Merge pull request #610 from hapifhir/cr-6.9.6-snapshot

6.10.0 release merge with Clinical Reasoning config

README.md

@@ -336,12 +336,12 @@ NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause
 It is recommended to deploy a case-sensitive database prior to running HAPI FHIR when using MS SQL Server to avoid these and potentially other issues.
 
 ## Adding custom interceptors
-Custom interceptors can be registered with the server by including the property `hapi.fhir.custom-interceptor-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server. 
-Interceptors will be discovered in one of two ways: 
+Custom interceptors can be registered with the server by including the property `hapi.fhir.custom-interceptor-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server.
+Interceptors will be discovered in one of two ways:
 
 1) discovered from the Spring application context as existing Beans (can be used in conjunction with `hapi.fhir.custom-bean-packages`) or registered with Spring via other methods
 
-or 
+or
 
 2) classes will be instantiated via reflection if no matching Bean is found
 

pom.xml

@@ -131,6 +131,16 @@
             <artifactId>hapi-fhir-jpaserver-mdm</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-context</artifactId>
+        </dependency>
+        <!-- This dependency includes the CDS Hooks Server -->
+        <dependency>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>hapi-fhir-server-cds-hooks</artifactId>
+          <version>${project.version}</version>
+        </dependency>
         <!-- This dependency includes the OpenAPI Server -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>

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

@@ -865,4 +865,4 @@ public boolean getEnable_index_of_type() {
   public void setEnable_index_of_type(boolean enable_index_of_type) {
     this.enable_index_of_type = enable_index_of_type;
   }
-}
+}

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

@@ -3,7 +3,10 @@
 import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 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;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -29,6 +32,9 @@
 @ServletComponentScan(basePackageClasses = {RestfulServer.class})
 @SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})
 @Import({
+	StarterCrR4Config.class,
+	StarterCrDstu3Config.class,
+	StarterCdsHooksConfig.class,
 	SubscriptionSubmitterConfig.class,
 	SubscriptionProcessorConfig.class,
 	SubscriptionChannelConfig.class,
@@ -39,51 +45,54 @@
 })
 public class Application extends SpringBootServletInitializer {
 
-  public static void main(String[] args) {
+	public static void main(String[] args) {
 
-    SpringApplication.run(Application.class, args);
+		SpringApplication.run(Application.class, args);
 
-    //Server is now accessible at eg. http://localhost:8080/fhir/metadata
-    //UI is now accessible at http://localhost:8080/
-  }
+		// Server is now accessible at eg. http://localhost:8080/fhir/metadata
+		// UI is now accessible at http://localhost:8080/
+	}
 
-  @Override
-  protected SpringApplicationBuilder configure(
-    SpringApplicationBuilder builder) {
-    return builder.sources(Application.class);
-  }
+	@Override
+	protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
+		return builder.sources(Application.class);
+	}
 
-  @Autowired
-  AutowireCapableBeanFactory beanFactory;
+	@Autowired
+	AutowireCapableBeanFactory beanFactory;
 
-  @Bean
-  @Conditional(OnEitherVersion.class)
-  public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
-    ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
-    beanFactory.autowireBean(restfulServer);
-    servletRegistrationBean.setServlet(restfulServer);
-    servletRegistrationBean.addUrlMappings("/fhir/*");
-    servletRegistrationBean.setLoadOnStartup(1);
+	@Bean
+	@Conditional(OnEitherVersion.class)
+	public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
+		ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
+		beanFactory.autowireBean(restfulServer);
+		servletRegistrationBean.setServlet(restfulServer);
+		servletRegistrationBean.addUrlMappings("/fhir/*");
+		servletRegistrationBean.setLoadOnStartup(1);
 
-    return servletRegistrationBean;
-  }
+		return servletRegistrationBean;
+	}
 
-  @Bean
-  public ServletRegistrationBean overlayRegistrationBean() {
+	@Bean
+	public ServletRegistrationBean overlayRegistrationBean() {
 
-    AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
-    annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
+		AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext =
+				new AnnotationConfigWebApplicationContext();
+		annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
 
-    DispatcherServlet dispatcherServlet = new DispatcherServlet(
-      annotationConfigWebApplicationContext);
-    dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
-    dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
+		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;
+		ServletRegistrationBean registrationBean = new ServletRegistrationBean();
+		registrationBean.setServlet(dispatcherServlet);
+		registrationBean.addUrlMappings("/*");
+		registrationBean.setLoadOnStartup(1);
+		return registrationBean;
+	}
 
-  }
+	//	@Bean
+	//	IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
+	//		return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
+	//	}
 }

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

@@ -19,33 +19,32 @@ public class ExtraStaticFilesConfigurer implements WebMvcConfigurer {
 	public ExtraStaticFilesConfigurer(AppProperties appProperties) {
 
 		rootContextPath = appProperties.getStaticLocationPrefix();
-		if(rootContextPath.endsWith("/"))
+		if (rootContextPath.endsWith("/"))
 			rootContextPath = rootContextPath.substring(0, rootContextPath.lastIndexOf('/'));
 
 		staticLocation = appProperties.getStaticLocation();
-		if(staticLocation.endsWith("/"))
-			staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
-
+		if (staticLocation.endsWith("/")) staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
 	}
 
-
 	@Override
-    public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
-        theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
-    }
-
-    @Override
-    public void addViewControllers(ViewControllerRegistry registry) {
-        String path = URI.create(staticLocation).getPath();
-        String lastSegment = path.substring(path.lastIndexOf('/') + 1);
+	public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
+		theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
+	}
 
-        registry.addViewController(rootContextPath).setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
+	@Override
+	public void addViewControllers(ViewControllerRegistry registry) {
+		String path = URI.create(staticLocation).getPath();
+		String lastSegment = path.substring(path.lastIndexOf('/') + 1);
 
-        registry.addViewController(rootContextPath + "/*").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
+		registry.addViewController(rootContextPath)
+				.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
 
-        registry.addViewController(rootContextPath + "/" + lastSegment + "/").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
+		registry.addViewController(rootContextPath + "/*")
+				.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
 
-        registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
-    }
+		registry.addViewController(rootContextPath + "/" + lastSegment + "/")
+				.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
 
-}
+		registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnCorsPresent.java

@@ -10,9 +10,11 @@ public class OnCorsPresent implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
 
-		AppProperties config = Binder.get(conditionContext.getEnvironment()).bind("hapi.fhir", AppProperties.class).orElse(null);
+		AppProperties config = Binder.get(conditionContext.getEnvironment())
+				.bind("hapi.fhir", AppProperties.class)
+				.orElse(null);
 		if (config == null) return false;
 		if (config.getCors() == null) return false;
 		return true;
 	}
-}
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java

@@ -6,14 +6,13 @@
 import org.springframework.core.type.AnnotatedTypeMetadata;
 
 public class OnDSTU2Condition implements Condition {
-  @Override
-  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
-      getEnvironment()
-      .getProperty("hapi.fhir.fhir_version")
-      .toUpperCase());
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
+				.getProperty("hapi.fhir.fhir_version")
+				.toUpperCase());
 
-    return version == FhirVersionEnum.DSTU2;
-
-  }
+		return version == FhirVersionEnum.DSTU2;
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java

@@ -6,14 +6,13 @@
 import org.springframework.core.type.AnnotatedTypeMetadata;
 
 public class OnDSTU3Condition implements Condition {
-  @Override
-  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
-      getEnvironment()
-      .getProperty("hapi.fhir.fhir_version")
-      .toUpperCase());
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
+				.getProperty("hapi.fhir.fhir_version")
+				.toUpperCase());
 
-    return version == FhirVersionEnum.DSTU3;
-
-  }
+		return version == FhirVersionEnum.DSTU3;
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java

@@ -6,34 +6,28 @@
 
 public class OnEitherVersion extends AnyNestedCondition {
 
-  OnEitherVersion() {
-    super(ConfigurationPhase.REGISTER_BEAN);
-  }
+	OnEitherVersion() {
+		super(ConfigurationPhase.REGISTER_BEAN);
+	}
 
-  @Override
-  protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) {
-    ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes);
-    return result;
-  }
+	@Override
+	protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) {
+		ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes);
+		return result;
+	}
 
-  @Conditional(OnDSTU2Condition.class)
-  static class OnDSTU2 {
-  }
+	@Conditional(OnDSTU2Condition.class)
+	static class OnDSTU2 {}
 
-  @Conditional(OnDSTU3Condition.class)
-  static class OnDSTU3 {
-  }
+	@Conditional(OnDSTU3Condition.class)
+	static class OnDSTU3 {}
 
-  @Conditional(OnR4Condition.class)
-  static class OnR4 {
-  }
+	@Conditional(OnR4Condition.class)
+	static class OnR4 {}
 
 	@Conditional(OnR4BCondition.class)
-	static class OnR4B {
-	}
-
-  @Conditional(OnR5Condition.class)
-  static class OnR5 {
-  }
+	static class OnR4B {}
 
-}
+	@Conditional(OnR5Condition.class)
+	static class OnR5 {}
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnImplementationGuidesPresent.java

@@ -10,9 +10,11 @@ public class OnImplementationGuidesPresent implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
 
-		AppProperties config = Binder.get(conditionContext.getEnvironment()).bind("hapi.fhir", AppProperties.class).orElse(null);
+		AppProperties config = Binder.get(conditionContext.getEnvironment())
+				.bind("hapi.fhir", AppProperties.class)
+				.orElse(null);
 		if (config == null) return false;
 		if (config.getImplementationGuides() == null) return false;
 		return !config.getImplementationGuides().isEmpty();
 	}
-}
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4BCondition.java

@@ -8,10 +8,10 @@
 public class OnR4BCondition implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-		String version = conditionContext.
-			getEnvironment()
-			.getProperty("hapi.fhir.fhir_version")
-			.toUpperCase();
+		String version = conditionContext
+				.getEnvironment()
+				.getProperty("hapi.fhir.fhir_version")
+				.toUpperCase();
 
 		return FhirVersionEnum.R4B.name().equals(version);
 	}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java

@@ -6,14 +6,13 @@
 import org.springframework.core.type.AnnotatedTypeMetadata;
 
 public class OnR4Condition implements Condition {
-  @Override
-  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
-      getEnvironment()
-      .getProperty("hapi.fhir.fhir_version")
-      .toUpperCase());
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
+				.getProperty("hapi.fhir.fhir_version")
+				.toUpperCase());
 
-    return version == FhirVersionEnum.R4;
-
-  }
+		return version == FhirVersionEnum.R4;
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java

@@ -6,14 +6,13 @@
 import org.springframework.core.type.AnnotatedTypeMetadata;
 
 public class OnR5Condition implements Condition {
-  @Override
-  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
-      getEnvironment()
-      .getProperty("hapi.fhir.fhir_version")
-      .toUpperCase());
+	@Override
+	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
+				.getProperty("hapi.fhir.fhir_version")
+				.toUpperCase());
 
-    return version == FhirVersionEnum.R5;
-
-  }
+		return version == FhirVersionEnum.R5;
+	}
 }