[
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=432815&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-432815
]
ASF GitHub Bot logged work on BEAM-9468:
----------------------------------------
Author: ASF GitHub Bot
Created on: 13/May/20 20:41
Start Date: 13/May/20 20:41
Worklog Time Spent: 10m
Work Description: pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424715107
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -0,0 +1,1144 @@
+/*
+ * 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>
+ *
+ * <h3>Reading</h3>
+ *
+ * <p>FHIR resources can be read with {@link FhirIO.Read}, which 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 retrieve 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.
+ *
+ * <h3>Writing</h3>
+ *
+ * <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.getExistingFhirStore()));
+ *
+ * PCollection<HealthcareIOError<String>> failedBundles =
writeResult.getFailedInsertsWithErr();
+ *
+ * failedBundles.apply("Write failed bundles to BigQuery",
+ * BigQueryIO
+ * .write()
+ * .to(option.getBQFhirExecuteBundlesDeadLetterTable())
+ * .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ *
+ * // Alternatively you could use import for high throughput to a new store.
+ * FhirIO.Write.Result writeResult =
+ * output.apply("Import FHIR Resources",
FhirIO.executeBundles(options.getNewFhirStore()));
+ * }***
+ * </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
+ */
+ 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>
+ */
+ 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 ReadResourceFn())
+ .withOutputTags(FhirIO.Read.OUT,
TupleTagList.of(FhirIO.Read.DEAD_LETTER))));
+ }
+
+ /** DoFn for fetching messages from the Fhir store with error handling.
*/
+ static class ReadResourceFn extends DoFn<String, String> {
+
+ private Counter failedMessageGets =
+ Metrics.counter(ReadResourceFn.class, "failed-message-reads");
+ private static final Logger LOG =
LoggerFactory.getLogger(ReadResourceFn.class);
+ private final Counter successfulStringGets =
+ Metrics.counter(ReadResourceFn.class,
"successful-hl7v2-message-gets");
+ private HealthcareApiClient client;
+ private ObjectMapper mapper;
+
+ /** Instantiates a new Hl 7 v 2 message get fn. */
+ ReadResourceFn() {}
+
+ /**
+ * 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));
+ } 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 String fetchResource(HealthcareApiClient client, String
resourceId)
+ throws IOException, IllegalArgumentException {
+ long startTime = System.currentTimeMillis();
+
+ HttpBody resource = client.readFhirResource(resourceId);
+
+ if (resource == null) {
+ throw new IOException(String.format("GET request for %s returned
null", resourceId));
+ }
+ this.successfulStringGets.inc();
+ return mapper.writeValueAsString(resource);
+ }
+ }
+ }
+ }
+
+ /** The type Write. */
+ @AutoValue
+ public abstract static class Write extends PTransform<PCollection<String>,
Write.Result> {
+
+ /** The tag for the failed writes to FHIR store`. */
+ public static final TupleTag<HealthcareIOError<String>> FAILED_BODY =
+ new TupleTag<HealthcareIOError<String>>() {};
+ /** The tag for the files that failed to FHIR store`. */
+ public static final TupleTag<HealthcareIOError<String>> FAILED_FILES =
+ new TupleTag<HealthcareIOError<String>>() {};
+ /** The tag for temp files for import to FHIR store`. */
+ public static final TupleTag<ResourceId> TEMP_FILES = new
TupleTag<ResourceId>() {};
+
+ /** 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
+ }
+
+ /** The type Result. */
+ public static class Result implements POutput {
+ private final Pipeline pipeline;
+ private final PCollection<HealthcareIOError<String>> failedBodies;
+ private final PCollection<HealthcareIOError<String>> failedFiles;
+
+ /**
+ * Creates a {@link FhirIO.Write.Result} in the given {@link Pipeline}.
@param pipeline the
+ * pipeline
+ *
+ * @param failedBodies the failed inserts
+ * @return the result
+ */
+ static Result in(Pipeline pipeline,
PCollection<HealthcareIOError<String>> failedBodies) {
+ return new Result(pipeline, failedBodies, null);
+ }
+
+ static Result in(
+ Pipeline pipeline,
+ PCollection<HealthcareIOError<String>> failedBodies,
+ PCollection<HealthcareIOError<String>> failedFiles) {
+ return new Result(pipeline, failedBodies, failedFiles);
+ }
+
+ /**
+ * Gets failed bodies with err.
+ *
+ * @return the failed inserts with err
+ */
+ public PCollection<HealthcareIOError<String>> getFailedBodies() {
+ return this.failedBodies;
+ }
+
+ /**
+ * Gets failed file imports with err.
+ *
+ * @return the failed GCS uri with err
+ */
+ public PCollection<HealthcareIOError<String>> getFailedFiles() {
+ return this.failedFiles;
+ }
+
+ @Override
+ public Pipeline getPipeline() {
+ return this.pipeline;
+ }
+
+ @Override
+ public Map<TupleTag<?>, PValue> expand() {
+ return ImmutableMap.of(Write.FAILED_BODY, failedBodies,
Write.FAILED_FILES, failedFiles);
+ }
+
+ @Override
+ public void finishSpecifyingOutput(
+ String transformName, PInput input, PTransform<?, ?> transform) {}
+
+ private Result(
+ Pipeline pipeline,
+ PCollection<HealthcareIOError<String>> failedBodies,
+ @Nullable PCollection<HealthcareIOError<String>> failedFiles) {
+ this.pipeline = pipeline;
+ this.failedBodies = failedBodies;
+ if (failedFiles == null) {
+ failedFiles =
+ (PCollection<HealthcareIOError<String>>)
+
pipeline.apply(Create.empty(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
+ }
+ this.failedFiles = failedFiles;
+ }
+ }
+
+ /**
+ * Gets Fhir store.
+ *
+ * @return the Fhir store
+ */
+ abstract String getFhirStore();
+
+ /**
+ * Gets write method.
+ *
+ * @return the write method
+ */
+ abstract WriteMethod getWriteMethod();
+
+ /**
+ * Gets content structure.
+ *
+ * @return the content structure
+ */
+ abstract Optional<FhirIO.Import.ContentStructure> getContentStructure();
+
+ /**
+ * Gets import gcs temp path.
+ *
+ * @return the import gcs temp path
+ */
+ abstract Optional<String> getImportGcsTempPath();
+
+ /**
+ * Gets import gcs dead letter path.
+ *
+ * @return the import gcs dead letter path
+ */
+ 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);
+
+ /**
+ * Sets content structure.
+ *
+ * @param contentStructure the content structure
+ * @return the content structure
+ */
+ abstract Builder setContentStructure(FhirIO.Import.ContentStructure
contentStructure);
+
+ /**
+ * Sets import gcs temp path.
+ *
+ * @param gcsTempPath the gcs temp path
+ * @return the import gcs temp path
+ */
+ abstract Builder setImportGcsTempPath(String gcsTempPath);
+
+ /**
+ * Sets import gcs dead letter path.
+ *
+ * @param gcsDeadLetterPath the gcs dead letter path
+ * @return the import gcs dead letter path
+ */
+ 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
+ * @param gcsTempPath the gcs temp path
+ * @param gcsDeadLetterPath the gcs dead letter path
+ * @param contentStructure the content structure
+ * @return the write
+ */
+ public static Write fhirStoresImport(
+ String fhirStore,
+ String gcsTempPath,
+ String gcsDeadLetterPath,
+ @Nullable FhirIO.Import.ContentStructure contentStructure) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore)
+ .setWriteMethod(Write.WriteMethod.IMPORT)
+ .setContentStructure(contentStructure)
+ .setImportGcsTempPath(gcsTempPath)
+ .setImportGcsDeadLetterPath(gcsDeadLetterPath)
+ .build();
+ }
+
+ public static Write fhirStoresImport(
+ String fhirStore,
+ String gcsDeadLetterPath,
+ @Nullable FhirIO.Import.ContentStructure contentStructure) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore)
+ .setWriteMethod(Write.WriteMethod.IMPORT)
+ .setContentStructure(contentStructure)
+ .setImportGcsDeadLetterPath(gcsDeadLetterPath)
+ .build();
+ }
+
+ public static Write fhirStoresImport(
+ ValueProvider<String> fhirStore,
+ ValueProvider<String> gcsTempPath,
+ ValueProvider<String> gcsDeadLetterPath,
+ @Nullable FhirIO.Import.ContentStructure contentStructure) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore.get())
+ .setWriteMethod(Write.WriteMethod.IMPORT)
+ .setContentStructure(contentStructure)
+ .setImportGcsTempPath(gcsTempPath.get())
+ .setImportGcsDeadLetterPath(gcsDeadLetterPath.get())
+ .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();
+ }
+
+ /**
+ * Execute bundles write.
+ *
+ * @param fhirStore the fhir store
+ * @return the write
+ */
+ public static Write executeBundles(ValueProvider<String> fhirStore) {
+ return new AutoValue_FhirIO_Write.Builder()
+ .setFhirStore(fhirStore.get())
+ .setWriteMethod(WriteMethod.EXECUTE_BUNDLE)
+ .build();
+ }
+
+ private static final Logger LOG = LoggerFactory.getLogger(Write.class);
+
+ @Override
+ public Result expand(PCollection<String> input) {
+ PCollection<HealthcareIOError<String>> 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 deadPath =
getImportGcsDeadLetterPath().orElseThrow(IllegalArgumentException::new);
+ FhirIO.Import.ContentStructure contentStructure =
+ getContentStructure().orElseThrow(IllegalArgumentException::new);
+ String tempPath =
+
getImportGcsTempPath().orElse(input.getPipeline().getOptions().getTempLocation());
+
+ return input.apply(new Import(getFhirStore(), tempPath, deadPath,
contentStructure));
+ case EXECUTE_BUNDLE:
+ default:
+ failedBundles =
+ input
+ .apply(
+ "Execute FHIR Bundles",
+ ParDo.of(new
ExecuteBundles.ExecuteBundlesFn(this.getFhirStore())))
+ .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+ }
+ 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. This is intended for batch use
only to facilitate
+ * large backfills to empty FHIR stores and should not be used with
unbounded PCollections. If
+ * your use case is streaming checkout using {@link ExecuteBundles} to more
safely execute bundles
+ * as transactions which is safer practice for a use on a "live" FHIR store.
+ */
+ public static class Import extends Write {
+
+ private final String fhirStore;
+ private final String deadLetterGcsPath;
+ private final ContentStructure contentStructure;
+ private static final int DEFAULT_FILES_PER_BATCH = 10000;
+ private static final Logger LOG = LoggerFactory.getLogger(Import.class);
+ private String tempGcsPath;
+
+ /**
+ * Instantiates a new Import.
+ *
+ * @param fhirStore the fhir store
+ * @param tempGcsPath the temp gcs path
+ * @param deadLetterGcsPath the dead letter gcs path
+ * @param contentStructure the content structure
+ */
+ Import(
+ ValueProvider<String> fhirStore,
+ ValueProvider<String> tempGcsPath,
+ ValueProvider<String> deadLetterGcsPath,
+ @Nullable ContentStructure contentStructure) {
+ this.fhirStore = fhirStore.get();
+ this.tempGcsPath = tempGcsPath.get();
+ this.deadLetterGcsPath = deadLetterGcsPath.get();
+ if (contentStructure == null) {
+ this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+ } else {
+ this.contentStructure = contentStructure;
+ }
+ }
+
+ Import(
+ ValueProvider<String> fhirStore,
+ ValueProvider<String> deadLetterGcsPath,
+ @Nullable ContentStructure contentStructure) {
+ this.fhirStore = fhirStore.get();
+ this.deadLetterGcsPath = deadLetterGcsPath.get();
+ if (contentStructure == null) {
+ this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+ } else {
+ this.contentStructure = contentStructure;
+ }
+ }
+ /**
+ * Instantiates a new Import.
+ *
+ * @param fhirStore the fhir store
+ * @param tempGcsPath the temp gcs path
+ * @param deadLetterGcsPath the dead letter gcs path
+ * @param contentStructure the content structure
+ */
+ 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
+ String getFhirStore() {
+ return fhirStore;
+ }
+
+ @Override
+ WriteMethod getWriteMethod() {
+ return WriteMethod.IMPORT;
+ }
+
+ @Override
+ Optional<ContentStructure> getContentStructure() {
+ return Optional.of(contentStructure);
+ }
+
+ @Override
+ Optional<String> getImportGcsTempPath() {
+ return Optional.of(tempGcsPath);
+ }
+
+ @Override
+ Optional<String> getImportGcsDeadLetterPath() {
+ return Optional.of(deadLetterGcsPath);
+ }
+
+ @Override
+ public Write.Result expand(PCollection<String> input) {
+ checkState(
+ input.isBounded() == IsBounded.BOUNDED,
+ "FhirIO.Import should only be used on unbounded PCollections as it
is"
+ + "intended for batch use only.");
+
+ // fall back on pipeline's temp location.
+ String tempPath = tempGcsPath;
+ if (tempPath == null) {
+ tempPath = input.getPipeline().getOptions().getTempLocation();
+ }
+
+ // Write bundles of String to GCS
+ PCollectionTuple writeTmpFileResults =
+ input.apply(
+ "Write nd json to GCS",
+ ParDo.of(new WriteBundlesToFilesFn(fhirStore, tempPath,
deadLetterGcsPath))
+ .withOutputTags(Write.TEMP_FILES,
TupleTagList.of(Write.FAILED_BODY)));
+
+ PCollection<HealthcareIOError<String>> failedBodies =
+ writeTmpFileResults
+ .get(Write.FAILED_BODY)
+ .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+ int numShards = 100;
+ PCollection<HealthcareIOError<String>> failedFiles =
+ writeTmpFileResults
+ .get(Write.TEMP_FILES)
+ .apply(
+ "Shard files", // to paralelize group into batches
+ WithKeys.of(ThreadLocalRandom.current().nextInt(0,
numShards)))
Review comment:
This is providing a static key, not a key-generating function, right?
```suggestion
WithKeys.of(elm -> ThreadLocalRandom.current().nextInt(0,
numShards)))
```
(I think)
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Issue Time Tracking
-------------------
Worklog Id: (was: 432815)
Time Spent: 39h (was: 38h 50m)
> Add Google Cloud Healthcare API IO Connectors
> ---------------------------------------------
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
> Issue Type: New Feature
> Components: io-java-gcp
> Reporter: Jacob Ferriero
> Assignee: Jacob Ferriero
> Priority: Minor
> Time Spent: 39h
> Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM
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