jaketf commented on a change in pull request #11151: [BEAM-9468] Hl7v2 io URL: https://github.com/apache/beam/pull/11151#discussion_r398215206
########## 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(); + } + + @Override + public HttpBody fhirSearch(String fhirStore, SearchResourcesRequest query) throws IOException { + return client + .projects() + .locations() + .datasets() + .fhirStores() + .fhir() + .search(fhirStore, query) + .execute(); + } + + @Override + public Message createHL7v2Message(String hl7v2Store, Message msg) throws IOException { + CreateMessageRequest createMessageRequest = new CreateMessageRequest(); + createMessageRequest.setMessage(msg); + return client + .projects() + .locations() + .datasets() + .hl7V2Stores() + .messages() + .create(hl7v2Store, createMessageRequest) + .execute(); + } + + @Override + public HttpBody createFhirResource(String fhirStore, String type, HttpBody body) + throws IOException { + return client + .projects() + .locations() + .datasets() + .fhirStores() + .fhir() + .create(fhirStore, type, body) + .execute(); + } + + @Override + public HttpBody executeFhirBundle(String fhirStore, HttpBody bundle) throws IOException { + return client + .projects() + .locations() + .datasets() + .fhirStores() + .fhir() + .executeBundle(fhirStore, bundle) + .execute(); + } + + @Override + public HttpBody listFHIRResourceForPatient(String fhirStore, String patient) throws IOException { + return client + .projects() + .locations() + .datasets() + .fhirStores() + .fhir() + .patientEverything(patient) + .execute(); + } + + @Override + public HttpBody readFHIRResource(String fhirStore, String resource) throws IOException { + return client.projects().locations().datasets().fhirStores().fhir().read(resource).execute(); + } + + private static class AuthenticatedRetryInitializer extends RetryHttpRequestInitializer { + GoogleCredentials credentials; + + public AuthenticatedRetryInitializer(GoogleCredentials credentials) { + super(); + this.credentials = credentials; + } + + @Override + public void initialize(HttpRequest request) throws IOException { + super.initialize(request); + if (!credentials.hasRequestMetadata()) { + return; + } + HttpHeaders requestHeaders = request.getHeaders(); + requestHeaders.setUserAgent("apache-beam-hl7v2-io"); + URI uri = null; + if (request.getUrl() != null) { + uri = request.getUrl().toURI(); + } + Map<String, List<String>> credentialHeaders = credentials.getRequestMetadata(uri); + if (credentialHeaders == null) { + return; + } + for (Map.Entry<String, List<String>> entry : credentialHeaders.entrySet()) { + String headerName = entry.getKey(); + List<String> requestValues = new ArrayList<>(entry.getValue()); + requestHeaders.put(headerName, requestValues); + } + } + } + + private void initClient() throws IOException { + // Create a HttpRequestInitializer, which will provide a baseline configuration to all requests. + // HttpRequestInitializer requestInitializer = new RetryHttpRequestInitializer(); + // GoogleCredentials credentials = GoogleCredentials.getApplicationDefault(); + HttpRequestInitializer requestInitializer = + new AuthenticatedRetryInitializer( + GoogleCredentials.getApplicationDefault() + .createScoped(CloudHealthcareScopes.CLOUD_PLATFORM)); + + client = + new CloudHealthcare.Builder(new NetHttpTransport(), new GsonFactory(), requestInitializer) + .setApplicationName("apache-beam-hl7v2-io") + .build(); + } + + public static class HL7v2MessageIDPages implements Iterable<List<String>> { + + private final String hl7v2Store; + private final String filter; + private transient HealthcareApiClient client; + + /** + * Instantiates a new HL7v2 message id pages. + * + * @param client the client + * @param hl7v2Store the HL7v2 store + */ + HL7v2MessageIDPages(HealthcareApiClient client, String hl7v2Store) { + this.client = client; + this.hl7v2Store = hl7v2Store; + this.filter = null; + } + + /** + * Instantiates a new HL7v2 message id pages. + * + * @param client the client + * @param hl7v2Store the HL7v2 store + * @param filter the filter + */ + HL7v2MessageIDPages(HealthcareApiClient client, String hl7v2Store, @Nullable String filter) { + this.client = client; + this.hl7v2Store = hl7v2Store; + this.filter = filter; + } + + /** + * Make list request list messages response. + * + * @param client the client + * @param hl7v2Store the hl 7 v 2 store + * @param filter the filter + * @param pageToken the page token + * @return the list messages response + * @throws IOException the io exception + */ + public static ListMessagesResponse makeListRequest( + HealthcareApiClient client, + String hl7v2Store, + @Nullable String filter, + @Nullable String pageToken) + throws IOException { + return client.makeHL7v2ListRequest(hl7v2Store, filter, pageToken); + } + + @Override + public Iterator<List<String>> iterator() { + return new HL7v2MessageIDPagesIterator(this.client, this.hl7v2Store, this.filter); + } + + /** The type Hl7v2 message id pages iterator. */ + public static class HL7v2MessageIDPagesIterator implements Iterator<List<String>> { + + private final String hl7v2Store; + private final String filter; + private HealthcareApiClient client; + private String pageToken; + private boolean isFirstRequest; + + /** + * Instantiates a new Hl 7 v 2 message id pages iterator. + * + * @param client the client + * @param hl7v2Store the hl 7 v 2 store + * @param filter the filter + */ + HL7v2MessageIDPagesIterator( + HealthcareApiClient client, String hl7v2Store, @Nullable String filter) { + this.client = client; + this.hl7v2Store = hl7v2Store; + this.filter = filter; + this.pageToken = null; + this.isFirstRequest = true; + } + + @Override + public boolean hasNext() throws NoSuchElementException { + if (isFirstRequest) { + try { + ListMessagesResponse response = makeListRequest(client, hl7v2Store, filter, pageToken); + List<String> msgs = response.getMessages(); + if (msgs == null) { + if (response.get("hl7V2Messages") != null) { + return ((ArrayList<ArrayMap<String, String>>) response.get("hl7V2Messages")).size() + > 0; + } + return false; + } else { + return !msgs.isEmpty(); + } + } catch (IOException e) { + throw new NoSuchElementException( + String.format( + "Failed to list first page of HL7v2 messages from %s: %s", + hl7v2Store, e.getMessage())); + } + } + return this.pageToken != null; + } + + @Override + public List<String> next() throws NoSuchElementException { + try { + ListMessagesResponse response = makeListRequest(client, hl7v2Store, filter, pageToken); + this.isFirstRequest = false; + this.pageToken = response.getNextPageToken(); + List<String> msgs = response.getMessages(); + if (msgs == null && response.get("hl7V2Messages") != null) { Review comment: Note, this `ArrayMap<String, String>` is basically the `Message` model. If you use the alpha API to query an beta HL7v2 store, there will be a single key `name` with the message ID value. If you use the alpha API to query an alpha HL7v2 store, there will be all of the keys in the `Message` model. ---------------------------------------------------------------- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. For queries about this service, please contact Infrastructure at: us...@infra.apache.org With regards, Apache Git Services
