[
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=405808&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-405808
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ASF GitHub Bot logged work on BEAM-9468:
----------------------------------------
Author: ASF GitHub Bot
Created on: 18/Mar/20 22:52
Start Date: 18/Mar/20 22:52
Worklog Time Spent: 10m
Work Description: pabloem commented on pull request #11151: [BEAM-9468]
Hl7v2 io
URL: https://github.com/apache/beam/pull/11151#discussion_r394668514
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java
##########
@@ -0,0 +1,620 @@
+/*
+ * 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.v1alpha2.model.IngestMessageResponse;
+import com.google.api.services.healthcare.v1alpha2.model.Message;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.Collections;
+import java.util.List;
+import org.apache.beam.sdk.io.gcp.datastore.AdaptiveThrottler;
+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.PDone;
+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.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 HL7v2 Messages are fetched from the HL7v2 store based on the {@link
PCollection} of of
+ * message IDs {@link String}s produced by the {@link
AutoValue_HL7v2IO_Read#getMessageIDTransform}
+ * as {@link PCollectionTuple}*** containing an {@link HL7v2IO.Read#OUT} tag
for successfully
+ * fetched messages and a {@link HL7v2IO.Read#DEAD_LETTER} tag for message IDs
that could not be
+ * fetched.
+ *
+ * <p>HL7v2 stores can be read in several ways: - Unbounded: based on the
Pub/Sub Notification
+ * Channel {@link HL7v2IO#readNotificationSubscription(String)} - Bounded:
based on reading an
+ * entire HL7v2 store (or stores) {@link HL7v2IO#readHL7v2Store(String)} -
Bounded: based on reading
+ * an HL7v2 store with a filter
+ *
+ * <p>Note, due to the flexibility of this Read transform, this must output a
dead letter queue.
+ * This handles the scenario where the the PTransform that populates a
PCollection of message IDs
+ * contains message IDs that do not exist in the HL7v2 stores.
+ *
+ * <p>Example:
+ *
+ * <pre>{@code
+ * PipelineOptions options = ...;
+ * Pipeline pipeline = Pipeline.create(options)
+ *
+ *
+ * PCollectionTuple messages = pipeline.apply(
+ * new HLv2IO.readNotifications(options.getNotificationSubscription())
+ *
+ * // Write errors to your favorite dead letter queue (e.g. Pub/Sub, GCS,
BigQuery)
+ * messages.get(PubsubNotificationToHL7v2Message.DEAD_LETTER)
+ * .apply("WriteToDeadLetterQueue", ...);
+ *
+ * PCollection<Message> fetchedMessages =
fetchResults.get(PubsubNotificationToHL7v2Message.OUT)
+ * .apply("ExtractFetchedMessage",
+ * MapElements
+ * .into(TypeDescriptor.of(Message.class))
+ * .via(FailsafeElement::getPayload));
+ *
+ * // Go about your happy path transformations.
+ * PCollection<Message> out = fetchedMessages.apply("ProcessFetchedMessages",
...);
+ *
+ * // Write using the Message.Ingest method of the HL7v2 REST API.
+ * out.apply(HL7v2IO.ingestMessages(options.getOutputHL7v2Store()));
+ *
+ * pipeline.run();
+ *
+ * }***
+ * </pre>
+ */
+public class HL7v2IO {
+ // TODO add metrics for failed records.
+
+ private static Read.Builder read(PTransform<PBegin, PCollection<String>>
messageIDTransform) {
Review comment:
Under this interface, you would do something like this:
```
Pipeline p = ....
PCollectionTuple pct =
p.apply(HL7v2IO.read(PubSubIO.read().fromTopic(....)));
```
This is a little odd. A more natural way of doing this would be something
like this:
```
Pipeline p = ....
PCollection<String> messageIds = p.apply(PubSubIO.read().fromTopic(....));
HL7v2IO.Read.Result result = messageIds.apply(HL7v2IO.readAll());
```
This way, `HL7v2IO.Read` takes in a `PCollection<String>` containing the
message IDs, instead of having a PTransform be a parameter, which is not
commonly done elsewhere.
This is similar to how FileIO transforms work. Check out the functions
`match`, `matchAll`, `readMatches`.
https://beam.apache.org/releases/javadoc/2.19.0/index.html?org/apache/beam/sdk/io/FileIO.html
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Issue Time Tracking
-------------------
Worklog Id: (was: 405808)
Time Spent: 2h 40m (was: 2.5h)
> 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: 2h 40m
> 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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