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Posted to github@beam.apache.org by GitBox <gi...@apache.org> on 2020/04/08 19:27:10 UTC
[GitHub] [beam] lastomato commented on a change in pull request #11339:
[BEAM-9468] [WIP] Fhir io
lastomato commented on a change in pull request #11339: [BEAM-9468] [WIP] Fhir io
URL: https://github.com/apache/beam/pull/11339#discussion_r405761171
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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 +1,662 @@
+/*
+ * 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.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.Collection;
+import java.util.Collections;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.annotations.Experimental;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure;
+import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result;
+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.transforms.DoFn;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.util.Sleeper;
+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.base.Throwables;
+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 HttpBody}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 HttpBody} can be ingested into an Fhir store using {@link
+ * FhirIO.Write#fhirStoresImport(String, String, String, ContentStructure)} This will return a
+ * {@link FhirIO.Write.Result} on which you can call {@link
+ * FhirIO.Write.Result#getFailedInsertsWithErr()} to retrieve a {@link PCollection} of {@link
+ * HealthcareIOError} containing the {@link HttpBody} that failed to be ingested and the
+ * exception.
+ */
+public class FhirIO {
+
+ @Experimental
+ public static class Read extends PTransform<PCollection<String>, FhirIO.Read.Result> {
+ private static final Logger LOG = LoggerFactory.getLogger(Read.class);
+
+ public Read() {
+ LOG.warn("FhirIO.Read is experimental and has not been tested.");
+ }
+
+ public static class Result implements POutput, PInput {
+ private PCollection<HttpBody> resources;
+
+ private PCollection<HealthcareIOError<String>> failedReads;
+ PCollectionTuple pct;
+
+ 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).setCoder(new HttpBodyCoder());
+ this.failedReads =
+ pct.get(DEAD_LETTER).setCoder(new HealthcareIOErrorCoder<>(StringUtf8Coder.of()));
+ }
+
+ public PCollection<HealthcareIOError<String>> getFailedReads() {
+ return failedReads;
+ }
+
+ public PCollection<HttpBody> 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<HttpBody> OUT = new TupleTag<HttpBody>() {};
+ /** 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 FhirIO.Read.FetchHttpBody());
+ }
+
+ /**
+ * 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 HttpBody} 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 FetchHttpBody extends PTransform<PCollection<String>, FhirIO.Read.Result> {
+
+ /** Instantiates a new Fetch Fhir message DoFn. */
+ public FetchHttpBody() {}
+
+ @Override
+ public FhirIO.Read.Result expand(PCollection<String> resourceIds) {
+ return new FhirIO.Read.Result(
+ resourceIds.apply(
+ ParDo.of(new FhirIO.Read.FetchHttpBody.HttpBodyGetFn())
+ .withOutputTags(FhirIO.Read.OUT, TupleTagList.of(FhirIO.Read.DEAD_LETTER))));
+ }
+
+ /** DoFn for fetching messages from the Fhir store with error handling. */
+ public static class HttpBodyGetFn extends DoFn<String, HttpBody> {
+
+ private Counter failedMessageGets =
+ Metrics.counter(FhirIO.Read.FetchHttpBody.HttpBodyGetFn.class, "failed-message-reads");
+ private static final Logger LOG =
+ LoggerFactory.getLogger(FhirIO.Read.FetchHttpBody.HttpBodyGetFn.class);
+ private final Counter successfulHttpBodyGets =
+ Metrics.counter(
+ FhirIO.Read.FetchHttpBody.HttpBodyGetFn.class, "successful-hl7v2-message-gets");
+ private HealthcareApiClient client;
+
+ /** Instantiates a new Hl 7 v 2 message get fn. */
+ HttpBodyGetFn() {}
+
+ /**
+ * Instantiate healthcare client.
+ *
+ * @throws IOException the io exception
+ */
+ @Setup
+ public void instantiateHealthcareClient() throws IOException {
+ this.client = new HttpHealthcareApiClient();
+ }
+
+ /**
+ * Process element.
+ *
+ * @param context the context
+ */
+ @ProcessElement
+ public void processElement(ProcessContext context) {
+ String resourceId = context.element();
+ try {
+ context.output(fetchResource(this.client, resourceId));
+ } catch (Exception e) {
+ failedMessageGets.inc();
+ LOG.warn(
+ String.format(
+ "Error fetching Fhir message with ID %s writing to Dead Letter "
+ + "Queue. Cause: %s Stack Trace: %s",
+ resourceId, e.getMessage(), Throwables.getStackTraceAsString(e)));
+ context.output(FhirIO.Read.DEAD_LETTER, HealthcareIOError.of(resourceId, e));
+ }
+ }
+
+ private HttpBody fetchResource(HealthcareApiClient client, String resourceId)
+ throws IOException, IllegalArgumentException, InterruptedException {
+ long startTime = System.currentTimeMillis();
+ Sleeper sleeper = Sleeper.DEFAULT;
+
+ com.google.api.services.healthcare.v1beta1.model.HttpBody resource =
+ client.readFhirResource(resourceId);
+
+ if (resource == null) {
+ throw new IOException(String.format("GET request for %s returned null", resourceId));
+ }
+ this.successfulHttpBodyGets.inc();
+ return resource;
+ }
+ }
+ }
+ }
+
+ /** The type Write. */
+ @AutoValue
+ public abstract static class Write extends PTransform<PCollection<HttpBody>, Write.Result> {
+
+ /** The tag for the failed writes to FHIR store`. */
+ public static final TupleTag<HealthcareIOError<HttpBody>> FAILED_BODY =
+ new TupleTag<HealthcareIOError<HttpBody>>() {};
+
+ /** The enum Write method. */
+ public enum WriteMethod {
+ /**
+ * Execute Bundle Method executes a batch of requests as a single transaction @see <a
+ * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle></a>.
+ */
+ EXECUTE_BUNDLE,
+ /**
+ * Import Method bulk imports resources from GCS. This is ideal for initial loads to empty
+ * FHIR stores. <a
+ * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import></a>.
+ */
+ IMPORT
+ }
+
+ public static class Result implements POutput {
+ private final Pipeline pipeline;
+ private final PCollection<HealthcareIOError<HttpBody>> failedInsertsWithErr;
+
+ /** Creates a {@link FhirIO.Write.Result} in the given {@link Pipeline}. */
+ static Result in(Pipeline pipeline, PCollection<HealthcareIOError<HttpBody>> failedInserts) {
+ return new Result(pipeline, failedInserts);
+ }
+
+ public PCollection<HealthcareIOError<HttpBody>> getFailedInsertsWithErr() {
+ return this.failedInsertsWithErr;
+ }
+
+ @Override
+ public Pipeline getPipeline() {
+ return this.pipeline;
+ }
+
+ @Override
+ public Map<TupleTag<?>, PValue> expand() {
+ failedInsertsWithErr.setCoder(new HealthcareIOErrorCoder<HttpBody>(new HttpBodyCoder()));
+ return ImmutableMap.of(Write.FAILED_BODY, failedInsertsWithErr);
+ }
+
+ @Override
+ public void finishSpecifyingOutput(
+ String transformName, PInput input, PTransform<?, ?> transform) {}
+
+ private Result(
+ Pipeline pipeline, PCollection<HealthcareIOError<HttpBody>> failedInsertsWithErr) {
+ this.pipeline = pipeline;
+ this.failedInsertsWithErr = failedInsertsWithErr;
+ }
+ }
+
+ /**
+ * Gets Fhir store.
+ *
+ * @return the Fhir store
+ */
+ abstract String getFhirStore();
+
+ /**
+ * Gets write method.
+ *
+ * @return the write method
+ */
+ abstract WriteMethod getWriteMethod();
+
+ abstract Optional<ContentStructure> getContentStructure();
+
+ abstract Optional<String> getImportGcsTempPath();
+
+ abstract Optional<String> getImportGcsDeadLetterPath();
+
+ /** The type Builder. */
+ @AutoValue.Builder
+ abstract static class Builder {
+
+ /**
+ * Sets Fhir store.
+ *
+ * @param fhirStore the Fhir store
+ * @return the Fhir store
+ */
+ abstract Builder setFhirStore(String fhirStore);
+
+ /**
+ * Sets write method.
+ *
+ * @param writeMethod the write method
+ * @return the write method
+ */
+ abstract Builder setWriteMethod(WriteMethod writeMethod);
+
+ abstract Builder setContentStructure(ContentStructure contentStructure);
+
+ abstract Builder setImportGcsTempPath(String gcsTempPath);
+
+ abstract Builder setImportGcsDeadLetterPath(String gcsDeadLetterPath);
+
+ /**
+ * Build write.
+ *
+ * @return the write
+ */
+ abstract Write build();
+ }
+
+ private static Write.Builder write(String fhirStore) {
+ return new AutoValue_FhirIO_Write.Builder().setFhirStore(fhirStore);
+ }
+
+ /**
+ * Create Method creates a single FHIR resource. @see <a
+ * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create></a>
+ *
+ * @param fhirStore the hl 7 v 2 store
+ * @return the write
+ */
+ public static Write fhirStoresImport(
+ String fhirStore,
+ String gcsTempPath,
+ String gcsDeadLetterPath,
+ @Nullable ContentStructure contentStructure) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore)
+ .setWriteMethod(Write.WriteMethod.IMPORT)
+ .setContentStructure(contentStructure)
+ .setImportGcsTempPath(gcsTempPath)
+ .setImportGcsDeadLetterPath(gcsDeadLetterPath)
+ .build();
+ }
+
+ /**
+ * Execute Bundle Method executes a batch of requests as a single transaction @see <a
+ * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle></a>.
+ *
+ * @param fhirStore the hl 7 v 2 store
+ * @return the write
+ */
+ public static Write executeBundles(String fhirStore) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore)
+ .setWriteMethod(WriteMethod.EXECUTE_BUNDLE)
+ .build();
+ }
+
+ private static final Logger LOG = LoggerFactory.getLogger(Write.class);
+
+ @Override
+ public Result expand(PCollection<HttpBody> input) {
+ PCollection<HealthcareIOError<HttpBody>> failedBundles;
+ PCollection<HealthcareIOError<String>> failedImports;
+ switch (this.getWriteMethod()) {
+ case IMPORT:
+ LOG.warn(
+ "Make sure the Cloud Healthcare Service Agent has permissions when using import:"
+ + " https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions");
+ String tempPath = getImportGcsTempPath().orElseThrow(IllegalArgumentException::new);
+ String deadPath = getImportGcsDeadLetterPath().orElseThrow(IllegalArgumentException::new);
+ ContentStructure contentStructure =
+ getContentStructure().orElseThrow(IllegalArgumentException::new);
+
+ failedBundles =
+ input
+ .apply(new Import(getFhirStore(), tempPath, deadPath, contentStructure))
+ .setCoder(new HealthcareIOErrorCoder<>(new HttpBodyCoder()));
+ // fall through
+ case EXECUTE_BUNDLE:
+ default:
+ failedBundles =
+ input.apply(
+ "Execute FHIR Bundles",
+ ParDo.of(new ExecuteBundles.ExecuteBundlesFn(this.getFhirStore())));
+ }
+ return Result.in(input.getPipeline(), failedBundles);
+ }
+ }
+
+ /**
+ * Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a
+ * fhirStores.import Request for that file.
+ */
+ public static class Import
+ extends PTransform<PCollection<HttpBody>, PCollection<HealthcareIOError<HttpBody>>> {
+
+ private final String fhirStore;
+ private final String tempGcsPath;
+ private final String deadLetterGcsPath;
+ private final ContentStructure contentStructure;
+
+ Import(
+ String fhirStore,
+ String tempGcsPath,
+ String deadLetterGcsPath,
+ @Nullable ContentStructure contentStructure) {
+ this.fhirStore = fhirStore;
+ this.tempGcsPath = tempGcsPath;
+ this.deadLetterGcsPath = deadLetterGcsPath;
+ if (contentStructure == null) {
+ this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+ } else {
+ this.contentStructure = contentStructure;
+ }
+ }
+
+ @Override
+ public PCollection<HealthcareIOError<HttpBody>> expand(PCollection<HttpBody> input) {
+ return input.apply(
+ ParDo.of(new ImportFn(fhirStore, tempGcsPath, deadLetterGcsPath, contentStructure)));
+ }
+
+ public enum ContentStructure {
+ /** If the content structure is not specified, the default value BUNDLE will be used. */
+ CONTENT_STRUCTURE_UNSPECIFIED,
+ /**
+ * The source file contains one or more lines of newline-delimited JSON (ndjson). Each line is
+ * a bundle, which contains one or more resources. Set the bundle type to history to import
+ * resource versions.
+ */
+ BUNDLE,
+ /**
+ * The source file contains one or more lines of newline-delimited JSON (ndjson). Each line is
+ * a single resource.
+ */
+ RESOURCE,
+ /** The entire file is one JSON bundle. The JSON can span multiple lines. */
+ BUNDLE_PRETTY,
+ /** The entire file is one JSON resource. The JSON can span multiple lines. */
+ RESOURCE_PRETTY
+ }
+
+ static class ImportFn extends DoFn<HttpBody, HealthcareIOError<HttpBody>> {
+ private final String fhirStore;
+ private final String tempGcsPath;
+ private final String deadLetterGcsPath;
+ private final ContentStructure contentStructure;
+ private ObjectMapper mapper;
+ private ResourceId resourceId;
+ private ResourceId deadLetterResourceId;
+ private WritableByteChannel ndJsonChannel;
+
+ private transient HealthcareApiClient client;
+ private static final Logger LOG = LoggerFactory.getLogger(ImportFn.class);
+
+ ImportFn(
+ String fhirStore,
+ String tempGcsPath,
+ String deadLetterGcsPath,
+ @Nullable ContentStructure contentStructure) {
+ this.fhirStore = fhirStore;
+ this.tempGcsPath = tempGcsPath;
+ this.deadLetterGcsPath = deadLetterGcsPath;
+ if (contentStructure == null) {
+ this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+ } else {
+ this.contentStructure = contentStructure;
+ }
+ }
+
+ @Setup
+ public void initClient() throws IOException {
+ this.client = new HttpHealthcareApiClient();
+ }
+
+ @StartBundle
+ public void initBatch() throws IOException {
Review comment:
I am a little worried about the fact that the bundle size is unknown. In extreme (though unlikely) cases, we could be making one import API call per resource.
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