[GitHub] [beam] pabloem commented on a change in pull request #11151: [BEAM-9468] Hl7v2 io

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pabloem commented on a change in pull request #11151: [BEAM-9468]  Hl7v2 io
URL: https://github.com/apache/beam/pull/11151#discussion_r404353084
 
 

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 File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java
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+/*
+ * 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.api.services.healthcare.v1beta1.model.Message;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+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.Create;
+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.PBegin;
+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.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link HL7v2IO} provides an API for reading from and writing to <a
+ * href="https://cloud.google.com/healthcare/docs/concepts/hl7v2">Google Cloud Healthcare HL7v2 API.
+ * </a>
+ *
+ * <p>Read
+ *
+ * <p>HL7v2 Messages can be fetched from the HL7v2 store in two ways Message Fetching and Message
+ * Listing.
+ *
+ * <p>Message Fetching
+ *
+ * <p>Message Fetching with {@link HL7v2IO.Read} supports use cases where you have a ${@link
+ * PCollection} of message IDS. This is appropriate for reading the HL7v2 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 Message contents from HL7v2 Store based on the {@link PCollection} of message ID strings
+ * {@link HL7v2IO.Read.Result} where one can call {@link Read.Result#getMessages()} to retrived a
+ * {@link PCollection} containing the successfully fetched {@link HL7v2Message}s and/or {@link
+ * Read.Result#getFailedReads()} to retrieve a {@link PCollection} of {@link HealthcareIOError}
+ * containing the msgID 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 catch scenarios where the upstream {@link PCollection} contains IDs that are not
+ * valid or are not reachable due to permissions issues.
+ *
+ * <p>Message Listing Message Listing with {@link HL7v2IO.ListHL7v2Messages} supports batch use
+ * cases where you want to process all the messages in an HL7v2 store or those matching a
+ * filter @see <a
+ * href=>https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.hl7V2Stores.messages/list#query-parameters</a>
+ * This paginates through results of a Messages.List call @see <a
+ * href=>https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.hl7V2Stores.messages/list</a>
+ * and outputs directly to a {@link PCollection} of {@link HL7v2Message}. In these use cases, the
+ * error handling similar to above is unnecessary because we are listing from the source of truth
+ * the pipeline should fail transparently if this transform fails to paginate through all the
+ * results.
+ *
+ * <p>Write
+ *
+ * <p>A bounded or unbounded {@link PCollection} of {@link HL7v2Message} can be ingested into an
+ * HL7v2 store using {@link HL7v2IO#ingestMessages(String)}. This will return a {@link
+ * HL7v2IO.Write.Result} on which you can call {@link Write.Result#getFailedInsertsWithErr()} to
+ * retrieve a {@link PCollection} of {@link HealthcareIOError} containing the {@link HL7v2Message}
+ * that failed to be ingested and the exception. This can be used to write to the dead letter
+ * storage system of your chosing.
+ *
+ * <p>Unbounded Example:
+ *
+ * <pre>{@code
+ * PipelineOptions options = ...;
+ * Pipeline p = Pipeline.create(options);
+ *
+ * HL7v2IO.Read.Result readResult = p
+ *   .apply(
+ *     "Read HL7v2 notifications",
+ *     PubSubIO.readStrings().fromTopic(options.getNotificationSubscription()))
+ *   .apply(HL7v2IO.readAll());
+ *
+ * // Write errors to your favorite dead letter  queue (e.g. Pub/Sub, GCS, BigQuery)
+ * readResult.getFailedReads().apply("WriteToDeadLetterQueue", ...);
+ *
+ *
+ * // Go about your happy path transformations.
+ * PCollection<HL7v2Message> out = readResult.getMessages().apply("ProcessFetchedMessages", ...);
+ *
+ * // Write using the Message.Ingest method of the HL7v2 REST API.
+ * out.apply(HL7v2IO.ingestMessages(options.getOutputHL7v2Store()));
+ *
+ * pipeline.run();
+ *
+ * }***
+ * </pre>
+ *
+ * <p>Bounded Read Example:
+ *
+ * <pre>{@code
+ * PipelineOptions options = ...;
+ * Pipeline p = Pipeline.create(options);
+ *
+ * PCollection<HL7v2Message> out = p
+ *   .apply(
+ *       "List messages in HL7v2 store with filter",
+ *       ListHL7v2Messages(
+ *           Collections.singletonList(options.getInputHL7v2Store()), option.getHL7v2Filter()))
+ *    // Go about your happy path transformations.
+ *   .apply("Process HL7v2 Messages", ...);
+ * pipeline.run().waitUntilFinish();
+ * }***
+ * </pre>
+ */
+public class HL7v2IO {
+
+  private static Write.Builder write(String hl7v2Store) {
+    return new AutoValue_HL7v2IO_Write.Builder().setHL7v2Store(hl7v2Store);
+  }
+
+  public static Read readAll() {
+    return new Read();
+  }
+
+  /**
+   * Write with Messages.Ingest method. @see <a
+   * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.hl7V2Stores.messages/ingest></a>
+   *
+   * @param hl7v2Store the hl 7 v 2 store
+   * @return the write
+   */
+  public static Write ingestMessages(String hl7v2Store) {
+    return write(hl7v2Store).setWriteMethod(Write.WriteMethod.INGEST).build();
+  }
+
+  // TODO add hyper links to this doc string.
+  /**
+   * The type Read that reads HL7v2 message contents given a PCollection of message IDs strings.
+   *
+   * <p>These could be sourced from any {@link PCollection} of {@link String}s but the most popular
+   * patterns would be {@link PubsubIO#readStrings()} reading a subscription on an HL7v2 Store's
+   * notification channel topic or using {@link ListHL7v2Messages} to list HL7v2 message IDs with an
+   * optional filter using Ingest write method. @see <a
+   * href=https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.hl7V2Stores.messages/list></a>.
+   */
+  public static class Read extends PTransform<PCollection<String>, Read.Result> {
+
+    public Read() {}
+
+    public static class Result implements POutput, PInput {
+      private PCollection<HL7v2Message> messages;
+
+      private PCollection<HealthcareIOError<String>> failedReads;
+      PCollectionTuple pct;
+
+      public static Result of(PCollectionTuple pct) throws IllegalArgumentException {
+        if (pct.getAll()
+            .keySet()
+            .containsAll((Collection<?>) TupleTagList.of(OUT).and(DEAD_LETTER))) {
+          return new Result(pct);
+        } else {
+          throw new IllegalArgumentException(
+              "The PCollection tuple must have the HL7v2IO.Read.OUT "
+                  + "and HL7v2IO.Read.DEAD_LETTER tuple tags");
+        }
+      }
+
+      private Result(PCollectionTuple pct) {
+        this.pct = pct;
+        this.messages = pct.get(OUT).setCoder(new HL7v2MessageCoder());
+        this.failedReads =
+            pct.get(DEAD_LETTER).setCoder(new HealthcareIOErrorCoder<>(StringUtf8Coder.of()));
+      }
+
+      public PCollection<HealthcareIOError<String>> getFailedReads() {
+        return failedReads;
+      }
+
+      public PCollection<HL7v2Message> getMessages() {
+        return messages;
+      }
+
+      @Override
+      public Pipeline getPipeline() {
+        return this.pct.getPipeline();
+      }
+
+      @Override
+      public Map<TupleTag<?>, PValue> expand() {
+        return ImmutableMap.of(OUT, messages);
+      }
+
+      @Override
+      public void finishSpecifyingOutput(
+          String transformName, PInput input, PTransform<?, ?> transform) {}
+    }
+
+    /** The tag for the main output of HL7v2 Messages. */
+    public static final TupleTag<HL7v2Message> OUT = new TupleTag<HL7v2Message>() {};
+    /** The tag for the deadletter output of HL7v2 Messages. */
+    public static final TupleTag<HealthcareIOError<String>> DEAD_LETTER =
+        new TupleTag<HealthcareIOError<String>>() {};
+
+    @Override
+    public Result expand(PCollection<String> input) {
+      return input.apply("Fetch HL7v2 messages", new FetchHL7v2Message());
+    }
+
+    /**
+     * DoFn to fetch a message from an Google Cloud Healthcare HL7v2 store based on msgID
 
 Review comment:
   I guess it's not a DoFn?

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