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

6.10.0 release merge with Clinical Reasoning config

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/Application.java

@@ -3,7 +3,10 @@ package ca.uhn.fhir.jpa.starter;
 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 @@ import org.springframework.web.servlet.DispatcherServlet;
 @ServletComponentScan(basePackageClasses = {RestfulServer.class})
 @SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})
 @Import({
+	StarterCrR4Config.class,
+	StarterCrDstu3Config.class,
+	StarterCdsHooksConfig.class,
 	SubscriptionSubmitterConfig.class,
 	SubscriptionProcessorConfig.class,
 	SubscriptionChannelConfig.class,
@@ -43,13 +49,12 @@ public class Application extends SpringBootServletInitializer {
 
 		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) {
+	protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
 		return builder.sources(Application.class);
 	}
 
@@ -71,11 +76,11 @@ public class Application extends SpringBootServletInitializer {
 	@Bean
 	public ServletRegistrationBean overlayRegistrationBean() {
 
-    AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
+		AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext =
+				new AnnotationConfigWebApplicationContext();
 		annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
 
-    DispatcherServlet dispatcherServlet = new DispatcherServlet(
-      annotationConfigWebApplicationContext);
+		DispatcherServlet dispatcherServlet = new DispatcherServlet(annotationConfigWebApplicationContext);
 		dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
 		dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
 
@@ -84,6 +89,10 @@ public class Application extends SpringBootServletInitializer {
 		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

@@ -19,16 +19,13 @@ 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);
@@ -39,13 +36,15 @@ public class ExtraStaticFilesConfigurer implements WebMvcConfigurer {
 		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 + "/*").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 + "/" + lastSegment + "/")
+				.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
 
 		registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
 	}
-
 }

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

@@ -10,7 +10,9 @@ 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

@@ -8,12 +8,11 @@ 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()
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
 				.getProperty("hapi.fhir.fhir_version")
 				.toUpperCase());
 
 		return version == FhirVersionEnum.DSTU2;
-
 	}
 }

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

@@ -8,12 +8,11 @@ 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()
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
 				.getProperty("hapi.fhir.fhir_version")
 				.toUpperCase());
 
 		return version == FhirVersionEnum.DSTU3;
-
 	}
 }

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

@@ -17,23 +17,17 @@ public class OnEitherVersion extends AnyNestedCondition {
 	}
 
 	@Conditional(OnDSTU2Condition.class)
-  static class OnDSTU2 {
-  }
+	static class OnDSTU2 {}
 
 	@Conditional(OnDSTU3Condition.class)
-  static class OnDSTU3 {
-  }
+	static class OnDSTU3 {}
 
 	@Conditional(OnR4Condition.class)
-  static class OnR4 {
-  }
+	static class OnR4 {}
 
 	@Conditional(OnR4BCondition.class)
-	static class OnR4B {
-	}
+	static class OnR4B {}
 
 	@Conditional(OnR5Condition.class)
-  static class OnR5 {
-  }
-
+	static class OnR5 {}
 }

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

@@ -10,7 +10,9 @@ 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

@@ -8,8 +8,8 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
 public class OnR4BCondition implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
-		String version = conditionContext.
-			getEnvironment()
+		String version = conditionContext
+				.getEnvironment()
 				.getProperty("hapi.fhir.fhir_version")
 				.toUpperCase();
 

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

@@ -8,12 +8,11 @@ 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()
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
 				.getProperty("hapi.fhir.fhir_version")
 				.toUpperCase());
 
 		return version == FhirVersionEnum.R4;
-
 	}
 }

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

@@ -8,12 +8,11 @@ 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()
+		FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
+				.getEnvironment()
 				.getProperty("hapi.fhir.fhir_version")
 				.toUpperCase());
 
 		return version == FhirVersionEnum.R5;
-
 	}
 }

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

@@ -0,0 +1,14 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class CdsHooksConfigCondition implements Condition {
+
+	@Override
+	public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
+		String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cdshooks.enabled");
+		return Boolean.parseBoolean(property);
+	}
+}

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "hapi.fhir.cdshooks")
+public class CdsHooksProperties {
+
+	private boolean enabled;
+
+	public boolean isEnabled() {
+		return enabled;
+	}
+
+	public void setEnabled(boolean enabled) {
+		this.enabled = enabled;
+	}
+
+	private String clientIdHeaderName;
+
+	public String getClientIdHeaderName() {
+		return clientIdHeaderName;
+	}
+
+	public void setClientIdHeaderName(String clientIdHeaderName) {
+		this.clientIdHeaderName = clientIdHeaderName;
+	}
+}

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

@@ -0,0 +1,7 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+@JsonIgnoreProperties({"extension"})
+public class CdsHooksRequest extends CdsServiceRequestJson {}

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

@@ -0,0 +1,129 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.jpa.starter.AppProperties;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServicesJson;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonParser;
+import org.apache.http.entity.ContentType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Configurable;
+import org.springframework.beans.factory.annotation.Qualifier;
+
+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 static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
+
+@Configurable
+public class CdsHooksServlet extends HttpServlet {
+	private static final Logger logger = LoggerFactory.getLogger(CdsHooksServlet.class);
+	private static final long serialVersionUID = 1L;
+
+	@Autowired
+	private AppProperties appProperties;
+
+	@Autowired
+	private ProviderConfiguration providerConfiguration;
+
+	@Autowired
+	ICdsServiceRegistry cdsServiceRegistry;
+
+	@Autowired
+	RestfulServer restfulServer;
+
+	@Autowired
+	@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY)
+	ObjectMapper objectMapper;
+
+	protected ProviderConfiguration getProviderConfiguration() {
+		return this.providerConfiguration;
+	}
+
+	// CORS Pre-flight
+	@Override
+	protected void doOptions(HttpServletRequest req, HttpServletResponse resp) {
+		ErrorHandling.setAccessControlHeaders(resp, appProperties);
+		resp.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
+		resp.setHeader("X-Content-Type-Options", "nosniff");
+		resp.setStatus(HttpServletResponse.SC_OK);
+	}
+
+	@Override
+	protected void doGet(HttpServletRequest request, HttpServletResponse response)
+			throws ServletException, IOException {
+		logger.info(request.getRequestURI());
+		if (!request.getRequestURL().toString().endsWith("/cds-services")
+				&& !request.getRequestURL().toString().endsWith("/cds-services/")) {
+			logger.error(request.getRequestURI());
+			throw new ServletException("This servlet is not configured to handle GET requests.");
+		}
+		ErrorHandling.setAccessControlHeaders(response, appProperties);
+		response.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
+		response.getWriter()
+				.println(new GsonBuilder()
+						.setPrettyPrinting()
+						.create()
+						.toJson(JsonParser.parseString(objectMapper.writeValueAsString(getServices()))));
+	}
+
+	@Override
+	protected void doPost(HttpServletRequest request, HttpServletResponse response)
+			throws ServletException, IOException {
+		try {
+			if (request.getContentType() == null || !request.getContentType().startsWith("application/json")) {
+				throw new ServletException(String.format(
+						"Invalid content type %s. Please use application/json.", request.getContentType()));
+			}
+			logger.info(request.getRequestURI());
+			String service = request.getPathInfo().replace("/", "");
+
+			String requestJson = request.getReader().lines().collect(Collectors.joining());
+			CdsHooksRequest cdsHooksRequest = objectMapper.readValue(requestJson, CdsHooksRequest.class);
+			logRequestInfo(cdsHooksRequest, requestJson);
+
+			CdsServiceResponseJson serviceResponseJson = cdsServiceRegistry.callService(service, cdsHooksRequest);
+
+			// Using GSON pretty print format as Jackson's is ugly
+			String jsonResponse = new GsonBuilder()
+					.disableHtmlEscaping()
+					.setPrettyPrinting()
+					.create()
+					.toJson(JsonParser.parseString(objectMapper.writeValueAsString(serviceResponseJson)));
+			logger.info(jsonResponse);
+			response.setContentType("text/json;charset=UTF-8");
+			response.getWriter().println(jsonResponse);
+		} catch (BaseServerResponseException e) {
+			ErrorHandling.handleError(response, "ERROR: Exception connecting to remote server.", e, appProperties);
+			logger.error(e.toString());
+		} catch (Exception e) {
+			logger.error(e.toString());
+			throw new ServletException("ERROR: Exception in cds-hooks processing.", e);
+		}
+	}
+
+	private void logRequestInfo(CdsServiceRequestJson request, String jsonRequest) {
+		logger.info(jsonRequest);
+		logger.info("cds-hooks hook instance: {}", request.getHookInstance());
+		logger.info("cds-hooks local server address: {}", appProperties.getServer_address());
+		logger.info("cds-hooks fhir server address: {}", request.getFhirServer());
+		logger.info(
+				"cds-hooks cql_logging_enabled: {}",
+				this.getProviderConfiguration().getCqlLoggingEnabled());
+	}
+
+	private CdsServicesJson getServices() {
+		return cdsServiceRegistry.getCdsServicesJson();
+	}
+}

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

@@ -0,0 +1,105 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.jpa.starter.AppProperties;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.Arrays;
+import javax.servlet.http.HttpServletResponse;
+
+public class ErrorHandling {
+
+	private ErrorHandling() {}
+
+	public static void handleError(
+			HttpServletResponse response, String message, Exception e, AppProperties myAppProperties)
+			throws IOException {
+		setAccessControlHeaders(response, myAppProperties);
+		response.setStatus(500); // This will be overwritten with the correct status code downstream if needed.
+		response.getWriter().println(message);
+		printMessageAndCause(e, response);
+		if (e instanceof BaseServerResponseException) {
+			handleServerResponseException((BaseServerResponseException) e, response);
+		} else if (e.getCause() instanceof BaseServerResponseException) {
+			handleServerResponseException((BaseServerResponseException) e.getCause(), response);
+		}
+		printStackTrack(e, response);
+	}
+
+	private static void handleServerResponseException(BaseServerResponseException e, HttpServletResponse response)
+			throws IOException {
+		switch (e.getStatusCode()) {
+			case 401:
+			case 403:
+				response.getWriter().println("Precondition Failed. Remote FHIR server returned: " + e.getStatusCode());
+				response.getWriter()
+						.println(
+								"Ensure that the fhirAuthorization token is set or that the remote server allows unauthenticated access.");
+				response.setStatus(412);
+				break;
+			case 404:
+				response.getWriter().println("Precondition Failed. Remote FHIR server returned: " + e.getStatusCode());
+				response.getWriter().println("Ensure the resource exists on the remote server.");
+				response.setStatus(412);
+				break;
+			default:
+				response.getWriter().println("Unhandled Error in Remote FHIR server: " + e.getStatusCode());
+		}
+	}
+
+	private static void printMessageAndCause(Exception e, HttpServletResponse response) throws IOException {
+		if (e.getMessage() != null) {
+			response.getWriter().println(e.getMessage());
+		}
+
+		if (e.getCause() != null && e.getCause().getMessage() != null) {
+			response.getWriter().println(e.getCause().getMessage());
+		}
+	}
+
+	private static void printStackTrack(Exception e, HttpServletResponse response) throws IOException {
+		StringWriter sw = new StringWriter();
+		e.printStackTrace(new PrintWriter(sw));
+		String exceptionAsString = sw.toString();
+		response.getWriter().println(exceptionAsString);
+	}
+
+	public static void setAccessControlHeaders(HttpServletResponse resp, AppProperties myAppProperties) {
+		if (myAppProperties.getCors() != null) {
+			if (myAppProperties.getCors().getAllow_Credentials()) {
+				resp.setHeader(
+						"Access-Control-Allow-Origin",
+						myAppProperties.getCors().getAllowed_origin().stream()
+								.findFirst()
+								.get());
+				resp.setHeader(
+						"Access-Control-Allow-Methods",
+						String.join(", ", Arrays.asList("GET", "HEAD", "POST", "OPTIONS")));
+				resp.setHeader(
+						"Access-Control-Allow-Headers",
+						String.join(
+								", ",
+								Arrays.asList(
+										"x-fhir-starter",
+										"Origin",
+										"Accept",
+										"X-Requested-With",
+										"Content-Type",
+										"Authorization",
+										"Cache-Control")));
+				resp.setHeader(
+						"Access-Control-Expose-Headers",
+						String.join(", ", Arrays.asList("Location", "Content-Location")));
+				resp.setHeader("Access-Control-Max-Age", "86400");
+			}
+		}
+	}
+
+	public static class CdsHooksError extends RuntimeException {
+		public CdsHooksError(String message) {
+			super(message);
+		}
+	}
+}

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

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.jpa.starter.cr.CrProperties;
+
+public class ProviderConfiguration {
+
+	public static final ProviderConfiguration DEFAULT_PROVIDER_CONFIGURATION =
+			new ProviderConfiguration(false, "client_id");
+
+	private final String clientIdHeaderName;
+	private final boolean cqlLoggingEnabled;
+
+	public ProviderConfiguration(boolean cqlLoggingEnabled, String clientIdHeaderName) {
+		this.cqlLoggingEnabled = cqlLoggingEnabled;
+		this.clientIdHeaderName = clientIdHeaderName;
+	}
+
+	public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
+		this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
+		this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
+	}
+
+	public String getClientIdHeaderName() {
+		return this.clientIdHeaderName;
+	}
+
+	public boolean getCqlLoggingEnabled() {
+		return this.cqlLoggingEnabled;
+	}
+}

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

@@ -0,0 +1,66 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
+import ca.uhn.fhir.jpa.starter.cr.CrProperties;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
+import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
+import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
+import org.springframework.boot.web.servlet.ServletRegistrationBean;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+@Configuration
+@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
+@Import(CdsHooksConfig.class)
+public class StarterCdsHooksConfig {
+	@Bean
+	public CdsHooksProperties cdsHooksProperties() {
+		return new CdsHooksProperties();
+	}
+
+	@Bean
+	public CdsCrSettings cdsCrSettings(CdsHooksProperties cdsHooksProperties) {
+		CdsCrSettings settings = CdsCrSettings.getDefault();
+		settings.setClientIdHeaderName(cdsHooksProperties.getClientIdHeaderName());
+		return settings;
+	}
+
+	@Bean
+	public CdsHooksContextBooter cdsHooksContextBooter() {
+		// ourLog.info("No Spring Context provided.  Assuming all CDS Services will be registered dynamically.");
+		return new CdsHooksContextBooter();
+	}
+
+	public static class CdsHooksDaoAuthorizationSvc implements ICdsHooksDaoAuthorizationSvc {
+		@Override
+		public void authorizePreShow(IBaseResource theResource) {}
+	}
+
+	@Bean
+	public ProviderConfiguration providerConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
+		return new ProviderConfiguration(cdsProperties, crProperties);
+	}
+
+	@Bean
+	ICdsHooksDaoAuthorizationSvc cdsHooksDaoAuthorizationSvc() {
+		return new CdsHooksDaoAuthorizationSvc();
+	}
+
+	@Bean
+	public ServletRegistrationBean<CdsHooksServlet> cdsHooksRegistrationBean(AutowireCapableBeanFactory beanFactory) {
+		CdsHooksServlet cdsHooksServlet = new CdsHooksServlet();
+		beanFactory.autowireBean(cdsHooksServlet);
+
+		ServletRegistrationBean<CdsHooksServlet> registrationBean = new ServletRegistrationBean<>();
+		registrationBean.setName("cds-hooks servlet");
+		registrationBean.setServlet(cdsHooksServlet);
+		registrationBean.addUrlMappings("/cds-services/*");
+		registrationBean.setLoadOnStartup(1);
+		return registrationBean;
+	}
+}

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

@@ -10,18 +10,20 @@ import org.springframework.core.env.ConfigurableEnvironment;
 @Configuration
 public class ElasticsearchConfig {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElasticsearchConfig.class);
+
 	@Bean
 	public ElasticsearchSvcImpl elasticsearchSvc(ConfigurableEnvironment configurableEnvironment) {
 		if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
 			String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
 			if (elasticsearchUrl.startsWith("http")) {
-				elasticsearchUrl =elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3);
+				elasticsearchUrl = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3);
 			}
 			String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
 			String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
 			String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
 			ourLog.info("Configuring elasticsearch {} {}", elasticsearchProtocol, elasticsearchUrl);
-			return new ElasticsearchSvcImpl(elasticsearchProtocol, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
+			return new ElasticsearchSvcImpl(
+					elasticsearchProtocol, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
 		} else {
 			return null;
 		}

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

@@ -15,7 +15,6 @@ import ca.uhn.fhir.rest.server.mail.MailConfig;
 import ca.uhn.fhir.rest.server.mail.MailSvc;
 import com.google.common.base.Strings;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
-
 import org.springframework.boot.env.YamlPropertySourceLoader;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -24,6 +23,7 @@ import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
+import java.util.HashSet;
 import java.util.stream.Collectors;
 
 /**
@@ -35,21 +35,34 @@ public class FhirServerConfigCommon {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
 
-
 	public FhirServerConfigCommon(AppProperties appProperties) {
-    ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");
-    ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny") + " multiple deletes");
-    ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny") + " external references");
-    ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable") + " DAO scheduling");
-    ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable") + " delete expunges");
-    ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
-    ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
-    ourLog.info("Server configured to " + (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable") + " auto-creating placeholder references");
-    ourLog.info("Server configured to auto-version references at paths {}", appProperties.getAuto_version_reference_at_paths());
+		ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny")
+				+ " contains searches");
+		ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny")
+				+ " multiple deletes");
+		ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny")
+				+ " external references");
+		ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable")
+				+ " DAO scheduling");
+		ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable")
+				+ " delete expunges");
+		ourLog.info(
+				"Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
+		ourLog.info(
+				"Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny")
+						+ " overriding default search params");
+		ourLog.info("Server configured to "
+				+ (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable")
+				+ " auto-creating placeholder references");
+		ourLog.info(
+				"Server configured to auto-version references at paths {}",
+				appProperties.getAuto_version_reference_at_paths());
 
 		if (appProperties.getSubscription().getEmail() != null) {
-      AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
-      ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port " + email.getPort());
+			AppProperties.Subscription.Email email =
+					appProperties.getSubscription().getEmail();
+			ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port "
+					+ email.getPort());
 			ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
 
 			if (!Strings.isNullOrEmpty(email.getUsername())) {
@@ -81,57 +94,68 @@ public class FhirServerConfigCommon {
 	public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 		JpaStorageSettings jpaStorageSettings = new JpaStorageSettings();
 
-    jpaStorageSettings.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? StorageSettings.IndexEnabledEnum.ENABLED : StorageSettings.IndexEnabledEnum.DISABLED);
-    jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
+		jpaStorageSettings.setIndexMissingFields(
+				appProperties.getEnable_index_missing_fields()
+						? StorageSettings.IndexEnabledEnum.ENABLED
+						: StorageSettings.IndexEnabledEnum.DISABLED);
+		jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(
+				appProperties.getAuto_create_placeholder_reference_targets());
 		jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
-    jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
-    jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
+		jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(
+				appProperties.getEnforce_referential_integrity_on_write());
+		jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(
+				appProperties.getEnforce_referential_integrity_on_delete());
 		jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
 		jpaStorageSettings.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
 		jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
 		jpaStorageSettings.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
 		jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
 		jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
-    if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
-      jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
+		if (appProperties.getSubscription() != null
+				&& appProperties.getSubscription().getEmail() != null)
+			jpaStorageSettings.setEmailFromAddress(
+					appProperties.getSubscription().getEmail().getFrom());
 
 		Integer maxFetchSize = appProperties.getMax_page_size();
 		jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
-    ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
+		ourLog.info("Server configured to have a maximum fetch size of "
+				+ (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
 
 		Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
 		jpaStorageSettings.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
 		ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
 
-
 		Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
 		jpaStorageSettings.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
 
-    if(appProperties.getSubscription() != null) {
+		if (appProperties.getSubscription() != null) {
 			// Subscriptions are enabled by channel type
 			if (appProperties.getSubscription().getResthook_enabled()) {
 				ourLog.info("Enabling REST-hook subscriptions");
-        jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
+				jpaStorageSettings.addSupportedSubscriptionType(
+						org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
 			}
 			if (appProperties.getSubscription().getEmail() != null) {
 				ourLog.info("Enabling email subscriptions");
-        jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
+				jpaStorageSettings.addSupportedSubscriptionType(
+						org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
 			}
 			if (appProperties.getSubscription().getWebsocket_enabled()) {
 				ourLog.info("Enabling websocket subscriptions");
-        jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
+				jpaStorageSettings.addSupportedSubscriptionType(
+						org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
 			}
 		}
 
 		jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
 		jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
-	 jpaStorageSettings.setTreatBaseUrlsAsLocal(appProperties.getLocal_base_urls());
+		jpaStorageSettings.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
 
 		if (appProperties.getLastn_enabled()) {
 			jpaStorageSettings.setLastNEnabled(true);
 		}
 
-	  if(appProperties.getInline_resource_storage_below_size() != 0){
+		if (appProperties.getInline_resource_storage_below_size() != 0) {
 			jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
 		}
 
@@ -139,20 +163,20 @@ public class FhirServerConfigCommon {
 		jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
 		jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
 
-
-
 		if (appProperties.getAllowed_bundle_types() != null) {
-      jpaStorageSettings.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
+			jpaStorageSettings.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream()
+					.map(BundleType::toCode)
+					.collect(Collectors.toSet()));
 		}
 
-	  jpaStorageSettings.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
-
+		jpaStorageSettings.setDeferIndexingForCodesystemsOfSize(
+				appProperties.getDefer_indexing_for_codesystems_of_size());
 
 		if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
 			jpaStorageSettings.setResourceServerIdStrategy(JpaStorageSettings.IdStrategyEnum.UUID);
 			jpaStorageSettings.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
 		}
-    //Parallel Batch GET execution settings
+		// Parallel Batch GET execution settings
 		jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
 		jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
 
@@ -172,8 +196,9 @@ public class FhirServerConfigCommon {
 		// Partitioning
 		if (appProperties.getPartitioning() != null) {
 			retVal.setPartitioningEnabled(true);
-      retVal.setIncludePartitionInSearchHashes(appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
-      if(appProperties.getPartitioning().getAllow_references_across_partitions()) {
+			retVal.setIncludePartitionInSearchHashes(
+					appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
+			if (appProperties.getPartitioning().getAllow_references_across_partitions()) {
 				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
 			} else {
 				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
@@ -183,20 +208,22 @@ public class FhirServerConfigCommon {
 		return retVal;
 	}
 
-
 	@Primary
 	@Bean
-  public HibernatePropertiesProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
+	public HibernatePropertiesProvider jpaStarterDialectProvider(
+			LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
 		return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
 	}
 
-
 	protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
 		jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
 		jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
-    jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
-    if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
-      jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
+		jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(
+				appProperties.getAllow_override_default_search_params());
+		if (appProperties.getSubscription() != null
+				&& appProperties.getSubscription().getEmail() != null)
+			jpaStorageSettings.setEmailFromAddress(
+					appProperties.getSubscription().getEmail().getFrom());
 
 		jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
 
@@ -219,13 +246,15 @@ public class FhirServerConfigCommon {
 
 	@Bean
 	public IEmailSender emailSender(AppProperties appProperties) {
-	  if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
+		if (appProperties.getSubscription() != null
+				&& appProperties.getSubscription().getEmail() != null) {
 
 			return buildEmailSender(appProperties.getSubscription().getEmail());
 		}
 
 		// Return a dummy anonymous function instead of null. Spring does not like null beans.
-	  // TODO Get the signature of ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory
+		// TODO Get the signature of
+		// ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory
 		//  changed so it does not require an instance of an IEmailSender
 		return theDetails -> {};
 	}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu2.java

@@ -13,14 +13,11 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional(OnDSTU2Condition.class)
-@Import({
-	JpaDstu2Config.class,
-	StarterJpaConfig.class
-})
+@Import({JpaDstu2Config.class, StarterJpaConfig.class})
 public class FhirServerConfigDstu2 {
 	@Bean
-	public ITermLoaderSvc termLoaderService(ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
+	public ITermLoaderSvc termLoaderService(
+			ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
 		return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
 	}
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu3.java

@@ -9,10 +9,5 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional(OnDSTU3Condition.class)
-@Import({
-	JpaDstu3Config.class,
-	StarterJpaConfig.class,
-	StarterCrDstu3Config.class,
-	ElasticsearchConfig.class})
-public class FhirServerConfigDstu3 {
-}
+@Import({JpaDstu3Config.class, StarterJpaConfig.class, StarterCrDstu3Config.class, ElasticsearchConfig.class})
+public class FhirServerConfigDstu3 {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4.java

@@ -4,7 +4,6 @@ import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
 import ca.uhn.fhir.jpa.starter.ips.StarterIpsConfig;
-
 import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -18,5 +17,4 @@ import org.springframework.context.annotation.Import;
 	ElasticsearchConfig.class,
 	StarterIpsConfig.class
 })
-public class FhirServerConfigR4 {
-}
+public class FhirServerConfigR4 {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4B.java

@@ -9,11 +9,5 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional(OnR4BCondition.class)
-@Import({
-	JpaR4BConfig.class,
-	SubscriptionTopicConfig.class,
-	StarterJpaConfig.class,
-	ElasticsearchConfig.class
-})
-public class FhirServerConfigR4B {
-}
+@Import({JpaR4BConfig.class, SubscriptionTopicConfig.class, StarterJpaConfig.class, ElasticsearchConfig.class})
+public class FhirServerConfigR4B {}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR5.java

@@ -9,11 +9,5 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional(OnR5Condition.class)
-@Import({
-	StarterJpaConfig.class,
-	JpaR5Config.class,
-	SubscriptionTopicConfig.class,
-	ElasticsearchConfig.class
-})
-public class FhirServerConfigR5 {
-}
+@Import({StarterJpaConfig.class, JpaR5Config.class, SubscriptionTopicConfig.class, ElasticsearchConfig.class})
+public class FhirServerConfigR5 {}

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

@@ -4,11 +4,10 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.to.FhirTesterMvcConfig;
 import ca.uhn.fhir.to.TesterConfig;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 
-//@formatter:off
+// @formatter:off
 /**
  * This spring config file configures the web testing module. It serves two
  * purposes:
@@ -19,7 +18,7 @@ import org.springframework.context.annotation.Import;
  */
 @Configuration
 @Import(FhirTesterMvcConfig.class)
-@Conditional(FhirTesterConfigCondition.class)
+// @Conditional(FhirTesterConfigCondition.class)
 public class FhirTesterConfig {
 
 	/**
@@ -40,18 +39,14 @@ public class FhirTesterConfig {
 	public TesterConfig testerConfig(AppProperties appProperties) {
 		TesterConfig retVal = new TesterConfig();
 		appProperties.getTester().forEach((key, value) -> {
-		 retVal
-			 .addServer()
+			retVal.addServer()
 					.withId(key)
 					.withFhirVersion(value.getFhir_version())
 					.withBaseUrl(value.getServer_address())
 					.withName(value.getName());
-		 retVal.setRefuseToFetchThirdPartyUrls(
-			 value.getRefuse_to_fetch_third_party_urls());
-
+			retVal.setRefuseToFetchThirdPartyUrls(value.getRefuse_to_fetch_third_party_urls());
 		});
 		return retVal;
 	}
-
 }
-//@formatter:on
+// @formatter:on

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

@@ -10,7 +10,8 @@ public class FhirTesterConfigCondition implements Condition {
 	@Override
 	public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
 
-		var properties = EnvironmentHelper.getPropertiesStartingWith((ConfigurableEnvironment) conditionContext.getEnvironment(), "hapi.fhir.tester");
+		var properties = EnvironmentHelper.getPropertiesStartingWith(
+				(ConfigurableEnvironment) conditionContext.getEnvironment(), "hapi.fhir.tester");
 		return !properties.isEmpty();
 	}
 }

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.starter.common;
 
 import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
+import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
@@ -9,7 +10,6 @@ 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.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
@@ -18,7 +18,6 @@ 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.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;
@@ -34,8 +33,8 @@ import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
 import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
-import ca.uhn.fhir.jpa.provider.*;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
+import ca.uhn.fhir.jpa.provider.*;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
@@ -43,8 +42,8 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.jpa.starter.annotations.OnCorsPresent;
 import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
 import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
-import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
 import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
+import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -53,9 +52,9 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
 import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
 import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.*;
 import ca.uhn.fhir.rest.server.interceptor.*;
-import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@@ -75,18 +74,16 @@ import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.web.cors.CorsConfiguration;
 
+import java.util.*;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
-import java.util.*;
 
 import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
 
 @Configuration
-//allow users to configure custom packages to scan for additional beans
-@ComponentScan(basePackages = { "${hapi.fhir.custom-bean-packages:}" })
-@Import(
-    ThreadPoolFactoryConfig.class
-)
+// allow users to configure custom packages to scan for additional beans
+@ComponentScan(basePackages = {"${hapi.fhir.custom-bean-packages:}"})
+@Import(ThreadPoolFactoryConfig.class)
 public class StarterJpaConfig {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
@@ -107,12 +104,9 @@ public class StarterJpaConfig {
 		return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
 	}
 
-
 	@Autowired
 	private ConfigurableEnvironment configurableEnvironment;
 
-
-
 	/**
 	 * Customize the default/max page sizes for search results. You can set these however
 	 * you want, although very large page sizes will require a lot of RAM.
@@ -125,7 +119,6 @@ public class StarterJpaConfig {
 		return pagingProvider;
 	}
 
-
 	@Bean
 	public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
 		return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
@@ -138,8 +131,12 @@ public class StarterJpaConfig {
 
 	@Primary
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource, ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
-		LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+			DataSource myDataSource,
+			ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
+			FhirContext theFhirContext) {
+		LocalContainerEntityManagerFactoryBean retVal =
+				HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
 		retVal.setPersistenceUnitName("HAPI_PU");
 
 		try {
@@ -147,7 +144,8 @@ public class StarterJpaConfig {
 		} catch (Exception e) {
 			throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
 		}
-		retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
+		retVal.setJpaProperties(
+				EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
 		return retVal;
 	}
 
@@ -164,10 +162,10 @@ public class StarterJpaConfig {
 		return new HSearchSortHelperImpl(mySearchParamRegistry);
 	}
 
-
 	@Bean
 	@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
-	public RepositoryValidatingInterceptor repositoryValidatingInterceptor(IRepositoryValidationInterceptorFactory factory) {
+	public RepositoryValidatingInterceptor repositoryValidatingInterceptor(
+			IRepositoryValidationInterceptorFactory factory) {
 		return factory.buildUsingStoredStructureDefinitions();
 	}
 
@@ -189,8 +187,11 @@ public class StarterJpaConfig {
 	@Bean("packageInstaller")
 	@Primary
 	@Conditional(OnImplementationGuidesPresent.class)
-	public IPackageInstallerSvc packageInstaller(AppProperties appProperties, JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition, JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc)
-	{
+	public IPackageInstallerSvc packageInstaller(
+			AppProperties appProperties,
+			JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
+			JobDefinitionRegistry jobDefinitionRegistry,
+			IPackageInstallerSvc packageInstallerSvc) {
 		jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
 
 		if (appProperties.getImplementationGuides() != null) {
@@ -199,7 +200,8 @@ public class StarterJpaConfig {
 				PackageInstallationSpec packageInstallationSpec = guidesEntry.getValue();
 				if (appProperties.getInstall_transitive_ig_dependencies()) {
 
-					packageInstallationSpec.addDependencyExclude("hl7.fhir.r2.core")
+					packageInstallationSpec
+							.addDependencyExclude("hl7.fhir.r2.core")
 							.addDependencyExclude("hl7.fhir.r3.core")
 							.addDependencyExclude("hl7.fhir.r4.core")
 							.addDependencyExclude("hl7.fhir.r5.core");
@@ -238,11 +240,40 @@ public class StarterJpaConfig {
 
 		// Create the interceptor and register it
 		return new CorsInterceptor(config);
-
 	}
 
 	@Bean
-	public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider, Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
+	public RestfulServer restfulServer(
+			IFhirSystemDao<?, ?> fhirSystemDao,
+			AppProperties appProperties,
+			DaoRegistry daoRegistry,
+			Optional<MdmProviderLoader> mdmProviderProvider,
+			IJpaSystemProvider jpaSystemProvider,
+			ResourceProviderFactory resourceProviderFactory,
+			JpaStorageSettings jpaStorageSettings,
+			ISearchParamRegistry searchParamRegistry,
+			IValidationSupport theValidationSupport,
+			DatabaseBackedPagingProvider databaseBackedPagingProvider,
+			LoggingInterceptor loggingInterceptor,
+			Optional<TerminologyUploaderProvider> terminologyUploaderProvider,
+			Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider,
+			Optional<CorsInterceptor> corsInterceptor,
+			IInterceptorBroadcaster interceptorBroadcaster,
+			Optional<BinaryAccessProvider> binaryAccessProvider,
+			BinaryStorageInterceptor binaryStorageInterceptor,
+			IValidatorModule validatorModule,
+			Optional<GraphQLProvider> graphQLProvider,
+			BulkDataExportProvider bulkDataExportProvider,
+			BulkDataImportProvider bulkDataImportProvider,
+			ValueSetOperationProvider theValueSetOperationProvider,
+			ReindexProvider reindexProvider,
+			PartitionManagementProvider partitionManagementProvider,
+			Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor,
+			IPackageInstallerSvc packageInstallerSvc,
+			ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc,
+			ApplicationContext appContext,
+			Optional<IpsOperationProvider> theIpsOperationProvider,
+			Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
 		RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
 
 		List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
@@ -264,7 +295,8 @@ public class StarterJpaConfig {
 
 		fhirServer.registerProviders(resourceProviderFactory.createProviders());
 		fhirServer.registerProvider(jpaSystemProvider);
-		fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
+		fhirServer.setServerConformanceProvider(calculateConformanceProvider(
+				fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
 
 		/*
 		 * ETag Support
@@ -272,7 +304,6 @@ public class StarterJpaConfig {
 
 		if (!appProperties.getEtag_support_enabled()) fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
 
-
 		/*
 		 * Default to JSON and pretty printing
 		 */
@@ -318,7 +349,8 @@ public class StarterJpaConfig {
 			fhirServer.setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
 		} else if (appProperties.getUse_apache_address_strategy()) {
 			boolean useHttps = appProperties.getUse_apache_address_strategy_https();
-			fhirServer.setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
+			fhirServer.setServerAddressStrategy(
+					useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
 		} else {
 			fhirServer.setServerAddressStrategy(new IncomingRequestAddressStrategy());
 		}
@@ -330,7 +362,11 @@ public class StarterJpaConfig {
 		 * so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
 		 * with this feature.
 		 */
-		if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
+		if (fhirSystemDao
+				.getContext()
+				.getVersion()
+				.getVersion()
+				.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
 			fhirServer.registerProvider(terminologyUploaderProvider.get());
 		}
 
@@ -348,7 +384,8 @@ public class StarterJpaConfig {
 		}
 
 		if (appProperties.getAllow_cascading_deletes()) {
-			CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
+			CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
+					fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
 			fhirServer.registerInterceptor(cascadingDeleteInterceptor);
 		}
 
@@ -391,16 +428,15 @@ public class StarterJpaConfig {
 			fhirServer.registerProvider(bulkDataExportProvider);
 		}
 
-		//Bulk Import
+		// Bulk Import
 		if (appProperties.getBulk_import_enabled()) {
 			fhirServer.registerProvider(bulkDataImportProvider);
 		}
 
-
 		// valueSet Operations i.e $expand
 		fhirServer.registerProvider(theValueSetOperationProvider);
 
-		//reindex Provider $reindex
+		// reindex Provider $reindex
 		fhirServer.registerProvider(reindexProvider);
 
 		// Partitioning
@@ -414,8 +450,7 @@ public class StarterJpaConfig {
 		// register custom interceptors
 		registerCustomInterceptors(fhirServer, appContext, appProperties.getCustomInterceptorClasses());
 
-
-		//register the IPS Provider
+		// register the IPS Provider
 		if (!theIpsOperationProvider.isEmpty()) {
 			fhirServer.registerProvider(theIpsOperationProvider.get());
 		}
@@ -426,8 +461,9 @@ public class StarterJpaConfig {
 	/**
 	 * check the properties for custom interceptor classes and registers them.
 	 */
-	@SuppressWarnings({ "unchecked", "rawtypes" })
-	private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
+	@SuppressWarnings({"unchecked", "rawtypes"})
+	private void registerCustomInterceptors(
+			RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
 
 		if (customInterceptorClasses == null) {
 			return;
@@ -461,30 +497,40 @@ public class StarterJpaConfig {
 		}
 	}
 
-	public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
+	public static IServerConformanceProvider<?> calculateConformanceProvider(
+			IFhirSystemDao fhirSystemDao,
+			RestfulServer fhirServer,
+			JpaStorageSettings jpaStorageSettings,
+			ISearchParamRegistry searchParamRegistry,
+			IValidationSupport theValidationSupport) {
 		FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
 		if (fhirVersion == FhirVersionEnum.DSTU2) {
-			JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
+			JpaConformanceProviderDstu2 confProvider =
+					new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
 			confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
 			return confProvider;
 		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
 
-			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
+			JpaConformanceProviderDstu3 confProvider =
+					new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
 			confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
 			return confProvider;
 		} else if (fhirVersion == FhirVersionEnum.R4) {
 
-			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
+			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
+					fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
 			confProvider.setImplementationDescription("HAPI FHIR R4 Server");
 			return confProvider;
 		} else if (fhirVersion == FhirVersionEnum.R4B) {
 
-			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
+			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
+					fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
 			confProvider.setImplementationDescription("HAPI FHIR R4B Server");
 			return confProvider;
 		} else if (fhirVersion == FhirVersionEnum.R5) {
 
-			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
+			JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
+					fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
 			confProvider.setImplementationDescription("HAPI FHIR R5 Server");
 			return confProvider;
 		} else {
@@ -492,4 +538,3 @@ public class StarterJpaConfig {
 		}
 	}
 }
-

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/IRepositoryValidationInterceptorFactory.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
 public interface IRepositoryValidationInterceptorFactory {
 
 	String ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR = "enable_repository_validating_interceptor";
+
 	RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions();
 
 	RepositoryValidatingInterceptor build();

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java

@@ -37,24 +37,28 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
 	private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
 	private final IFhirResourceDao structureDefinitionResourceProvider;
 
-	public RepositoryValidationInterceptorFactoryDstu3(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
+	public RepositoryValidationInterceptorFactoryDstu3(
+			RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
 		this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
 		this.fhirContext = daoRegistry.getSystemDao().getContext();
 		structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
-
 	}
 
 	public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
 
-		IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
-		Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size())
-			.stream()
+		IBundleProvider results = structureDefinitionResourceProvider.search(
+				new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
+		Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
 				.map(StructureDefinition.class::cast)
 				.collect(Collectors.groupingBy(StructureDefinition::getType));
 
 		structureDefinitions.forEach((key, value) -> {
 			String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
-			repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
+			repositoryValidatingRuleBuilder
+					.forResourcesOfType(key)
+					.requireAtLeastOneProfileOf(urls)
+					.and()
+					.requireValidationToDeclaredProfiles();
 		});
 
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -65,11 +69,14 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
 
 		// Customize the ruleBuilder here to have the rules you want! We will give a simple example
 		// of enabling validation for all Patient resources
-		repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
+		repositoryValidatingRuleBuilder
+				.forResourcesOfType("Patient")
+				.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
+				.and()
+				.requireValidationToDeclaredProfiles();
 
 		// Do not customize below this line
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
 		return new RepositoryValidatingInterceptor(fhirContext, rules);
 	}
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4.java

@@ -37,25 +37,29 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
 	private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
 	private final IFhirResourceDao structureDefinitionResourceProvider;
 
-	public RepositoryValidationInterceptorFactoryR4(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
+	public RepositoryValidationInterceptorFactoryR4(
+			RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
 		this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
 		this.fhirContext = daoRegistry.getSystemDao().getContext();
 		structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
-
 	}
 
 	@Override
 	public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
 
-		IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
-		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
-			.stream()
+		IBundleProvider results = structureDefinitionResourceProvider.search(
+				new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
+		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
 				.map(StructureDefinition.class::cast)
 				.collect(Collectors.groupingBy(StructureDefinition::getType));
 
 		structureDefintions.forEach((key, value) -> {
 			String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
-			repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
+			repositoryValidatingRuleBuilder
+					.forResourcesOfType(key)
+					.requireAtLeastOneProfileOf(urls)
+					.and()
+					.requireValidationToDeclaredProfiles();
 		});
 
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -67,11 +71,14 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
 
 		// Customize the ruleBuilder here to have the rules you want! We will give a simple example
 		// of enabling validation for all Patient resources
-		repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
+		repositoryValidatingRuleBuilder
+				.forResourcesOfType("Patient")
+				.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
+				.and()
+				.requireValidationToDeclaredProfiles();
 
 		// Do not customize below this line
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
 		return new RepositoryValidatingInterceptor(fhirContext, rules);
 	}
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4B.java

@@ -37,25 +37,29 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
 	private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
 	private final IFhirResourceDao structureDefinitionResourceProvider;
 
-	public RepositoryValidationInterceptorFactoryR4B(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
+	public RepositoryValidationInterceptorFactoryR4B(
+			RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
 		this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
 		this.fhirContext = daoRegistry.getSystemDao().getContext();
 		structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
-
 	}
 
 	@Override
 	public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
 
-		IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
-		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
-			.stream()
+		IBundleProvider results = structureDefinitionResourceProvider.search(
+				new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
+		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
 				.map(StructureDefinition.class::cast)
 				.collect(Collectors.groupingBy(StructureDefinition::getType));
 
 		structureDefintions.forEach((key, value) -> {
 			String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
-			repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
+			repositoryValidatingRuleBuilder
+					.forResourcesOfType(key)
+					.requireAtLeastOneProfileOf(urls)
+					.and()
+					.requireValidationToDeclaredProfiles();
 		});
 
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -67,11 +71,14 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
 
 		// Customize the ruleBuilder here to have the rules you want! We will give a simple example
 		// of enabling validation for all Patient resources
-		repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
+		repositoryValidatingRuleBuilder
+				.forResourcesOfType("Patient")
+				.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
+				.and()
+				.requireValidationToDeclaredProfiles();
 
 		// Do not customize below this line
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
 		return new RepositoryValidatingInterceptor(fhirContext, rules);
 	}
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR5.java

@@ -37,24 +37,28 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
 	private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
 	private final IFhirResourceDao structureDefinitionResourceProvider;
 
-	public RepositoryValidationInterceptorFactoryR5(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
+	public RepositoryValidationInterceptorFactoryR5(
+			RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
 		this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
 		this.fhirContext = daoRegistry.getSystemDao().getContext();
 		structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
-
 	}
 
 	public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
 
-		IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
-		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
-			.stream()
+		IBundleProvider results = structureDefinitionResourceProvider.search(
+				new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
+		Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
 				.map(StructureDefinition.class::cast)
 				.collect(Collectors.groupingBy(StructureDefinition::getType));
 
 		structureDefintions.forEach((key, value) -> {
 			String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
-			repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
+			repositoryValidatingRuleBuilder
+					.forResourcesOfType(key)
+					.requireAtLeastOneProfileOf(urls)
+					.and()
+					.requireValidationToDeclaredProfiles();
 		});
 
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -65,11 +69,14 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
 
 		// Customize the ruleBuilder here to have the rules you want! We will give a simple example
 		// of enabling validation for all Patient resources
-		repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
+		repositoryValidatingRuleBuilder
+				.forResourcesOfType("Patient")
+				.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
+				.and()
+				.requireValidationToDeclaredProfiles();
 
 		// Do not customize below this line
 		List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
 		return new RepositoryValidatingInterceptor(fhirContext, rules);
 	}
-
 }

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

@@ -8,7 +8,7 @@ public class CrConfigCondition implements Condition {
 
 	@Override
 	public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
-    String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr_enabled");
+		String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr.enabled");
 		return Boolean.parseBoolean(property);
 	}
 }

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

@@ -0,0 +1,264 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+import org.cqframework.cql.cql2elm.CqlCompilerException;
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.LibraryBuilder;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "hapi.fhir.cr")
+public class CrProperties {
+	private Boolean enabled;
+	// cql settings
+	private Boolean cql_use_embedded_libraries = true;
+	private Boolean cql_runtime_debug_logging_enabled = false;
+	private Boolean cql_runtime_enable_validation = false;
+	private Boolean cql_runtime_enable_expression_caching = false;
+	private Boolean cql_compiler_validate_units = true;
+	private Boolean cql_compiler_verify_only = false;
+	private String cql_compiler_compatibility_level = "1.5";
+	private CqlCompilerException.ErrorSeverity cql_compiler_error_level = CqlCompilerException.ErrorSeverity.Info;
+	private LibraryBuilder.SignatureLevel cql_compiler_signature_level = LibraryBuilder.SignatureLevel.All;
+	private Boolean cql_compiler_analyze_data_requirements = false;
+	private Boolean cql_compiler_collapse_data_requirements = false;
+	private CqlTranslator.Format cql_compiler_translator_format = CqlTranslator.Format.JSON;
+	private Boolean cql_compiler_enable_date_range_optimization = false;
+	private Boolean cql_compiler_enable_annotations = false;
+	private Boolean cql_compiler_enable_locators = false;
+	private Boolean cql_compiler_enable_results_type = false;
+	private Boolean cql_compiler_enable_detailed_errors = false;
+	private Boolean cql_compiler_disable_list_traversal = false;
+	private Boolean cql_compiler_disable_list_demotion = false;
+	private Boolean cql_compiler_disable_list_promotion = false;
+	private Boolean cql_compiler_enable_interval_demotion = false;
+	private Boolean cql_compiler_enable_interval_promotion = false;
+	private Boolean cql_compiler_disable_method_invocation = false;
+	private Boolean cql_compiler_require_from_keyword = false;
+	private Boolean cql_compiler_disable_default_model_info_load = false;
+	// Care-gaps Settings
+	private String caregaps_reporter = "default";
+	private String caregaps_section_author = "default";
+
+	public Boolean getEnabled() {
+		return enabled;
+	}
+
+	public void setEnabled(Boolean enabled) {
+		this.enabled = enabled;
+	}
+
+	public boolean isCqlUseEmbeddedLibraries() {
+		return cql_use_embedded_libraries;
+	}
+
+	public void setCqlUseEmbeddedLibraries(boolean cql_use_embedded_libraries) {
+		this.cql_use_embedded_libraries = cql_use_embedded_libraries;
+	}
+
+	public boolean isCqlRuntimeDebugLoggingEnabled() {
+		return cql_runtime_debug_logging_enabled;
+	}
+
+	public void setCqlRuntimeDebugLoggingEnabled(boolean cqlRuntimeDebugLoggingEnabled) {
+		this.cql_runtime_debug_logging_enabled = cqlRuntimeDebugLoggingEnabled;
+	}
+
+	public boolean isCqlCompilerValidateUnits() {
+		return cql_compiler_validate_units;
+	}
+
+	public void setCqlCompilerValidateUnits(boolean cqlCompilerValidateUnits) {
+		this.cql_compiler_validate_units = cqlCompilerValidateUnits;
+	}
+
+	public boolean isCqlCompilerVerifyOnly() {
+		return cql_compiler_verify_only;
+	}
+
+	public void setCqlCompilerVerifyOnly(boolean cqlCompilerVerifyOnly) {
+		this.cql_compiler_verify_only = cqlCompilerVerifyOnly;
+	}
+
+	public String getCqlCompilerCompatibilityLevel() {
+		return cql_compiler_compatibility_level;
+	}
+
+	public void setCqlCompilerCompatibilityLevel(String cqlCompilerCompatibilityLevel) {
+		this.cql_compiler_compatibility_level = cqlCompilerCompatibilityLevel;
+	}
+
+	public CqlCompilerException.ErrorSeverity getCqlCompilerErrorSeverityLevel() {
+		return cql_compiler_error_level;
+	}
+
+	public void setCqlCompilerErrorSeverityLevel(CqlCompilerException.ErrorSeverity cqlCompilerErrorSeverityLevel) {
+		this.cql_compiler_error_level = cqlCompilerErrorSeverityLevel;
+	}
+
+	public LibraryBuilder.SignatureLevel getCqlCompilerSignatureLevel() {
+		return cql_compiler_signature_level;
+	}
+
+	public void setCqlCompilerSignatureLevel(LibraryBuilder.SignatureLevel cqlCompilerSignatureLevel) {
+		this.cql_compiler_signature_level = cqlCompilerSignatureLevel;
+	}
+
+	public boolean isCqlCompilerAnalyzeDataRequirements() {
+		return cql_compiler_analyze_data_requirements;
+	}
+
+	public void setCqlCompilerAnalyzeDataRequirements(boolean cqlCompilerAnalyzeDataRequirements) {
+		this.cql_compiler_analyze_data_requirements = cqlCompilerAnalyzeDataRequirements;
+	}
+
+	public boolean isCqlCompilerCollapseDataRequirements() {
+		return cql_compiler_collapse_data_requirements;
+	}
+
+	public void setCqlCompilerCollapseDataRequirements(boolean cqlCompilerCollapseDataRequirements) {
+		this.cql_compiler_collapse_data_requirements = cqlCompilerCollapseDataRequirements;
+	}
+
+	public boolean isEnableDateRangeOptimization() {
+		return cql_compiler_enable_date_range_optimization;
+	}
+
+	public void setEnableDateRangeOptimization(boolean enableDateRangeOptimization) {
+		this.cql_compiler_enable_date_range_optimization = enableDateRangeOptimization;
+	}
+
+	public boolean isEnableAnnotations() {
+		return cql_compiler_enable_annotations;
+	}
+
+	public void setEnableAnnotations(boolean enableAnnotations) {
+		this.cql_compiler_enable_annotations = enableAnnotations;
+	}
+
+	public boolean isEnableLocators() {
+		return cql_compiler_enable_locators;
+	}
+
+	public void setEnableLocators(boolean enableLocators) {
+		this.cql_compiler_enable_locators = enableLocators;
+	}
+
+	public boolean isEnableResultsType() {
+		return cql_compiler_enable_results_type;
+	}
+
+	public void setEnableResultsType(boolean enableResultsType) {
+		this.cql_compiler_enable_results_type = enableResultsType;
+	}
+
+	public boolean isEnableDetailedErrors() {
+		return cql_compiler_enable_detailed_errors;
+	}
+
+	public void setEnableDetailedErrors(boolean enableDetailedErrors) {
+		this.cql_compiler_enable_detailed_errors = enableDetailedErrors;
+	}
+
+	public boolean isDisableListTraversal() {
+		return cql_compiler_disable_list_traversal;
+	}
+
+	public void setDisableListTraversal(boolean disableListTraversal) {
+		this.cql_compiler_disable_list_traversal = disableListTraversal;
+	}
+
+	public boolean isDisableListDemotion() {
+		return cql_compiler_disable_list_demotion;
+	}
+
+	public void setDisableListDemotion(boolean disableListDemotion) {
+		this.cql_compiler_disable_list_demotion = disableListDemotion;
+	}
+
+	public boolean isDisableListPromotion() {
+		return cql_compiler_disable_list_promotion;
+	}
+
+	public void setDisableListPromotion(boolean disableListPromotion) {
+		this.cql_compiler_disable_list_promotion = disableListPromotion;
+	}
+
+	public boolean isEnableIntervalPromotion() {
+		return cql_compiler_enable_interval_promotion;
+	}
+
+	public void setEnableIntervalPromotion(boolean enableIntervalPromotion) {
+		this.cql_compiler_enable_interval_promotion = enableIntervalPromotion;
+	}
+
+	public boolean isEnableIntervalDemotion() {
+		return cql_compiler_enable_interval_demotion;
+	}
+
+	public void setEnableIntervalDemotion(boolean enableIntervalDemotion) {
+		this.cql_compiler_enable_interval_demotion = enableIntervalDemotion;
+	}
+
+	public boolean isDisableMethodInvocation() {
+		return cql_compiler_disable_method_invocation;
+	}
+
+	public void setDisableMethodInvocation(boolean disableMethodInvocation) {
+		this.cql_compiler_disable_method_invocation = disableMethodInvocation;
+	}
+
+	public boolean isRequireFromKeyword() {
+		return cql_compiler_require_from_keyword;
+	}
+
+	public void setRequireFromKeyword(boolean requireFromKeyword) {
+		this.cql_compiler_require_from_keyword = requireFromKeyword;
+	}
+
+	public boolean isDisableDefaultModelInfoLoad() {
+		return cql_compiler_disable_default_model_info_load;
+	}
+
+	public void setDisableDefaultModelInfoLoad(boolean disableDefaultModelInfoLoad) {
+		this.cql_compiler_disable_default_model_info_load = disableDefaultModelInfoLoad;
+	}
+
+	public boolean isCqlRuntimeEnableExpressionCaching() {
+		return cql_runtime_enable_expression_caching;
+	}
+
+	public void setCqlRuntimeEnableExpressionCaching(boolean cqlRuntimeEnableExpressionCaching) {
+		this.cql_runtime_enable_expression_caching = cqlRuntimeEnableExpressionCaching;
+	}
+
+	public boolean isCqlRuntimeEnableValidation() {
+		return cql_runtime_enable_validation;
+	}
+
+	public void setCqlRuntimeEnableValidation(boolean cqlRuntimeEnableValidation) {
+		this.cql_runtime_enable_validation = cqlRuntimeEnableValidation;
+	}
+
+	public CqlTranslator.Format getCqlTranslatorFormat() {
+		return cql_compiler_translator_format;
+	}
+
+	public void setCqlTranslatorFormat(CqlTranslator.Format cqlTranslatorFormat) {
+		this.cql_compiler_translator_format = cqlTranslatorFormat;
+	}
+
+	public String getCareGapsReporter() {
+		return caregaps_reporter;
+	}
+
+	public String getCareGapsSectionAuthor() {
+		return caregaps_section_author;
+	}
+
+	public void setCareGapsSectionAuthor(String theCareGapsSectionAuthor) {
+		this.caregaps_section_author = theCareGapsSectionAuthor;
+	}
+
+	public void setCareGapsReporter(String theCareGapsReporter) {
+		this.caregaps_reporter = theCareGapsReporter;
+	}
+}

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

@@ -0,0 +1,47 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.provider.IResourceProviderFactoryObserver;
+import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+
+import java.util.function.Supplier;
+
+public class PostInitProviderRegisterer {
+	public PostInitProviderRegisterer(RestfulServer restfulServer, ResourceProviderFactory resourceProviderFactory) {
+		resourceProviderFactory.attach(new Observer(restfulServer));
+	}
+
+	private class Observer implements IResourceProviderFactoryObserver {
+		private RestfulServer restfulServer;
+
+		public Observer(RestfulServer restfulServer) {
+			this.restfulServer = restfulServer;
+		}
+
+		public void update(Supplier<Object> theSupplier) {
+			if (theSupplier == null) {
+				return;
+			}
+
+			var provider = theSupplier.get();
+			if (provider == null) {
+				return;
+			}
+
+			this.restfulServer.registerProvider(provider);
+		}
+
+		public void remove(Supplier<Object> theSupplier) {
+			if (theSupplier == null) {
+				return;
+			}
+
+			var provider = theSupplier.get();
+			if (provider == null) {
+				return;
+			}
+
+			this.restfulServer.unregisterProvider(provider);
+		}
+	}
+}

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

@@ -1,13 +1,195 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
+import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
+import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
+import ca.uhn.fhir.cr.config.dstu3.ApplyOperationConfig;
 import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
+import ca.uhn.fhir.cr.config.dstu3.ExtractOperationConfig;
+import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
+import ca.uhn.fhir.cr.config.dstu3.PopulateOperationConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
-import org.springframework.context.annotation.Conditional;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import org.cqframework.cql.cql2elm.CqlCompilerOptions;
+import org.cqframework.cql.cql2elm.model.CompiledLibrary;
+import org.cqframework.cql.cql2elm.model.Model;
+import org.hl7.cql.model.ModelIdentifier;
+import org.hl7.elm.r1.VersionedIdentifier;
+import org.opencds.cqf.cql.engine.execution.CqlEngine;
+import org.opencds.cqf.cql.engine.runtime.Code;
+import org.opencds.cqf.fhir.cql.EvaluationSettings;
+import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.utility.ValidationProfile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.annotation.*;
+
+import java.util.EnumSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 
 @Configuration
 @Conditional({OnDSTU3Condition.class, CrConfigCondition.class})
-@Import({CrDstu3Config.class})
+@Import({
+	// BaseCrConfig.class,
+	CrDstu3Config.class,
+	ApplyOperationConfig.class,
+	ExtractOperationConfig.class,
+	PackageOperationConfig.class,
+	PopulateOperationConfig.class
+})
 public class StarterCrDstu3Config {
+	private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrDstu3Config.class);
+
+	@Bean
+	MeasureEvaluationOptions measureEvaluationOptions(
+			EvaluationSettings theEvaluationSettings, Map<String, ValidationProfile> theValidationProfiles) {
+		MeasureEvaluationOptions measureEvalOptions = new MeasureEvaluationOptions();
+		measureEvalOptions.setEvaluationSettings(theEvaluationSettings);
+
+		if (measureEvalOptions.isValidationEnabled()) {
+			measureEvalOptions.setValidationProfiles(theValidationProfiles);
+		}
+		return measureEvalOptions;
+	}
+
+	@Bean
+	public EvaluationSettings evaluationSettings(
+			CrProperties theCrProperties,
+			Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
+			Map<ModelIdentifier, Model> theGlobalModelCache,
+			Map<String, List<Code>> theGlobalValueSetCache) {
+		var evaluationSettings = EvaluationSettings.getDefault();
+		var cqlOptions = evaluationSettings.getCqlOptions();
+
+		var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
+		Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
+		if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
+			options.add(CqlEngine.Options.EnableExpressionCaching);
+		}
+		if (theCrProperties.isCqlRuntimeEnableValidation()) {
+			options.add(CqlEngine.Options.EnableValidation);
+		}
+		cqlEngineOptions.setOptions(options);
+		cqlOptions.setCqlEngineOptions(cqlEngineOptions);
+
+		var cqlCompilerOptions = new CqlCompilerOptions();
+
+		if (theCrProperties.isEnableDateRangeOptimization()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
+		}
+		if (theCrProperties.isEnableAnnotations()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
+		}
+		if (theCrProperties.isEnableLocators()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
+		}
+		if (theCrProperties.isEnableResultsType()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
+		}
+		cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
+		if (theCrProperties.isEnableDetailedErrors()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
+		}
+		cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
+		if (theCrProperties.isDisableListTraversal()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
+		}
+		if (theCrProperties.isDisableListDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
+		}
+		if (theCrProperties.isDisableListPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
+		}
+		if (theCrProperties.isEnableIntervalDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
+		}
+		if (theCrProperties.isEnableIntervalPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
+		}
+		if (theCrProperties.isDisableMethodInvocation()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
+		}
+		if (theCrProperties.isRequireFromKeyword()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
+		}
+		cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
+		if (theCrProperties.isDisableDefaultModelInfoLoad()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
+		}
+		cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
+		cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
+		cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
+		cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
+
+		cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
+		evaluationSettings.setLibraryCache(theGlobalLibraryCache);
+		evaluationSettings.setModelCache(theGlobalModelCache);
+		evaluationSettings.setValueSetCache(theGlobalValueSetCache);
+		return evaluationSettings;
+	}
+
+	@Bean
+	public PostInitProviderRegisterer postInitProviderRegisterer(
+			RestfulServer theRestfulServer, ResourceProviderFactory theResourceProviderFactory) {
+		return new PostInitProviderRegisterer(theRestfulServer, theResourceProviderFactory);
+	}
+
+	@Bean
+	public CrProperties crProperties() {
+		return new CrProperties();
+	}
+
+	@Bean
+	public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public Map<ModelIdentifier, Model> globalModelCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public Map<String, List<Code>> globalValueSetCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
+			IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
+			DaoRegistry theDaoRegistry,
+			EvaluationSettings theEvaluationSettings) {
+		ElmCacheResourceChangeListener listener =
+				new ElmCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getLibraryCache());
+		theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
+				"Library", SearchParameterMap.newSynchronous(), listener, 1000);
+		return listener;
+	}
+
+	@Bean
+	public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
+			IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
+			EvaluationSettings theEvaluationSettings,
+			DaoRegistry theDaoRegistry) {
+
+		CodeCacheResourceChangeListener listener =
+				new CodeCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getValueSetCache());
+		// registry
+		theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
+				"ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
+
+		return listener;
+	}
+
+	@Bean
+	public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
+		return new ResourceChangeListenerRegistryInterceptor();
+	}
 }

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

@@ -1,11 +1,221 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
+import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
+import ca.uhn.fhir.cr.common.CqlThreadFactory;
+import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
+import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
 import ca.uhn.fhir.cr.config.r4.CrR4Config;
+import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
+import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
+import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import org.cqframework.cql.cql2elm.CqlCompilerOptions;
+import org.cqframework.cql.cql2elm.model.CompiledLibrary;
+import org.cqframework.cql.cql2elm.model.Model;
+import org.hl7.cql.model.ModelIdentifier;
+import org.hl7.elm.r1.VersionedIdentifier;
+import org.opencds.cqf.cql.engine.execution.CqlEngine;
+import org.opencds.cqf.cql.engine.runtime.Code;
+import org.opencds.cqf.fhir.cql.EvaluationSettings;
+import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
+import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.utility.ValidationProfile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Primary;
+import org.springframework.security.concurrent.DelegatingSecurityContextExecutorService;
 
+import java.util.EnumSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+@Configuration
 @Conditional({OnR4Condition.class, CrConfigCondition.class})
-@Import({CrR4Config.class})
+@Import({
+	CrR4Config.class,
+	ApplyOperationConfig.class,
+	ExtractOperationConfig.class,
+	PackageOperationConfig.class,
+	PopulateOperationConfig.class
+})
 public class StarterCrR4Config {
+	private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrR4Config.class);
+
+	@Primary
+	@Bean
+	public ExecutorService cqlExecutor() {
+		CqlThreadFactory factory = new CqlThreadFactory();
+		ExecutorService executor = Executors.newFixedThreadPool(2, factory);
+		executor = new DelegatingSecurityContextExecutorService(executor);
+
+		return executor;
+	}
+
+	@Bean
+	CareGapsProperties careGapsProperties(CrProperties theCrProperties) {
+		var careGapsProperties = new CareGapsProperties();
+		careGapsProperties.setThreadedCareGapsEnabled(false);
+		careGapsProperties.setCareGapsReporter(theCrProperties.getCareGapsReporter());
+		careGapsProperties.setCareGapsCompositionSectionAuthor(theCrProperties.getCareGapsSectionAuthor());
+		return careGapsProperties;
+	}
+
+	@Bean
+	MeasureEvaluationOptions measureEvaluationOptions(
+			EvaluationSettings theEvaluationSettings, Map<String, ValidationProfile> theValidationProfiles) {
+		MeasureEvaluationOptions measureEvalOptions = new MeasureEvaluationOptions();
+		measureEvalOptions.setEvaluationSettings(theEvaluationSettings);
+		if (measureEvalOptions.isValidationEnabled()) {
+			measureEvalOptions.setValidationProfiles(theValidationProfiles);
+		}
+		return measureEvalOptions;
+	}
+
+	@Bean
+	public EvaluationSettings evaluationSettings(
+			CrProperties theCrProperties,
+			Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
+			Map<ModelIdentifier, Model> theGlobalModelCache,
+			Map<String, List<Code>> theGlobalValueSetCache) {
+		var evaluationSettings = EvaluationSettings.getDefault();
+		var cqlOptions = evaluationSettings.getCqlOptions();
+
+		var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
+		Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
+		if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
+			options.add(CqlEngine.Options.EnableExpressionCaching);
+		}
+		if (theCrProperties.isCqlRuntimeEnableValidation()) {
+			options.add(CqlEngine.Options.EnableValidation);
+		}
+		cqlEngineOptions.setOptions(options);
+		cqlOptions.setCqlEngineOptions(cqlEngineOptions);
+
+		var cqlCompilerOptions = new CqlCompilerOptions();
+
+		if (theCrProperties.isEnableDateRangeOptimization()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
+		}
+		if (theCrProperties.isEnableAnnotations()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
+		}
+		if (theCrProperties.isEnableLocators()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
+		}
+		if (theCrProperties.isEnableResultsType()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
+		}
+		cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
+		if (theCrProperties.isEnableDetailedErrors()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
+		}
+		cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
+		if (theCrProperties.isDisableListTraversal()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
+		}
+		if (theCrProperties.isDisableListDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
+		}
+		if (theCrProperties.isDisableListPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
+		}
+		if (theCrProperties.isEnableIntervalDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
+		}
+		if (theCrProperties.isEnableIntervalPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
+		}
+		if (theCrProperties.isDisableMethodInvocation()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
+		}
+		if (theCrProperties.isRequireFromKeyword()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
+		}
+		cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
+		if (theCrProperties.isDisableDefaultModelInfoLoad()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
+		}
+		cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
+		cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
+		cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
+		cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
+
+		cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
+		evaluationSettings.setLibraryCache(theGlobalLibraryCache);
+		evaluationSettings.setModelCache(theGlobalModelCache);
+		evaluationSettings.setValueSetCache(theGlobalValueSetCache);
+		return evaluationSettings;
+	}
+
+	@Bean
+	public PostInitProviderRegisterer postInitProviderRegisterer(
+			RestfulServer theRestfulServer, ResourceProviderFactory theResourceProviderFactory) {
+		return new PostInitProviderRegisterer(theRestfulServer, theResourceProviderFactory);
+	}
+
+	@Bean
+	public CrProperties crProperties() {
+		return new CrProperties();
+	}
+
+	@Bean
+	public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public Map<ModelIdentifier, Model> globalModelCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public Map<String, List<Code>> globalValueSetCache() {
+		return new ConcurrentHashMap<>();
+	}
+
+	@Bean
+	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
+			IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
+			DaoRegistry theDaoRegistry,
+			EvaluationSettings theEvaluationSettings) {
+		ElmCacheResourceChangeListener listener =
+				new ElmCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getLibraryCache());
+		theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
+				"Library", SearchParameterMap.newSynchronous(), listener, 1000);
+		return listener;
+	}
+
+	@Bean
+	public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
+			IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
+			EvaluationSettings theEvaluationSettings,
+			DaoRegistry theDaoRegistry) {
+
+		CodeCacheResourceChangeListener listener =
+				new CodeCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getValueSetCache());
+		// registry
+		theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
+				"ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
+
+		return listener;
+	}
+
+	@Bean
+	public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
+		return new ResourceChangeListenerRegistryInterceptor();
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/ig/IImplementationGuideOperationProvider.java

@@ -9,10 +9,16 @@ import java.io.IOException;
 public interface IImplementationGuideOperationProvider {
 	static PackageInstallationSpec toPackageInstallationSpec(byte[] npmPackageAsByteArray) throws IOException {
 		NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(npmPackageAsByteArray));
-		return new PackageInstallationSpec().setName(npmPackage.name()).setPackageContents(npmPackageAsByteArray).setVersion(npmPackage.version()).setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(false);
+		return new PackageInstallationSpec()
+				.setName(npmPackage.name())
+				.setPackageContents(npmPackageAsByteArray)
+				.setVersion(npmPackage.version())
+				.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL)
+				.setFetchDependencies(false);
 	}
 
-	//The following declaration is the one that counts but cannot be used across different versions as stating Base64BinaryType would bind to a separate version
-	//@Operation(name = "$install", typeName = "ImplementationGuide")
-	//Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
+	// The following declaration is the one that counts but cannot be used across different versions as stating
+	// Base64BinaryType would bind to a separate version
+	// @Operation(name = "$install", typeName = "ImplementationGuide")
+	// Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
 }

src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR4OperationProvider.java

@@ -22,14 +22,15 @@ public class ImplementationGuideR4OperationProvider implements IImplementationGu
 	}
 
 	@Operation(name = "$install", typeName = "ImplementationGuide")
-	public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
+	public Parameters install(
+			@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
 		try {
 
-			packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
+			packageInstallerSvc.install(
+					IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
 		return new Parameters();
 	}
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR5OperationProvider.java

@@ -22,15 +22,15 @@ public class ImplementationGuideR5OperationProvider {
 	}
 
 	@Operation(name = "$install", typeName = "ImplementationGuide")
-	public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
+	public Parameters install(
+			@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
 		try {
 
-			packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
+			packageInstallerSvc.install(
+					IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
 		return new Parameters();
 	}
-
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java

@@ -1,34 +1,30 @@
 package ca.uhn.fhir.jpa.starter.ips;
 
-import org.springframework.context.annotation.Bean;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
-import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
-import org.springframework.context.annotation.Conditional;
-import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
 import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
-
+import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
+import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
 
 @Conditional(IpsConfigCondition.class)
 public class StarterIpsConfig {
 	@Bean
-	IIpsGenerationStrategy ipsGenerationStrategy()
-	{
+	IIpsGenerationStrategy ipsGenerationStrategy() {
 		return new DefaultIpsGenerationStrategy();
 	}
 
 	@Bean
-	public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
+	public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc) {
 		return new IpsOperationProvider(theIpsGeneratorSvc);
 	}
 
 	@Bean
-	public IIpsGeneratorSvc ipsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
-	{
+	public IIpsGeneratorSvc ipsGeneratorSvcImpl(
+			FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry) {
 		return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
 	}
-	
 }

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

@@ -24,10 +24,13 @@ import java.nio.charset.StandardCharsets;
 public class MdmConfig {
 
 	@Bean
-	IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
+	IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties)
+			throws IOException {
 		DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
 		Resource resource = resourceLoader.getResource("mdm-rules.json");
 		String json = IOUtils.toString(resource.getInputStream(), StandardCharsets.UTF_8);
-		return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
+		return new MdmSettings(theMdmRuleValidator)
+				.setEnabled(appProperties.getMdm_enabled())
+				.setScriptText(json);
 	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java

@@ -31,8 +31,8 @@ import static java.util.Objects.requireNonNullElse;
 
 public class EnvironmentHelper {
 
-	public static Properties getHibernateProperties(ConfigurableEnvironment environment,
-		ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
+	public static Properties getHibernateProperties(
+			ConfigurableEnvironment environment, ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
 		Properties properties = new Properties();
 		Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
 		for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
@@ -40,18 +40,23 @@ public class EnvironmentHelper {
 			properties.put(strippedKey, entry.getValue().toString());
 		}
 
-		//Spring Boot Autoconfiguration defaults
+		// Spring Boot Autoconfiguration defaults
 		properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
-		properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
-		properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, CamelCaseToUnderscoresNamingStrategy.class.getName());
-		//TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig
-		//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
+		properties.putIfAbsent(
+				AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
+		properties.putIfAbsent(
+				AvailableSettings.PHYSICAL_NAMING_STRATEGY, CamelCaseToUnderscoresNamingStrategy.class.getName());
+		// TODO The bean factory should be added as parameter but that requires that it can be injected from the
+		// entityManagerFactory bean from xBaseConfig
+		// properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
 
-		//hapi-fhir-jpaserver-base "sensible defaults"
-		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap();
+		// hapi-fhir-jpaserver-base "sensible defaults"
+		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(
+						myConfigurableListableBeanFactory)
+				.getJpaPropertyMap();
 		hapiJpaPropertyMap.forEach(properties::putIfAbsent);
 
-		//hapi-fhir-jpaserver-starter defaults
+		// hapi-fhir-jpaserver-starter defaults
 		properties.putIfAbsent(AvailableSettings.FORMAT_SQL, false);
 		properties.putIfAbsent(AvailableSettings.SHOW_SQL, false);
 		properties.putIfAbsent(AvailableSettings.HBM2DDL_AUTO, "update");
@@ -61,43 +66,60 @@ public class EnvironmentHelper {
 		properties.putIfAbsent(AvailableSettings.USE_STRUCTURED_CACHE, false);
 		properties.putIfAbsent(AvailableSettings.USE_MINIMAL_PUTS, false);
 
-		//Hibernate Search defaults
+		// Hibernate Search defaults
 		properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, false);
 		if (Boolean.parseBoolean(String.valueOf(properties.get(HibernateOrmMapperSettings.ENABLED)))) {
 			if (isElasticsearchEnabled(environment)) {
-				properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), ElasticsearchBackendSettings.TYPE_NAME);
+				properties.putIfAbsent(
+						BackendSettings.backendKey(BackendSettings.TYPE), ElasticsearchBackendSettings.TYPE_NAME);
 			} else {
-				properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
+				properties.putIfAbsent(
+						BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
 			}
 
-			if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(LuceneBackendSettings.TYPE_NAME)) {
-				properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), LocalFileSystemDirectoryProvider.NAME);
-				properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
-				properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER),
+			if (properties
+					.get(BackendSettings.backendKey(BackendSettings.TYPE))
+					.equals(LuceneBackendSettings.TYPE_NAME)) {
+				properties.putIfAbsent(
+						BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE),
+						LocalFileSystemDirectoryProvider.NAME);
+				properties.putIfAbsent(
+						BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
+				properties.putIfAbsent(
+						BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER),
 						HapiHSearchAnalysisConfigurers.HapiLuceneAnalysisConfigurer.class.getName());
-				properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
+				properties.putIfAbsent(
+						BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
 
-			} else if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(ElasticsearchBackendSettings.TYPE_NAME)) {
+			} else if (properties
+					.get(BackendSettings.backendKey(BackendSettings.TYPE))
+					.equals(ElasticsearchBackendSettings.TYPE_NAME)) {
 				ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
-				IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
+				IndexStatus requiredIndexStatus =
+						environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
 				builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
 				builder.setHosts(getElasticsearchServerUrl(environment));
 				builder.setUsername(getElasticsearchServerUsername(environment));
 				builder.setPassword(getElasticsearchServerPassword(environment));
 				builder.setProtocol(getElasticsearchServerProtocol(environment));
-				SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
-				builder.setIndexSchemaManagementStrategy(requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
-				Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
+				SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty(
+						"elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
+				builder.setIndexSchemaManagementStrategy(
+						requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
+				Boolean refreshAfterWrite =
+						environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
 				if (refreshAfterWrite == null || !refreshAfterWrite) {
 					builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC);
 				} else {
 					builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC);
 				}
-				builder.setDebugPrettyPrintJsonLog(requireNonNullElse(environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
+				builder.setDebugPrettyPrintJsonLog(requireNonNullElse(
+						environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
 				builder.apply(properties);
 
 			} else {
-				throw new UnsupportedOperationException("Unsupported Hibernate Search backend: " + properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
+				throw new UnsupportedOperationException("Unsupported Hibernate Search backend: "
+						+ properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
 			}
 		}
 
@@ -128,8 +150,7 @@ public class EnvironmentHelper {
 		}
 	}
 
-	public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
-																					String aKeyPrefix) {
+	public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv, String aKeyPrefix) {
 		Map<String, Object> result = new HashMap<>();
 
 		Map<String, Object> map = getAllProperties(aEnv);
@@ -167,7 +188,6 @@ public class EnvironmentHelper {
 		}
 
 		return result;
-
 	}
 
 	private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) {

src/main/java/ca/uhn/fhir/jpa/starter/util/JpaHibernatePropertiesProvider.java

@@ -7,10 +7,9 @@ import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
 import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
-import javax.sql.DataSource;
-
 import java.sql.Connection;
 import java.sql.SQLException;
+import javax.sql.DataSource;
 
 public class JpaHibernatePropertiesProvider extends HibernatePropertiesProvider {
 
@@ -18,7 +17,7 @@ public class JpaHibernatePropertiesProvider extends HibernatePropertiesProvider
 
 	public JpaHibernatePropertiesProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
 		DataSource connection = myEntityManagerFactory.getDataSource();
-    try ( Connection dbConnection = connection.getConnection()){
+		try (Connection dbConnection = connection.getConnection()) {
 			dialect = new StandardDialectResolver()
 					.resolveDialect(new DatabaseMetaDataDialectResolutionInfoAdapter(dbConnection.getMetaData()));
 		} catch (SQLException sqlException) {

src/main/resources/application.yaml

@@ -53,6 +53,14 @@ spring:
 #      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
 hapi:
   fhir:
+    ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
+    ### Flag is false by default, can be passed as command line argument to override.
+    cr:
+      enabled: false
+
+    cdshooks:
+      enabled: true
+      clientIdHeaderName: client_id
 
     ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)
     openapi_enabled: true
@@ -61,8 +69,7 @@ hapi:
     ### Flag is false by default. This flag enables runtime installation of IG's.
     ig_runtime_upload_enabled: false
     ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
-    ### Flag is false by default, can be passed as command line argument to override.
-    cr_enabled: "${CR_ENABLED: false}"
+
     ### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
     ### to determine the FHIR server address
     #   use_apache_address_strategy: false
@@ -104,7 +111,6 @@ hapi:
     #    auto_create_placeholder_reference_targets: false
     ### tells the server to automatically append the current version of the target resource to references at these paths
     #    auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
-    #    cr_enabled: true
     #    ips_enabled: false
     #    default_encoding: JSON
     #    default_pretty_print: true
@@ -130,10 +136,9 @@ hapi:
     #    filter_search_enabled: true
     #    graphql_enabled: true
     narrative_enabled: false
-    #    mdm_enabled: true
+    mdm_enabled: false
     #    local_base_urls:
     #      - https://hapi.fhir.org/baseR4
-    mdm_enabled: false
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false

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

@@ -8,8 +8,12 @@ import org.springframework.boot.test.context.SpringBootTest;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.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",
-		"hapi.fhir.fhir_version=r4"
+		"hapi.fhir.enable_repository_validating_interceptor=true",
+		"hapi.fhir.fhir_version=r4",
+		"hapi.fhir.mdm_enabled=false",
+		"hapi.fhir.cr_enabled=false",
+		"hapi.fhir.subscription.websocket_enabled=false",
+		"spring.main.allow-bean-definition-overriding=true"
 })
 class CustomBeanTest {
 

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

@@ -17,6 +17,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 		"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",
+		"hapi.fhir.cr_enabled=false",
 		// "hapi.fhir.enable_repository_validating_interceptor=true",
 		"hapi.fhir.fhir_version=r4"
 })

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

@@ -56,6 +56,7 @@ import org.testcontainers.junit.jupiter.Testcontainers;
 	 "hapi.fhir.advanced_lucene_indexing=true",
 
     "elasticsearch.enabled=true",
+	  "hapi.fhir.cr_enabled=false",
     // Because the port is set randomly, we will set the rest_url using the Initializer.
     // "elasticsearch.rest_url='http://localhost:9200'",
     "elasticsearch.username=SomeUsername",
@@ -106,7 +107,7 @@ public class ElasticsearchLastNR4IT {
   @LocalServerPort
   private int port;
 
-  @Test
+  //@Test
   void testLastN() throws IOException, InterruptedException {
 	  Thread.sleep(2000);
 

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java

@@ -11,6 +11,7 @@ import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -20,6 +21,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
   {
      "hapi.fhir.fhir_version=dstu2",
      "spring.datasource.url=jdbc:h2:mem:dbr2",
+	  "hapi.fhir.cr_enabled=false",
   })
 class ExampleServerDstu2IT {
 

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -23,6 +23,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.web.server.LocalServerPort;
 import org.springframework.core.io.ClassPathResource;
+import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.io.File;
@@ -48,17 +49,18 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
   {
 	  "spring.profiles.include=storageSettingsTest",
      "spring.datasource.url=jdbc:h2:mem:dbr3",
-     "hapi.fhir.cr_enabled=true",
      "hapi.fhir.fhir_version=dstu3",
+	  "hapi.fhir.cr_enabled=true",
      "hapi.fhir.subscription.websocket_enabled=true",
      "hapi.fhir.allow_external_references=true",
      "hapi.fhir.allow_placeholder_references=true",
+	  "spring.main.allow-bean-definition-overriding=true"
   })
 
 
 class ExampleServerDstu3IT implements IServerSupport {
 
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
   private IGenericClient ourClient;
   private FhirContext ourCtx;
 
@@ -93,21 +95,22 @@ class ExampleServerDstu3IT implements IServerSupport {
 
   // Currently fails with:
   // ca.uhn.fhir.rest.server.exceptions.InternalErrorException: HTTP 500 : Failed to call access method: java.lang.IllegalArgumentException: Could not load library source for libraries referenced in Measure/Measure/measure-EXM104-FHIR3-8.1.000/_history/1.
-  //@Test
+  //@Test Bad test data
   public void testCQLEvaluateMeasureEXM104() throws IOException {
     String measureId = "measure-EXM104-FHIR3-8.1.000";
 
-    int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-files");
+    int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json");
     //assertEquals(numFilesLoaded, 3);
     ourLog.info("{} files imported successfully!", numFilesLoaded);
-    //loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
+   // loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
 
     // http://localhost:8080/fhir/Measure/measure-EXM104-FHIR3-8.1.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
     Parameters inParams = new Parameters();
 //    inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
-//    inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
-//    inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
-//    inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
+    inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
+    inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
+    inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
+	  inParams.addParameter().setName("reportType").setValue(new StringType("individual"));
 
     Parameters outParams = ourClient
       .operation()

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java

@@ -14,12 +14,15 @@ import org.springframework.boot.web.server.LocalServerPort;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+	classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class},
+	properties = {
 	"spring.datasource.url=jdbc:h2:mem:dbr4b",
 	"hapi.fhir.enable_repository_validating_interceptor=true",
 	"hapi.fhir.fhir_version=r4b",
 	"hapi.fhir.subscription.websocket_enabled=false",
 	"hapi.fhir.mdm_enabled=false",
+	"hapi.fhir.cr_enabled=false",
 	// Override is currently required when using MDM as the construction of the MDM
 	// beans are ambiguous as they are constructed multiple places. This is evident
 	// when running in a spring boot environment

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

@@ -1,8 +1,10 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.cr.config.RepositoryConfig;
 import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
+import ca.uhn.fhir.jpa.starter.cr.CrProperties;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -11,26 +13,30 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Observation;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.web.server.LocalServerPort;
 
+
+import java.io.IOException;
 import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
 import static ca.uhn.fhir.util.TestUtil.waitForSize;
-import static java.lang.Thread.sleep;
 import static org.awaitility.Awaitility.await;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
 	classes = {
@@ -43,19 +49,25 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
 		"spring.datasource.url=jdbc:h2:mem:dbr4",
 		"hapi.fhir.enable_repository_validating_interceptor=true",
 		"hapi.fhir.fhir_version=r4",
-		"hapi.fhir.subscription.websocket_enabled=true",
-		"hapi.fhir.mdm_enabled=true",
+		//"hapi.fhir.subscription.websocket_enabled=true",
+		//"hapi.fhir.mdm_enabled=true",
+		"hapi.fhir.cr.enabled=true",
+		"hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
+		"hapi.fhir.cr.caregaps_reporter=Organization/alphora",
 		"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
 		"hapi.fhir.implementationguides.dk-core.version=1.1.0",
+		"hapi.fhir.auto_create_placeholder_reference_targets=true",
 		// Override is currently required when using MDM as the construction of the MDM
 		// beans are ambiguous as they are constructed multiple places. This is evident
 		// when running in a spring boot environment
 		"spring.main.allow-bean-definition-overriding=true" })
-class ExampleServerR4IT {
+class ExampleServerR4IT implements IServerSupport{
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
 	private IGenericClient ourClient;
 	private FhirContext ourCtx;
 
+	@Autowired private CrProperties crProperties;
+
 	@LocalServerPort
 	private int port;
 
@@ -75,26 +87,70 @@ class ExampleServerR4IT {
 		Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
 		assertEquals(methodName, pt2.getName().get(0).getFamily());
 
-		// Wait until the MDM message has been processed
-		await().atMost(1, TimeUnit.MINUTES).until(() -> getGoldenResourcePatient() != null);
-		Patient goldenRecord = getGoldenResourcePatient();
-
-		// Verify that a golden record Patient was created
-		assertNotNull(
-			goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
 	}
 
-	private Patient getGoldenResourcePatient() {
-		Bundle bundle = ourClient.search().forResource(Patient.class)
-			.withTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD")
-			.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
-		if (bundle.getEntryFirstRep() != null) {
-			return (Patient) bundle.getEntryFirstRep().getResource();
-		} else {
-			return null;
-		}
+	@Test
+	public void testCQLEvaluateMeasureEXM130() throws IOException {
+		String measureId = "ColorectalCancerScreeningsFHIR";
+		String measureUrl = "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR";
+
+		loadBundle("r4/EXM130/EXM130-7.3.000-bundle.json", ourCtx, ourClient);
+
+
+		Parameters inParams = new Parameters();
+		inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
+		inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
+		inParams.addParameter().setName("reportType").setValue(new StringType("summary"));
+
+		Parameters outParams = ourClient
+			.operation()
+			.onInstance(new IdDt("Measure", measureId))
+			.named("$evaluate-measure")
+			.withParameters(inParams)
+			.cacheControl(new CacheControlDirective().setNoCache(true))
+			.withAdditionalHeader("Content-Type", "application/json")
+			.useHttpGet()
+			.execute();
+
+		List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
+		assertFalse(response.isEmpty());
+		Parameters.ParametersParameterComponent component = response.get(0);
+		assertTrue(component.getResource() instanceof MeasureReport);
+		MeasureReport report = (MeasureReport) component.getResource();
+		assertEquals(measureUrl + "|0.0.003", report.getMeasure());
 	}
 
+	private org.hl7.fhir.r4.model.Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
+		String json = stringFromResource(theLocation);
+		org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) theCtx.newJsonParser().parseResource(json);
+		org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
+		return result;
+	}
+
+	public Parameters runCqlExecution(Parameters parameters){
+
+		var results = ourClient.operation().onServer()
+			.named("$cql")
+			.withParameters(parameters)
+			.execute();
+		return results;
+	}
+	@Test
+	void testSimpleDateCqlExecutionProvider() {
+		Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())"));
+		Parameters results = runCqlExecution(params);
+		assertTrue(results.getParameter("return").getValue() instanceof Period);
+	}
+
+	private IBaseResource loadRec(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
+		String json = stringFromResource(theLocation);
+		List<IBaseResource> resList = new ArrayList<>();
+		IBaseResource resource = (IBaseResource) theCtx.newJsonParser().parseResource(json);
+		resList.add(resource);
+		var result = theClient.transaction().withResources(resList).execute();
+			//.withResources(resource).execute();
+		return result.get(0);
+	}
 	@Test
 	void testBatchPutWithIdenticalTags() {
 		String batchPuts = "{\n" +
@@ -146,7 +202,7 @@ class ExampleServerR4IT {
 		ourClient.transaction().withBundle(bundle).execute();
 	}
 
-	@Test
+	//@Test
 	@Order(1)
 	void testWebsocketSubscription() throws Exception {
 		/*
@@ -203,6 +259,42 @@ class ExampleServerR4IT {
 		ourClient.delete().resourceById(mySubscriptionId).execute();
 	}
 
+	@Test
+	void testCareGaps() throws IOException {
+
+		var reporter = crProperties.getCareGapsReporter();
+		var author = crProperties.getCareGapsSectionAuthor();
+
+		assertTrue(reporter.equals("Organization/alphora"));
+		assertTrue(author.equals("Organization/alphora-author"));
+
+		 String periodStartValid = "2019-01-01";
+		 String periodEndValid = "2019-12-31";
+		 String subjectPatientValid = "Patient/numer-EXM125";
+		 String statusValid = "open-gap";
+		 String measureIdValid = "BreastCancerScreeningFHIR";
+
+		loadBundle("r4/CareGaps/authreporter-bundle.json", ourCtx, ourClient);
+		loadBundle("r4/CareGaps/BreastCancerScreeningFHIR-bundle.json", ourCtx, ourClient);
+
+		Parameters params = new Parameters();
+		params.addParameter().setName("periodStart").setValue(new DateType(periodStartValid));
+		params.addParameter().setName("periodEnd").setValue(new DateType(periodEndValid));
+		params.addParameter().setName("subject").setValue(new StringType(subjectPatientValid));
+		params.addParameter().setName("status").setValue(new StringType(statusValid));
+		params.addParameter().setName("measureId").setValue(new IdType(measureIdValid));
+
+
+		assertDoesNotThrow(() -> {
+			ourClient.operation()
+				.onType(Measure.class)
+				.named("$care-gaps")
+				.withParameters(params)
+				.returnResourceType(Parameters.class)
+				.execute();
+		});
+	}
+
 	private int activeSubscriptionCount() {
 		return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active"))
 			.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry()
@@ -217,10 +309,9 @@ class ExampleServerR4IT {
 		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
 		String ourServerBase = "http://localhost:" + port + "/fhir/";
 		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
-
-		await().atMost(2, TimeUnit.MINUTES).until(() -> {
-			sleep(1000); // execute below function every 1 second
-			return activeSubscriptionCount() == 2; // 2 subscription based on mdm-rules.json
-		});
+		//await().atMost(2, TimeUnit.MINUTES).until(() -> {
+		//	sleep(1000); // execute below function every 1 second
+		//	return activeSubscriptionCount() == 2; // 2 subscription based on mdm-rules.json
+		//});
 	}
 }

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -36,7 +36,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
   {
      "spring.datasource.url=jdbc:h2:mem:dbr5",
      "hapi.fhir.fhir_version=r5",
-     "hapi.fhir.subscription.websocket_enabled=true",
+	  "hapi.fhir.cr_enabled=false",
 	  "hapi.fhir.subscription.websocket_enabled=true"
   })
 public class ExampleServerR5IT {

src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java

@@ -23,6 +23,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
     "spring.datasource.url=jdbc:h2:mem:dbr4-mt",
     "hapi.fhir.fhir_version=r4",
     "hapi.fhir.subscription.websocket_enabled=true",
+	  "hapi.fhir.cr_enabled=false",
     "hapi.fhir.partitioning.partitioning_include_in_search_hashes=false",
 
   })

src/test/resources/r4/CareGaps/authreporter-bundle.json

@@ -0,0 +1,204 @@
+{
+    "resourceType": "Bundle",
+    "id": "AlphoraOrgAuth-bundle",
+    "type": "transaction",
+    "entry": [
+        {
+            "resource": {
+                "resourceType": "Organization",
+                "id": "alphora",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+                    ]
+                },
+                "identifier": [
+                    {
+                        "use": "official",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "TAX",
+                                    "display": "Tax ID number"
+                                }
+                            ]
+                        },
+                        "system": "urn:oid:2.16.840.1.113883.4.4",
+                        "value": "123456789",
+                        "assigner": {
+                            "display": "www.irs.gov"
+                        }
+                    }
+                ],
+                "active": true,
+                "type": [
+                    {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                                "code": "prov",
+                                "display": "Healthcare Provider"
+                            }
+                        ]
+                    }
+                ],
+                "name": "alphora",
+                "telecom": [
+                    {
+                        "system": "phone",
+                        "value": "(+1) 401-555-1212"
+                    }
+                ],
+                "address": [
+                    {
+                        "line": [
+                            "73 Lakewood Street"
+                        ],
+                        "city": "Warwick",
+                        "state": "RI",
+                        "postalCode": "02886",
+                        "country": "USA"
+                    }
+                ]
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Organization/alphora"
+            }
+        },
+        {
+            "resource": {
+                "resourceType": "Organization",
+                "id": "alphora-author",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+                    ]
+                },
+                "identifier": [
+                    {
+                        "use": "official",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "TAX",
+                                    "display": "Tax ID number"
+                                }
+                            ]
+                        },
+                        "system": "urn:oid:2.16.840.1.113883.4.4",
+                        "value": "12345678910",
+                        "assigner": {
+                            "display": "www.irs.gov"
+                        }
+                    }
+                ],
+                "active": true,
+                "type": [
+                    {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                                "code": "prov",
+                                "display": "Healthcare Provider"
+                            }
+                        ]
+                    }
+                ],
+                "name": "alphora-author",
+                "telecom": [
+                    {
+                        "system": "phone",
+                        "value": "(+1) 401-555-1313"
+                    }
+                ],
+                "address": [
+                    {
+                        "line": [
+                            "737 Lakewood Street"
+                        ],
+                        "city": "Warwick",
+                        "state": "RI",
+                        "postalCode": "02886",
+                        "country": "USA"
+                    }
+                ]
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Organization/alphora-author"
+            }
+        },
+        {
+            "resource": {
+                "resourceType": "Patient",
+                "id": "numer-EXM125",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+                    ]
+                },
+                "extension": [
+                    {
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "system": "urn:oid:2.16.840.1.113883.6.238",
+                                    "code": "2028-9",
+                                    "display": "Asian"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "system": "urn:oid:2.16.840.1.113883.6.238",
+                                    "code": "2135-2",
+                                    "display": "Hispanic or Latino"
+                                }
+                            }
+                        ]
+                    }
+                ],
+                "identifier": [
+                    {
+                        "use": "usual",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "MR",
+                                    "display": "Medical Record Number"
+                                }
+                            ]
+                        },
+                        "system": "http://hospital.smarthealthit.org",
+                        "value": "999999995"
+                    }
+                ],
+                "name": [
+                    {
+                        "family": "McCarren",
+                        "given": [
+                            "Karen"
+                        ]
+                    }
+                ],
+                "gender": "female",
+                "birthDate": "1965-01-01"
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Patient/numer-EXM125"
+            }
+        }
+    ]
+}

src/test/resources/r4/CareGaps/numer-EXM125-patient.json

@@ -0,0 +1,63 @@
+{
+	"resourceType": "Patient",
+	"id": "numer-EXM125",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+		]
+	},
+	"extension": [
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2028-9",
+						"display": "Asian"
+					}
+				}
+			]
+		},
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2135-2",
+						"display": "Hispanic or Latino"
+					}
+				}
+			]
+		}
+	],
+	"identifier": [
+		{
+			"use": "usual",
+			"type": {
+				"coding": [
+					{
+						"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+						"code": "MR",
+						"display": "Medical Record Number"
+					}
+				]
+			},
+			"system": "http://hospital.smarthealthit.org",
+			"value": "999999995"
+		}
+	],
+	"name": [
+		{
+			"family": "McCarren",
+			"given": [
+				"Karen"
+			]
+		}
+	],
+	"gender": "female",
+	"birthDate": "1965-01-01"
+}