Update to HAPI FHIR 7.0.0

.github/workflows/smoke-tests.yml

@@ -33,7 +33,7 @@ jobs:
       run: docker pull jetbrains/intellij-http-client
     - name: Start server with jetty
       run: |
-        mvn -Pjetty jetty:run & export JPA_PROCESS=$!
+        mvn -P jetty spring-boot:run & export JPA_PROCESS=$!
         sleep 80
     - name: Execute smoke tests
       run: docker run --rm -v $PWD:/workdir --add-host host.docker.internal:host-gateway jetbrains/intellij-http-client -D src/test/smoketest/plain_server.http --env-file src/test/smoketest/http-client.env.json --env default

pom.xml

@@ -14,16 +14,14 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>6.10.0</version>
+        <version>7.0.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
     <packaging>war</packaging>
 
     <properties>
         <java.version>11</java.version>
-        <logback-classic.version>1.2.11</logback-classic.version>
-        <slf4j-api.version>1.7.25</slf4j-api.version>
     </properties>
 
     <prerequisites>
@@ -53,16 +51,7 @@
     </dependencyManagement>
 
     <dependencies>
-        <dependency>
-            <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-jetty-api</artifactId>
-            <version>${jetty_version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-jetty-client</artifactId>
-            <version>${jetty_version}</version>
-        </dependency>
+
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
@@ -180,11 +169,15 @@
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
         </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-core</artifactId>
+        </dependency>
 
         <!-- Needed for JEE/Servlet support -->
         <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>javax.servlet-api</artifactId>
+            <groupId>jakarta.servlet</groupId>
+            <artifactId>jakarta.servlet-api</artifactId>
             <scope>provided</scope>
         </dependency>
 
@@ -201,6 +194,14 @@
             <artifactId>spring-web</artifactId>
         </dependency>
 
+        <!-- commons-logging is provided by jcl-over-slf4j, and the jar often shows up because of transitive dependencies; this dependency should avoid it -->
+        <dependency>
+            <groupId>commons-logging</groupId>
+            <artifactId>commons-logging</artifactId>
+            <version>1.2</version>
+            <scope>provided</scope>
+        </dependency>
+
         <!-- You may not need this if you are deploying to an application server which provides database connection pools itself. -->
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -251,6 +252,12 @@
         </dependency>
 
         <!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
+        <dependency>
+            <groupId>co.elastic.clients</groupId>
+            <artifactId>elasticsearch-java</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
@@ -263,36 +270,7 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-servlets</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-servlet</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty.websocket</groupId>
-            <artifactId>websocket-jetty-server</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-server</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-util</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.eclipse.jetty</groupId>
-            <artifactId>jetty-webapp</artifactId>
-            <scope>test</scope>
-        </dependency>
+
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
@@ -314,8 +292,8 @@
         For some reason JavaDoc crashed during site generation unless we have this dependency
         -->
         <dependency>
-            <groupId>javax.interceptor</groupId>
-            <artifactId>javax.interceptor-api</artifactId>
+            <groupId>jakarta.interceptor</groupId>
+            <artifactId>jakarta.interceptor-api</artifactId>
             <scope>provided</scope>
         </dependency>
 
@@ -324,6 +302,24 @@
             <artifactId>hapi-fhir-test-utilities</artifactId>
             <version>${project.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.eclipse.jetty.ee10</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty.ee10.websocket</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty.websocket</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <dependency>
@@ -369,40 +365,20 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-api</artifactId>
-            <version>5.7.2</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-engine</artifactId>
-            <version>5.7.2</version>
             <scope>test</scope>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-test</artifactId>
-            <version>${spring_boot_version}</version>
             <scope>test</scope>
         </dependency>
 
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-            <version>${slf4j-api.version}</version>
-        </dependency>
-
-        <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-classic</artifactId>
-            <version>${logback-classic.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-core</artifactId>
-            <version>${logback-classic.version}</version>
-        </dependency>
-
     </dependencies>
 
     <build>
@@ -429,6 +405,14 @@
             <plugin>
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
+                <configuration>
+                    <!--
+                    java -jar ROOT.war doesn't work; there is a bug in spring-boot-3.2.0 due to hibernate search,
+                    probably solved in 3.2.1 https://github.com/spring-projects/spring-boot/issues/38585
+                    (at the moment only tomcat works)
+                    -->
+                    <loaderImplementation>CLASSIC</loaderImplementation>
+                </configuration>
                 <executions>
                     <execution>
                         <goals>
@@ -629,6 +613,11 @@
                         </exclusion>
                     </exclusions>
                 </dependency>
+                <dependency>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-jetty</artifactId>
+                    <version>${spring_boot_version}</version>
+                </dependency>
             </dependencies>
         </profile>
         <profile>

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -4,7 +4,6 @@
 import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
 import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
-import ca.uhn.fhir.jpa.starter.common.FhirTesterConfig;
 import ca.uhn.fhir.jpa.starter.cr.StarterCrDstu3Config;
 import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
 import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
@@ -19,15 +18,12 @@
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
 import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
-import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.web.servlet.ServletComponentScan;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Import;
-import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
-import org.springframework.web.servlet.DispatcherServlet;
 
 @ServletComponentScan(basePackageClasses = {RestfulServer.class})
 @SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java

@@ -19,10 +19,10 @@
 
 import java.io.IOException;
 import java.util.stream.Collectors;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
 

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ErrorHandling.java

@@ -7,7 +7,7 @@
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.util.Arrays;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 
 public class ErrorHandling {
 

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

@@ -62,6 +62,7 @@
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Strings;
+import jakarta.persistence.EntityManagerFactory;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.springframework.beans.factory.NoSuchBeanDefinitionException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -76,7 +77,6 @@
 import org.springframework.web.cors.CorsConfiguration;
 
 import java.util.*;
-import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
@@ -133,11 +133,11 @@ public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao)
 	@Primary
 	@Bean
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory(
-			DataSource myDataSource,
-			ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
-			FhirContext theFhirContext) {
+		DataSource myDataSource,
+		ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
+		FhirContext theFhirContext, JpaStorageSettings theStorageSettings) {
 		LocalContainerEntityManagerFactoryBean retVal =
-				HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
+				HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext, theStorageSettings);
 		retVal.setPersistenceUnitName("HAPI_PU");
 
 		try {

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

@@ -5,7 +5,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties = {
 		"hapi.fhir.custom-bean-packages=some.custom.pkg1,some.custom.pkg2",
 		"spring.datasource.url=jdbc:h2:mem:dbr4",
 		"hapi.fhir.enable_repository_validating_interceptor=true",

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

@@ -13,7 +13,7 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties = {
 		"hapi.fhir.custom-bean-packages=some.custom.pkg1",
 		"hapi.fhir.custom-interceptor-classes=some.custom.pkg1.CustomInterceptorBean,some.custom.pkg1.CustomInterceptorPojo",
 		"spring.datasource.url=jdbc:h2:mem:dbr4",

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

@@ -14,12 +14,11 @@
 import java.util.Date;
 import java.util.GregorianCalendar;
 import java.util.List;
-import javax.annotation.PreDestroy;
 
+import co.elastic.clients.elasticsearch.ElasticsearchClient;
+import co.elastic.clients.json.JsonData;
+import jakarta.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;
@@ -30,13 +29,11 @@
 import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.util.TestPropertyValues;
-import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.boot.test.web.server.LocalServerPort;
 import org.springframework.context.ApplicationContextInitializer;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.test.context.ContextConfiguration;
@@ -47,7 +44,7 @@
 
 @ExtendWith(SpringExtension.class)
 @Testcontainers
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties =
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties =
   {
     "spring.datasource.url=jdbc:h2:mem:dbr4",
     "hapi.fhir.fhir_version=r4",
@@ -83,19 +80,20 @@ public class ElasticsearchLastNR4IT {
   @BeforeAll
   public static void beforeClass() throws IOException {
 	  //Given
-	  RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
+	  ElasticsearchClient 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);
 
+	  elasticsearchHighLevelRestClient.indices().putTemplate(t->{
+		  t.name("hapi_fhir_template");
+		  t.indexPatterns("*");
+		  t.settings("index.max_result_window", JsonData.of(50000));
+		  return t;
+	  });
 
   }