Merge pull request #572 from hapifhir/do-20230731-bump-to-hapi-6-8-0

Bump to HAPI 6.8.0

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-            <version>6.6.0</version>
+        <version>6.8.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -247,6 +247,12 @@
         </dependency>
 
         <!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
+            <version>${project.version}</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-servlets</artifactId>

src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java

@@ -9,7 +9,7 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
-import ca.uhn.fhir.cr.config.CrProviderLoader;
+
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
@@ -18,7 +18,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
-import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
+import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
 import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
 import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
@@ -111,8 +111,7 @@ public class StarterJpaConfig {
 	@Autowired
 	private ConfigurableEnvironment configurableEnvironment;
 
-	@Autowired(required=false)
+
-	private CrProviderLoader crProviderLoader;
 
 	/**
 	 * Customize the default/max page sizes for search results. You can set these however

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import ca.uhn.fhir.cr.config.CrDstu3Config;
+import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
 import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import ca.uhn.fhir.cr.config.CrR4Config;
+import ca.uhn.fhir.cr.config.r4.CrR4Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Import;

src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java

@@ -3,16 +3,23 @@ package ca.uhn.fhir.jpa.starter;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
 import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
+import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import java.io.IOException;
-import java.time.Duration;
+
-import java.time.temporal.ChronoUnit;
 import java.util.Date;
 import java.util.GregorianCalendar;
+import java.util.List;
 import javax.annotation.PreDestroy;
+
+import org.elasticsearch.client.RequestOptions;
+import org.elasticsearch.client.RestHighLevelClient;
+import org.elasticsearch.client.indices.PutIndexTemplateRequest;
+import org.elasticsearch.common.settings.Settings;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DateTimeType;
@@ -34,8 +41,11 @@ import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 import org.testcontainers.elasticsearch.ElasticsearchContainer;
+import org.testcontainers.junit.jupiter.Container;
+import org.testcontainers.junit.jupiter.Testcontainers;
 
 @ExtendWith(SpringExtension.class)
+@Testcontainers
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties =
   {
     "spring.datasource.url=jdbc:h2:mem:dbr4",
@@ -43,6 +53,7 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
     "hapi.fhir.lastn_enabled=true",
 	 "hapi.fhir.store_resource_in_lucene_index_enabled=true",
 	 "hapi.fhir.advanced_lucene_indexing=true",
+
     "elasticsearch.enabled=true",
     // Because the port is set randomly, we will set the rest_url using the Initializer.
     // "elasticsearch.rest_url='http://localhost:9200'",
@@ -61,19 +72,31 @@ public class ElasticsearchLastNR4IT {
 	private IGenericClient ourClient;
   private FhirContext ourCtx;
 
-  private static final String ELASTIC_VERSION = "7.16.3";
+	@Container
-  private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
+	public static ElasticsearchContainer embeddedElastic = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
-  private static ElasticsearchContainer embeddedElastic;
 
   @Autowired
   private ElasticsearchSvcImpl myElasticsearchSvc;
 
   @BeforeAll
-  public static void beforeClass() {
+  public static void beforeClass() throws IOException {
-	  embeddedElastic = new ElasticsearchContainer(ELASTIC_IMAGE).withStartupTimeout(Duration.of(300, ChronoUnit.SECONDS));
+	  //Given
-	  embeddedElastic.start();
+	  RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
+		  "http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
+
+	  /* As of 2023-08-10, HAPI FHIR sets SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS to 50000
+	  		which is in excess of elastic's default max_result_window. If MAX_SUBSCRIPTION_RESULTS is changed
+	  		to a value <= 10000, the following will no longer be necessary. - dotasek
+	  */
+	  PutIndexTemplateRequest putIndexTemplateRequest = new PutIndexTemplateRequest("hapi_fhir_template");
+	  putIndexTemplateRequest.patterns(List.of("*"));
+	  Settings settings = Settings.builder().put("index.max_result_window", 50000).build();
+	  putIndexTemplateRequest.settings(settings);
+	  elasticsearchHighLevelRestClient.indices().putTemplate(putIndexTemplateRequest, RequestOptions.DEFAULT);
+
+
   }
-  
+
   @PreDestroy
   public void stop() {
     embeddedElastic.stop();
@@ -115,7 +138,7 @@ public class ElasticsearchLastNR4IT {
   }
 
   @BeforeEach
-  void beforeEach() {
+  void beforeEach() throws IOException {
 
     ourCtx = FhirContext.forR4();
     ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
@@ -123,6 +146,7 @@ public class ElasticsearchLastNR4IT {
     String ourServerBase = "http://localhost:" + port + "/fhir/";
     ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
     ourClient.registerInterceptor(new LoggingInterceptor(true));
+
   }
 
   static class Initializer

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -30,7 +31,7 @@ import static org.awaitility.Awaitility.await;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class, NicknameServiceConfig.class}, properties = {
 		"spring.datasource.url=jdbc:h2:mem:dbr4",
 		"hapi.fhir.enable_repository_validating_interceptor=true",
 		"hapi.fhir.fhir_version=r4",