error with + * the body (string) as the data resource, for backwards compatibility. + */ +public class GetStringHealthcareIOErrorFn Review Comment: I agree with Mackenzie's comment: This shouldn't be it's own class/DoFN: you can just make a helper method somewhere local in FhirIO, like: ``` private HealthcareIOError<String> getStringHealthcareIOError(HealthcareIOError<FhirBundleWithMetadata> in) { return new HealthcareIOError<>( input.getDataResource().getBundle(), input.getErrorMessage(), input.getStackTrace(), input.getObservedTime(), input.getStatusCode())); } ``` and apply MapElements to the Results.getFailedBodies() method in-line (like some of the other results methods) ########## sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java: ########## @@ -1524,6 +1551,85 @@ private int parseBundleStatus(String status) { } } + /** + * ExecuteBundlesResult contains both successfully executed bundles and information help debugging + * failed executions (eg metadata & error msgs). + */ + public static class ExecuteBundlesResult extends Write.AbstractResult { + private final Pipeline pipeline; + private final PCollection<FhirBundleWithMetadata> successfulBundles; + private final PCollection<HealthcareIOError<FhirBundleWithMetadata>> failedBundles; + + private ExecuteBundlesResult( + Pipeline pipeline, + PCollection<FhirBundleWithMetadata> successfulBundles, + PCollection<HealthcareIOError<FhirBundleWithMetadata>> failedBundles) { + this.pipeline = pipeline; + this.successfulBundles = successfulBundles; + this.failedBundles = failedBundles; + } + + /** + * Entry point for the ExecuteBundlesResult, storing the successful and failed bundles and their + * metadata. + */ + public static ExecuteBundlesResult in( + Pipeline pipeline, + PCollection<FhirBundleWithMetadata> successfulBundles, + PCollection<HealthcareIOError<FhirBundleWithMetadata>> failedBundles) { + return new ExecuteBundlesResult(pipeline, successfulBundles, failedBundles); + } + + /** Gets successful FhirBundleWithMetadata from execute bundles operation. */ + public PCollection<FhirBundleWithMetadata> getSuccessfulBundlesWithMetadata() { + return this.successfulBundles; + } + + /** + * Gets failed FhirBundleWithMetadata with metadata wrapped inside HealthcareIOError. The bundle + * field could be null. + */ + public PCollection<HealthcareIOError<FhirBundleWithMetadata>> getFailedBundles() { + return this.failedBundles; + } + + @Override Review Comment: nit: order the methods to group success/fails, eg: getSuccessfulBodies() getSuccessfulBundlesWithMetadata() getFailedBodies() getFailedBundles() makes it easier to see the difference between methods. -- 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. To unsubscribe, e-mail: [email protected] For queries about this service, please contact Infrastructure at: [email protected]
