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Posted to github@beam.apache.org by GitBox <gi...@apache.org> on 2020/05/13 20:17:59 UTC
[GitHub] [beam] pabloem commented on a change in pull request #11339: [BEAM-9468] Fhir io
pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424706218
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File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
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@@ -0,0 +1,1107 @@
+/*
+ * 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 org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.coders.VoidCoder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.EmptyMatchTreatment;
+import org.apache.beam.sdk.io.fs.MatchResult.Metadata;
+import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollection.IsBounded;
+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.base.Throwables;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to <a
+ * href="https://cloud.google.com/healthcare/docs/concepts/fhir">Google Cloud Healthcare Fhir API.
+ * </a>
+ *
+ * <p>Read
+ *
+ * <p>FHIR resources can be read with {@link FhirIO.Read} supports use cases where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * <p>Fetch Resource contents from Fhir Store based on the {@link PCollection} of message ID strings
+ * {@link FhirIO.Read.Result} where one can call {@link Read.Result#getResources()} to retrieved a
+ * {@link PCollection} containing the successfully fetched {@link String}s and/or {@link
+ * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of {@link
+ * HealthcareIOError}* containing the resource ID that could not be fetched and the exception as a
+ * {@link HealthcareIOError}, this can be used to write to the dead letter storage system of your
+ * choosing. This error handling is mainly to transparently surface errors where the upstream {@link
+ * PCollection}* contains IDs that are not valid or are not reachable due to permissions issues.
+ *
+ * <p>Write Resources can be written to FHIR with two different methods: Import or Execute Bundle.
+ *
+ * <p>Execute Bundle This is best for use cases where you are writing to a non-empty FHIR store with
+ * other clients or otherwise need referential integrity (e.g. A Streaming HL7v2 to FHIR ETL
+ * pipeline).
+ *
+ * @see <a
+ * href=>https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle></a>
+ * <p>Import This is best for use cases where you are populating an empty FHIR store with no
+ * other clients. It is faster than the execute bundles method but does not respect referential
+ * integrity and the resources are not written transactionally (e.g. a historicaly backfill on a
+ * new FHIR store) This requires each resource to contain a client provided ID. It is important
+ * that when using import you give the appropriate permissions to the Google Cloud Healthcare
+ * Service Agent
+ * @see <a
+ * href=>https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions></a>
+ * @see <a
+ * href=>https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import></a>
+ * A {@link PCollection} of {@link String} can be ingested into an Fhir store using {@link
+ * FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This
+ * will return a {@link FhirIO.Write.Result} on which you can call {@link
+ * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link
+ * HealthcareIOError} containing the {@link String} that failed to be ingested and the
+ * exception.
+ * <p>Example
+ * <pre>{@code
+ * Pipeline pipeline = ...
+ *
+ * // Tail the FHIR store by retrieving resources based on Pub/Sub notifications.
+ * FhirIO.Read.Result readResult = p
+ * .apply("Read FHIR notifications",
+ * PubsubIO.readStrings().fromSubscription(options.getNotificationSubscription()))
+ * .apply(FhirIO.readResources());
+ *
+ * // happily retrived messages
+ * PCollection<String> resources = readResult.getResources();
+ * // message IDs that couldn't be retrieved + error context
+ * PCollection<HealthcareIOError<String>> failedReads = readResult.getFailedReads();
+ *
+ * failedReads.apply("Write Message IDs / Stacktrace for Failed Reads to BigQuery",
+ * BigQueryIO
+ * .write()
+ * .to(option.getBQFhirExecuteBundlesDeadLetterTable())
+ * .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ *
+ * output = resources.apply("Happy path transformations", ...);
+ * FhirIO.Write.Result writeResult =
+ * output.apply("Execute FHIR Bundles", FhirIO.executeBundles(options.getFhirStore()));
+ *
+ * PCollection<HealthcareIOError<String>> failedBundles = writeResult.getFailedInsertsWithErr();
+ *
+ * failedBundles.apply("Write failed bundles to BigQuery",
+ * BigQueryIO
+ * .write()
+ * .to(option.getBQFhirExecuteBundlesDeadLetterTable())
+ * .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ * }***
+ * </pre>
+ */
+public class FhirIO {
+
+ /**
+ * Read resources from a PCollection of resource IDs (e.g. when subscribing the pubsub
+ * notifications)
+ *
+ * @return the read
+ * @see Read
+ */
+ public static Read readResources() {
+ return new Read();
+ }
+
+ /**
+ * Import resources. Intended for use on empty FHIR stores
+ *
+ * @param fhirStore the fhir store
+ * @param tempDir the temp dir
+ * @param deadLetterDir the dead letter dir
+ * @param contentStructure the content structure
+ * @return the import
+ * @see Import
+ */
+ public static Import importResources(
+ String fhirStore,
+ String tempDir,
+ String deadLetterDir,
+ @Nullable FhirIO.Import.ContentStructure contentStructure) {
+ return new Import(fhirStore, tempDir, deadLetterDir, contentStructure);
+ }
+
+ /**
+ * Import resources. Intended for use on empty FHIR stores
+ *
+ * @param fhirStore the fhir store
+ * @param tempDir the temp dir
+ * @param deadLetterDir the dead letter dir
+ * @param contentStructure the content structure
+ * @return the import
+ * @see Import
+ */
+ public static Import importResources(
+ ValueProvider<String> fhirStore,
+ ValueProvider<String> tempDir,
+ ValueProvider<String> deadLetterDir,
+ @Nullable FhirIO.Import.ContentStructure contentStructure) {
+ return new Import(fhirStore, tempDir, deadLetterDir, contentStructure);
+ }
+
+ /** The type Read. */
+ public static class Read extends PTransform<PCollection<String>, FhirIO.Read.Result> {
+ private static final Logger LOG = LoggerFactory.getLogger(Read.class);
+
+ /** Instantiates a new Read. */
+ public Read() {}
+
+ /** The type Result. */
+ public static class Result implements POutput, PInput {
+ private PCollection<String> resources;
+
+ private PCollection<HealthcareIOError<String>> failedReads;
+ /** The Pct. */
+ PCollectionTuple pct;
+
+ /**
+ * Create FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags.
+ *
+ * @param pct the pct
+ * @return the read result
+ * @throws IllegalArgumentException the illegal argument exception
+ */
+ public static FhirIO.Read.Result of(PCollectionTuple pct) throws IllegalArgumentException {
+ if (pct.getAll()
+ .keySet()
+ .containsAll((Collection<?>) TupleTagList.of(OUT).and(DEAD_LETTER))) {
+ return new FhirIO.Read.Result(pct);
+ } else {
+ throw new IllegalArgumentException(
+ "The PCollection tuple must have the FhirIO.Read.OUT "
+ + "and FhirIO.Read.DEAD_LETTER tuple tags");
+ }
+ }
+
+ private Result(PCollectionTuple pct) {
+ this.pct = pct;
+ this.resources = pct.get(OUT);
+ this.failedReads =
+ pct.get(DEAD_LETTER).setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+ }
+
+ /**
+ * Gets failed reads.
+ *
+ * @return the failed reads
+ */
+ public PCollection<HealthcareIOError<String>> getFailedReads() {
+ return failedReads;
+ }
+
+ /**
+ * Gets resources.
+ *
+ * @return the resources
+ */
+ public PCollection<String> getResources() {
+ return resources;
+ }
+
+ @Override
+ public Pipeline getPipeline() {
+ return this.pct.getPipeline();
+ }
+
+ @Override
+ public Map<TupleTag<?>, PValue> expand() {
+ return ImmutableMap.of(OUT, resources);
+ }
+
+ @Override
+ public void finishSpecifyingOutput(
+ String transformName, PInput input, PTransform<?, ?> transform) {}
+ }
+
+ /** The tag for the main output of Fhir Messages. */
+ public static final TupleTag<String> OUT = new TupleTag<String>() {};
+ /** The tag for the deadletter output of Fhir Messages. */
+ public static final TupleTag<HealthcareIOError<String>> DEAD_LETTER =
+ new TupleTag<HealthcareIOError<String>>() {};
+
+ @Override
+ public FhirIO.Read.Result expand(PCollection<String> input) {
+ return input.apply("Fetch Fhir messages", new FetchResourceJsonString());
+ }
+
+ /**
+ * DoFn to fetch a resource from an Google Cloud Healthcare FHIR store based on resourceID
+ *
+ * <p>This DoFn consumes a {@link PCollection} of notifications {@link String}s from the FHIR
+ * store, and fetches the actual {@link String} object based on the id in the notification and
+ * will output a {@link PCollectionTuple} which contains the output and dead-letter {@link
+ * PCollection}*.
+ *
+ * <p>The {@link PCollectionTuple} output will contain the following {@link PCollection}:
+ *
+ * <ul>
+ * <li>{@link FhirIO.Read#OUT} - Contains all {@link PCollection} records successfully read
+ * from the Fhir store.
+ * <li>{@link FhirIO.Read#DEAD_LETTER} - Contains all {@link PCollection} of {@link
+ * HealthcareIOError}* of message IDs which failed to be fetched from the Fhir store, with
+ * error message and stacktrace.
+ * </ul>
+ */
+ public static class FetchResourceJsonString
+ extends PTransform<PCollection<String>, FhirIO.Read.Result> {
+
+ /** Instantiates a new Fetch Fhir message DoFn. */
+ public FetchResourceJsonString() {}
+
+ @Override
+ public FhirIO.Read.Result expand(PCollection<String> resourceIds) {
+ return new FhirIO.Read.Result(
+ resourceIds.apply(
+ ParDo.of(new FetchResourceJsonString.StringGetFn())
+ .withOutputTags(FhirIO.Read.OUT, TupleTagList.of(FhirIO.Read.DEAD_LETTER))));
+ }
+
+ /** DoFn for fetching messages from the Fhir store with error handling. */
+ public static class StringGetFn extends DoFn<String, String> {
+
+ private Counter failedMessageGets =
+ Metrics.counter(FetchResourceJsonString.StringGetFn.class, "failed-message-reads");
+ private static final Logger LOG =
+ LoggerFactory.getLogger(FetchResourceJsonString.StringGetFn.class);
+ private final Counter successfulStringGets =
+ Metrics.counter(
+ FetchResourceJsonString.StringGetFn.class, "successful-hl7v2-message-gets");
+ private HealthcareApiClient client;
+ private ObjectMapper mapper;
+
+ /** Instantiates a new Hl 7 v 2 message get fn. */
+ StringGetFn() {}
+
+ /**
+ * Instantiate healthcare client.
+ *
+ * @throws IOException the io exception
+ */
+ @Setup
+ public void instantiateHealthcareClient() throws IOException {
+ this.client = new HttpHealthcareApiClient();
+ this.mapper = new ObjectMapper();
+ }
+
+ /**
+ * Process element.
+ *
+ * @param context the context
+ */
+ @ProcessElement
+ public void processElement(ProcessContext context) {
+ String resourceId = context.element();
+ try {
+ context.output(fetchResource(this.client, resourceId));
Review comment:
You could perform multiple `Fhir.read` requests from separate threads? This may be fine for now, though, and if you find that the extra optimization will help, then add it later on?
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