[
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=410578&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-410578
]
ASF GitHub Bot logged work on BEAM-9468:
----------------------------------------
Author: ASF GitHub Bot
Created on: 26/Mar/20 20:07
Start Date: 26/Mar/20 20:07
Worklog Time Spent: 10m
Work Description: jaketf commented on pull request #11151: [BEAM-9468]
Hl7v2 io
URL: https://github.com/apache/beam/pull/11151#discussion_r398858533
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
##########
@@ -0,0 +1,452 @@
+/*
+ * 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.client.http.HttpHeaders;
+import com.google.api.client.http.HttpRequest;
+import com.google.api.client.http.HttpRequestInitializer;
+import com.google.api.client.http.javanet.NetHttpTransport;
+import com.google.api.client.json.JsonFactory;
+import com.google.api.client.json.gson.GsonFactory;
+import com.google.api.client.util.ArrayMap;
+import com.google.api.services.healthcare.v1alpha2.CloudHealthcare;
+import
com.google.api.services.healthcare.v1alpha2.CloudHealthcare.Projects.Locations.Datasets.Hl7V2Stores.Messages;
+import com.google.api.services.healthcare.v1alpha2.CloudHealthcareScopes;
+import com.google.api.services.healthcare.v1alpha2.model.CreateMessageRequest;
+import com.google.api.services.healthcare.v1alpha2.model.Empty;
+import com.google.api.services.healthcare.v1alpha2.model.Hl7V2Store;
+import com.google.api.services.healthcare.v1alpha2.model.HttpBody;
+import com.google.api.services.healthcare.v1alpha2.model.IngestMessageRequest;
+import com.google.api.services.healthcare.v1alpha2.model.IngestMessageResponse;
+import com.google.api.services.healthcare.v1alpha2.model.ListMessagesResponse;
+import com.google.api.services.healthcare.v1alpha2.model.Message;
+import
com.google.api.services.healthcare.v1alpha2.model.SearchResourcesRequest;
+import com.google.auth.oauth2.GoogleCredentials;
+import java.io.IOException;
+import java.io.Serializable;
+import java.net.URI;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.extensions.gcp.util.RetryHttpRequestInitializer;
+import
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Strings;
+
+/**
+ * A client that talks to the Cloud Healthcare API through HTTP requests. This
client is created
+ * mainly to encapsulate the unserializable dependencies, since most generated
classes are not
+ * serializable in the HTTP client.
+ */
+public class HttpHealthcareApiClient<T> implements HealthcareApiClient,
Serializable {
+
+ private transient CloudHealthcare client;
+
+ /**
+ * Instantiates a new Http healthcare api client.
+ *
+ * @throws IOException the io exception
+ */
+ public HttpHealthcareApiClient() throws IOException {
+ initClient();
+ }
+
+ /**
+ * Instantiates a new Http healthcare api client.
+ *
+ * @param client the client
+ * @throws IOException the io exception
+ */
+ public HttpHealthcareApiClient(CloudHealthcare client) throws IOException {
+ this.client = client;
+ initClient();
+ }
+
+ @VisibleForTesting
+ static <T, X extends Collection<T>> Stream<T>
flattenIteratorCollectionsToStream(
+ Iterator<X> iterator) {
+ Spliterator<Collection<T>> spliterator =
Spliterators.spliteratorUnknownSize(iterator, 0);
+ return StreamSupport.stream(spliterator,
false).flatMap(Collection::stream);
+ }
+
+ public JsonFactory getJsonFactory() {
+ return this.client.getJsonFactory();
+ }
+
+ @Override
+ public ListMessagesResponse makeHL7v2ListRequest(
+ String hl7v2Store, @Nullable String filter, @Nullable String pageToken)
throws IOException {
+
+ Messages.List baseRequest =
+ client
+ .projects()
+ .locations()
+ .datasets()
+ .hl7V2Stores()
+ .messages()
+ .list(hl7v2Store)
+ .setPageToken(pageToken);
+
+ if (Strings.isNullOrEmpty(filter)) {
+ return baseRequest.execute();
+ } else {
+ return baseRequest.setFilter(filter).execute();
+ }
+ }
+
+ /**
+ * Gets message id page iterator.
+ *
+ * @param hl7v2Store the HL7v2 store
+ * @return the message id page iterator
+ * @throws IOException the io exception
+ */
+ @Override
+ public Stream<String> getHL7v2MessageIDStream(String hl7v2Store) throws
IOException {
+ return getHL7v2MessageIDStream(hl7v2Store, null);
+ }
+
+ /**
+ * Get a {@link Stream} of message IDs from flattening the pages of a new
{@link
+ * HL7v2MessageIDPages}.
+ *
+ * @param hl7v2Store the HL7v2 store
+ * @param filter the filter
+ * @return the message id Stream
+ * @throws IOException the io exception
+ */
+ @Override
+ public Stream<String> getHL7v2MessageIDStream(String hl7v2Store, @Nullable
String filter)
+ throws IOException {
+ Iterator<List<String>> iterator = new HL7v2MessageIDPages(this,
hl7v2Store, filter).iterator();
+ return flattenIteratorCollectionsToStream(iterator);
+ }
+
+ /**
+ * Gets HL7v2 message.
+ *
+ * @param msgName the msg name
+ * @return the message
+ * @throws IOException the io exception
+ * @throws ParseException the parse exception
+ */
+ @Override
+ public Message getHL7v2Message(String msgName) throws IOException {
+ Message msg =
+
client.projects().locations().datasets().hl7V2Stores().messages().get(msgName).execute();
+ if (msg == null) {
+ throw new IOException(String.format("Couldn't find message: %s.",
msgName));
+ }
+ return msg;
+ }
+
+ @Override
+ public Empty deleteHL7v2Message(String msgName) throws IOException {
+ return client
+ .projects()
+ .locations()
+ .datasets()
+ .hl7V2Stores()
+ .messages()
+ .delete(msgName)
+ .execute();
+ }
+
+ /**
+ * Gets HL7v2 store.
+ *
+ * @param storeName the store name
+ * @return the HL7v2 store
+ * @throws IOException the io exception
+ */
+ @Override
+ public Hl7V2Store getHL7v2Store(String storeName) throws IOException {
+ return
client.projects().locations().datasets().hl7V2Stores().get(storeName).execute();
+ }
+
+ @Override
+ public IngestMessageResponse ingestHL7v2Message(String hl7v2Store, Message
msg)
+ throws IOException {
+ IngestMessageRequest ingestMessageRequest = new IngestMessageRequest();
+ ingestMessageRequest.setMessage(msg);
+ return client
+ .projects()
+ .locations()
+ .datasets()
+ .hl7V2Stores()
+ .messages()
+ .ingest(hl7v2Store, ingestMessageRequest)
+ .execute();
+ }
Review comment:
yes
[here](https://github.com/apache/beam/pull/11151/files/cac03ec30c77e6bd45954e659b875d0378370892#diff-3ab3eba677d52f20f1a688b1017adf84R274)
we extend
[`RetryHttpRequestInitializer`](https://beam.apache.org/releases/javadoc/2.13.0/org/apache/beam/sdk/extensions/gcp/util/RetryHttpRequestInitializer.html)
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Issue Time Tracking
-------------------
Worklog Id: (was: 410578)
Time Spent: 6h 20m (was: 6h 10m)
> 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: 6h 20m
> 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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