Merge branch 'master' into ja_20231203_hapi_7_0

.github/workflows/build-images.yaml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - name: Container meta for default (distroless) image
         id: docker_meta
-        uses: docker/metadata-action@v3
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGES }}
           tags: |
@@ -30,7 +30,7 @@ jobs:
 
       - name: Container meta for tomcat image
         id: docker_tomcat_meta
-        uses: docker/metadata-action@v3
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGES }}
           tags: |
@@ -39,20 +39,20 @@ jobs:
             suffix=-tomcat,onlatest=true
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         if: github.event_name != 'pull_request'
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}
@@ -61,7 +61,7 @@ jobs:
 
       - name: Build and push default (distroless) image
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           cache-from: type=local,src=/tmp/.buildx-cache
           cache-to: type=local,dest=/tmp/.buildx-cache
@@ -73,7 +73,7 @@ jobs:
 
       - name: Build and push tomcat image
         id: docker_build_tomcat
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           cache-from: type=local,src=/tmp/.buildx-cache
           cache-to: type=local,dest=/tmp/.buildx-cache

README.md

@@ -193,14 +193,14 @@ The easiest way to run this server entirely depends on your environment requirem
 
 ### Using jetty
 ```bash
-mvn jetty:run
+mvn -Pjetty jetty:run
 ```
 
 
 If you need to run this server on a different port (using Maven), you can change the port in the run command as follows:
 
 ```bash
-mvn -Djetty.port=8888 jetty:run
+mvn -Pjetty -Djetty.port=8888 jetty:run
 ```
 
 Server will then be accessible at http://localhost:8888/ and eg. http://localhost:8888/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.

pom.xml

@@ -624,11 +624,20 @@
         <!-- Use the boot profile for development and debugging options when using your IDE -->
         <profile>
             <id>boot</id>
+            <activation>
+                <activeByDefault>true</activeByDefault>
+            </activation>
             <dependencies>
                 <dependency>
                     <groupId>org.springframework.boot</groupId>
                     <artifactId>spring-boot-starter-web</artifactId>
                     <version>${spring_boot_version}</version>
+                    <exclusions>
+                        <exclusion>
+                            <groupId>org.springframework.boot</groupId>
+                            <artifactId>spring-boot-starter-tomcat</artifactId>
+                        </exclusion>
+                    </exclusions>
                 </dependency>
             </dependencies>
         </profile>

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

@@ -27,6 +27,7 @@ public class AppProperties {
   private Boolean ips_enabled = false;
   private Boolean openapi_enabled = false;
   private Boolean mdm_enabled = false;
+  private String mdm_rules_json_location = "mdm-rules.json";
   private boolean advanced_lucene_indexing = false;
   private boolean enable_index_of_type = false;
   private Boolean allow_cascading_deletes = false;
@@ -191,7 +192,15 @@ public class AppProperties {
     this.mdm_enabled = mdm_enabled;
   }
 
-  public Cors getCors() {
+  public String getMdm_rules_json_location() {
+	return mdm_rules_json_location;
+}
+
+public void setMdm_rules_json_location(String mdm_rules_json_location) {
+	this.mdm_rules_json_location = mdm_rules_json_location;
+}
+
+public Cors getCors() {
     return cors;
   }
 

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

@@ -55,10 +55,6 @@ public class Application extends SpringBootServletInitializer {
 		// UI is now accessible at http://localhost:8080/
 	}
 
-	@Override
-	protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
-		return builder.sources(Application.class);
-	}
 
 	@Autowired
 	AutowireCapableBeanFactory beanFactory;
@@ -75,31 +71,9 @@ public class Application extends SpringBootServletInitializer {
 		return servletRegistrationBean;
 	}
 
-	@Bean
-	public ServletRegistrationBean overlayRegistrationBean() {
-
-		AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext =
-				new AnnotationConfigWebApplicationContext();
-		annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
-
-		DispatcherServlet dispatcherServlet = new DispatcherServlet(annotationConfigWebApplicationContext);
-		dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
-		dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
-
-		ServletRegistrationBean registrationBean = new ServletRegistrationBean();
-		registrationBean.setServlet(dispatcherServlet);
-		registrationBean.addUrlMappings("/*");
-		registrationBean.setLoadOnStartup(1);
-		return registrationBean;
-	}
-
 	@Bean
 	public ServletWebServerFactory servletWebServerFactory() {
 		return new JettyServletWebServerFactory();
 	}
 
-	//	@Bean
-	//	IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
-	//		return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
-	//	}
 }

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

@@ -180,6 +180,13 @@ public class FhirServerConfigCommon {
 		jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
 		jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
 
+		if (appProperties.getMdm_enabled()) {
+			// MDM requires the subscription of type message
+			ourLog.info("Enabling message subscriptions");
+			jpaStorageSettings.addSupportedSubscriptionType(
+					org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.MESSAGE);
+		}
+
 		storageSettings(appProperties, jpaStorageSettings);
 		return jpaStorageSettings;
 	}

src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.starter.mdm;
 
 import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
 import ca.uhn.fhir.jpa.mdm.config.MdmSubmitterConfig;
+import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
 import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
@@ -20,14 +21,14 @@ import java.nio.charset.StandardCharsets;
 
 @Configuration
 @Conditional(MdmConfigCondition.class)
-@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})
+@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class, NicknameServiceConfig.class})
 public class MdmConfig {
 
 	@Bean
 	IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties)
 			throws IOException {
 		DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
-		Resource resource = resourceLoader.getResource("mdm-rules.json");
+		Resource resource = resourceLoader.getResource(appProperties.getMdm_rules_json_location());
 		String json = IOUtils.toString(resource.getInputStream(), StandardCharsets.UTF_8);
 		return new MdmSettings(theMdmRuleValidator)
 				.setEnabled(appProperties.getMdm_enabled())

src/main/resources/application.yaml

@@ -137,6 +137,7 @@ hapi:
     #    graphql_enabled: true
     narrative_enabled: false
     mdm_enabled: false
+    mdm_rules_json_location: "mdm-rules.json"
     #    local_base_urls:
     #      - https://hapi.fhir.org/baseR4
     #    partitioning:

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

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.starter;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.nickname.INicknameSvc;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties = {
+		"hapi.fhir.fhir_version=r4",
+		"hapi.fhir.mdm_enabled=true"
+})
+class MdmTest {
+	@Autowired
+	INicknameSvc nicknameService;
+	
+	@Autowired
+	JpaStorageSettings jpaStorageSettings;
+
+	@Test
+	void testApplicationStartedSuccessfully() {
+		assertThat(nicknameService).isNotNull();
+		assertThat(jpaStorageSettings.getSupportedSubscriptionTypes()).contains(SubscriptionChannelType.MESSAGE);
+	}
+}