Merge remote-tracking branch 'origin/master' into rel_7_3_tracking

.vscode/launch.json

@@ -7,7 +7,18 @@
             "cwd": "${workspaceFolder}",
             "mainClass": "ca.uhn.fhir.jpa.starter.Application",
             "projectName": "hapi-fhir-jpaserver-starter",
-            "args": "",
+            "vmArgs": [
+				"-XX:TieredStopAtLevel=1",
+				// "-Ddebug=true",
+				// "-Dloader.debug=true",
+				"-Dhapi.fhir.bulk_export_enabled=false",
+				"-Dspring.batch.job.enabled=false",
+				"-Dspring.main.allow-bean-definition-overriding=true",
+                "-Dhapi.fhir.cdshooks.enabled=true",
+				"-Dhapi.fhir.cr.enabled=true",
+				"-Dspring.main.allow-bean-definition-overriding=true"
+
+			],
             "envFile": "${workspaceFolder}/.env"
         }
     ]

.vscode/settings.json

@@ -5,5 +5,6 @@
         "**/.settings": true,
         "**/.factorypath": true
     },
-    "java.compile.nullAnalysis.mode": "disabled"
+    "java.compile.nullAnalysis.mode": "disabled",
+    "java.configuration.updateBuildConfiguration": "automatic"
 }

README.md

@@ -483,7 +483,11 @@ The server may be configured with subscription support by enabling properties in
 
 ## Enabling Clinical Reasoning
 
-Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server.
+Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server.  An alternate settings file, [cds.application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/cds.application.yaml), exists with the Clinical Reasoning module enabled and default settings that have been found to work with most CDS and dQM test cases.
+
+## Enabling CDS Hooks
+
+Set `hapi.fhir.cdshooks.enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [CDS Hooks](https://cds-hooks.org/) on this server.  The Clinical Reasoning module must also be enabled because this implementation of CDS Hooks includes [CDS on FHIR](https://build.fhir.org/clinicalreasoning-cds-on-fhir.html).  An example CDS Service using CDS on FHIR is available in the CdsHooksServletIT test class.
 
 ## Enabling MDM (EMPI)
 

pom.xml

@@ -42,6 +42,15 @@
 
     <dependencyManagement>
        <dependencies>
+
+            <!-- Temporarily override CR depedencies for debugging -->
+<!--            <dependency>-->
+<!--                <groupId>org.opencds.cqf.fhir</groupId>-->
+<!--                <artifactId>cqf-fhir-bom</artifactId>-->
+<!--                <version>3.4.0</version>-->
+<!--                <type>pom</type>-->
+<!--                <scope>import</scope>-->
+<!--            </dependency>-->
            <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>jaxb-runtime</artifactId>

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

@@ -3,10 +3,6 @@ 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;
 
@@ -16,8 +12,7 @@ public class ProviderConfiguration {
 	}
 
 	public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
-		this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
-		this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
+		this(crProperties.getCql().getRuntime().isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
 	}
 
 	public String getClientIdHeaderName() {

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

@@ -1,11 +1,21 @@
 package ca.uhn.fhir.jpa.starter.cdshooks;
 
+import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
 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 ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchDaoSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchFhirClientSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsResolutionStrategySvc;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
@@ -16,8 +26,38 @@ import org.springframework.context.annotation.Import;
 
 @Configuration
 @Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
-@Import(CdsHooksConfig.class)
+@Import({CdsHooksConfig.class, CrCommonConfig.class})
 public class StarterCdsHooksConfig {
+
+//	@Bean
+//	CdsPrefetchSvc cdsPrefetchSvc(
+//		CdsResolutionStrategySvc theCdsResolutionStrategySvc,
+//		CdsPrefetchDaoSvc theResourcePrefetchDao,
+//		CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
+//		ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
+//		return new ModuleConfigurationPrefetchSvc(
+//			theCdsResolutionStrategySvc,
+//			theResourcePrefetchDao,
+//			theResourcePrefetchFhirClient,
+//			theCdsHooksDaoAuthorizationSvc);
+//	}
+
+	@Bean
+	public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
+		CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
+		registry.unregister(FhirVersionEnum.R4);
+		registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryServiceR4.class);
+		return registry;
+	}
+
+	@Bean
+	public ICdsCrServiceRegistry cdsCrServiceRegistry() {
+		CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
+		registry.unregister(FhirVersionEnum.R4);
+		registry.register(FhirVersionEnum.R4, UpdatedCdsCrServiceR4.class);
+		return registry;
+	}
+
 	@Bean
 	public CdsHooksProperties cdsHooksProperties() {
 		return new CdsHooksProperties();

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrServiceR4.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.opencds.cqf.fhir.api.Repository;
+
+import java.util.stream.Collectors;
+
+import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
+import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA_ENDPOINT;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
+
+public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
+	public UpdatedCdsCrServiceR4(RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
+		super(theRequestDetails, theRepository, theCdsConfigService);
+	}
+
+	@Override
+	public Parameters encodeParams(CdsServiceRequestJson theJson) {
+		Parameters parameters = super.encodeParams(theJson);
+		if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
+			parameters.addParameter(part("useServerData", new BooleanType(false)));
+		}
+		return parameters;
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryServiceR4.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.opencds.cqf.fhir.api.Repository;
+
+public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
+	public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
+		super(thePlanDefinitionId, theRepository);
+		myMaxUriLength = 6000;
+	}
+}

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

@@ -0,0 +1,22 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+public class CareGapsProperties {
+    private String reporter = "default";
+	private String section_author = "default";
+
+    public String getReporter() {
+        return reporter;
+    }
+
+    public void setReporter(String reporter) {
+        this.reporter = reporter;
+    }
+
+    public String getSection_author() {
+        return section_author;
+    }
+
+    public void setSection_author(String section_author) {
+        this.section_author = section_author;
+    }
+}

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

@@ -0,0 +1,198 @@
+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;
+
+public class CqlCompilerProperties {
+    private Boolean validate_units = true;
+	private Boolean verify_only = false;
+	private String compatibility_level = "1.5";
+	private CqlCompilerException.ErrorSeverity error_level = CqlCompilerException.ErrorSeverity.Info;
+	private LibraryBuilder.SignatureLevel signature_level = LibraryBuilder.SignatureLevel.All;
+	private Boolean analyze_data_requirements = false;
+	private Boolean collapse_data_requirements = false;
+	private CqlTranslator.Format translator_format = CqlTranslator.Format.JSON;
+	private Boolean enable_date_range_optimization = true;
+	private Boolean enable_annotations = true;
+	private Boolean enable_locators = true;
+	private Boolean enable_results_type = true;
+	private Boolean enable_detailed_errors = true;
+	private Boolean disable_list_traversal = false;
+	private Boolean disable_list_demotion = false;
+	private Boolean disable_list_promotion = false;
+	private Boolean enable_interval_demotion = false;
+	private Boolean enable_interval_promotion = false;
+	private Boolean disable_method_invocation = false;
+	private Boolean require_from_keyword = false;
+	private Boolean disable_default_model_info_load = false;
+
+
+	public boolean isValidateUnits() {
+		return validate_units;
+	}
+
+	public void setValidateUnits(boolean validateUnits) {
+		this.validate_units = validateUnits;
+	}
+
+	public boolean isVerifyOnly() {
+		return verify_only;
+	}
+
+	public void setVerifyOnly(boolean verifyOnly) {
+		this.verify_only = verifyOnly;
+	}
+
+	public String getCompatibilityLevel() {
+		return compatibility_level;
+	}
+
+	public void setCompatibilityLevel(String compatibilityLevel) {
+		this.compatibility_level = compatibilityLevel;
+	}
+
+	public CqlCompilerException.ErrorSeverity getErrorSeverityLevel() {
+		return error_level;
+	}
+
+	public void setErrorSeverityLevel(CqlCompilerException.ErrorSeverity errorSeverityLevel) {
+		this.error_level = errorSeverityLevel;
+	}
+
+	public LibraryBuilder.SignatureLevel getSignatureLevel() {
+		return signature_level;
+	}
+
+	public void setSignatureLevel(LibraryBuilder.SignatureLevel signatureLevel) {
+		this.signature_level = signatureLevel;
+	}
+
+	public boolean isAnalyzeDataRequirements() {
+		return analyze_data_requirements;
+	}
+
+	public void setAnalyzeDataRequirements(boolean analyzeDataRequirements) {
+		this.analyze_data_requirements = analyzeDataRequirements;
+	}
+
+	public boolean isCollapseDataRequirements() {
+		return collapse_data_requirements;
+	}
+
+	public void setCollapseDataRequirements(boolean collapseDataRequirements) {
+		this.collapse_data_requirements = collapseDataRequirements;
+	}
+
+	public boolean isEnableDateRangeOptimization() {
+		return enable_date_range_optimization;
+	}
+
+	public void setEnableDateRangeOptimization(boolean enableDateRangeOptimization) {
+		this.enable_date_range_optimization = enableDateRangeOptimization;
+	}
+
+	public boolean isEnableAnnotations() {
+		return enable_annotations;
+	}
+
+	public void setEnableAnnotations(boolean enableAnnotations) {
+		this.enable_annotations = enableAnnotations;
+	}
+
+	public boolean isEnableLocators() {
+		return enable_locators;
+	}
+
+	public void setEnableLocators(boolean enableLocators) {
+		this.enable_locators = enableLocators;
+	}
+
+	public boolean isEnableResultsType() {
+		return enable_results_type;
+	}
+
+	public void setEnableResultsType(boolean enableResultsType) {
+		this.enable_results_type = enableResultsType;
+	}
+
+	public boolean isEnableDetailedErrors() {
+		return enable_detailed_errors;
+	}
+
+	public void setEnableDetailedErrors(boolean enableDetailedErrors) {
+		this.enable_detailed_errors = enableDetailedErrors;
+	}
+
+	public boolean isDisableListTraversal() {
+		return disable_list_traversal;
+	}
+
+	public void setDisableListTraversal(boolean disableListTraversal) {
+		this.disable_list_traversal = disableListTraversal;
+	}
+
+	public boolean isDisableListDemotion() {
+		return disable_list_demotion;
+	}
+
+	public void setDisableListDemotion(boolean disableListDemotion) {
+		this.disable_list_demotion = disableListDemotion;
+	}
+
+	public boolean isDisableListPromotion() {
+		return disable_list_promotion;
+	}
+
+	public void setDisableListPromotion(boolean disableListPromotion) {
+		this.disable_list_promotion = disableListPromotion;
+	}
+
+	public boolean isEnableIntervalPromotion() {
+		return enable_interval_promotion;
+	}
+
+	public void setEnableIntervalPromotion(boolean enableIntervalPromotion) {
+		this.enable_interval_promotion = enableIntervalPromotion;
+	}
+
+	public boolean isEnableIntervalDemotion() {
+		return enable_interval_demotion;
+	}
+
+	public void setEnableIntervalDemotion(boolean enableIntervalDemotion) {
+		this.enable_interval_demotion = enableIntervalDemotion;
+	}
+
+	public boolean isDisableMethodInvocation() {
+		return disable_method_invocation;
+	}
+
+	public void setDisableMethodInvocation(boolean disableMethodInvocation) {
+		this.disable_method_invocation = disableMethodInvocation;
+	}
+
+	public boolean isRequireFromKeyword() {
+		return require_from_keyword;
+	}
+
+	public void setRequireFromKeyword(boolean requireFromKeyword) {
+		this.require_from_keyword = requireFromKeyword;
+	}
+
+	public boolean isDisableDefaultModelInfoLoad() {
+		return disable_default_model_info_load;
+	}
+
+	public void setDisableDefaultModelInfoLoad(boolean disableDefaultModelInfoLoad) {
+		this.disable_default_model_info_load = disableDefaultModelInfoLoad;
+	}
+
+	public CqlTranslator.Format getTranslatorFormat() {
+		return translator_format;
+	}
+
+	public void setTranslatorFormat(CqlTranslator.Format translatorFormat) {
+		this.translator_format = translatorFormat;
+	}  
+}

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

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
+import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
+
+public class CqlProperties {
+
+    private Boolean use_embedded_libraries = true;
+    private CqlCompilerProperties compiler = new CqlCompilerProperties();
+    private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
+    private TerminologySettings terminology = new TerminologySettings();
+    private RetrieveSettings data = new RetrieveSettings();
+    
+    public Boolean getUse_embedded_libraries() {
+        return use_embedded_libraries;
+    }
+
+    public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
+        this.use_embedded_libraries = use_embedded_libraries;
+    }
+
+    public CqlCompilerProperties getCompiler() {
+        return compiler;
+    }
+
+    public void setCompiler(CqlCompilerProperties compiler) {
+        this.compiler = compiler;
+    }
+
+    public CqlRuntimeProperties getRuntime() {
+        return runtime;
+    }
+    
+    public void setRuntime(CqlRuntimeProperties runtime) {
+        this.runtime = runtime;
+    }
+
+    public TerminologySettings getTerminology() {
+        return terminology;
+    }
+
+    public void setTerminology(TerminologySettings terminology) {
+        this.terminology = terminology;
+    }
+
+    public RetrieveSettings getData() {
+        return data;
+    }
+
+    public void setData(RetrieveSettings data) {
+        this.data = data;
+    }
+}

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

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+public class CqlRuntimeProperties {
+
+    private Boolean debug_logging_enabled = false;
+	private Boolean enable_validation = false;
+	private Boolean enable_expression_caching = true;
+
+	public boolean isDebugLoggingEnabled() {
+		return debug_logging_enabled;
+	}
+
+	public void setDebugLoggingEnabled(boolean debug_logging_enabled) {
+		this.debug_logging_enabled = debug_logging_enabled;
+	}
+
+
+	public boolean isEnableExpressionCaching() {
+		return enable_expression_caching;
+	}
+
+	public void setEnableExpressionCaching(boolean enable_expression_caching) {
+		this.enable_expression_caching = enable_expression_caching;
+	}
+
+	public boolean isEnableValidation() {
+		return enable_validation;
+	}
+
+	public void EnableValidation(boolean enable_validation) {
+		this.enable_validation = enable_validation;
+	}
+
+    
+}

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

@@ -0,0 +1,228 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+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;
+
+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.cql.engine.retrieve.RetrieveSettings;
+import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
+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.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+import org.springframework.security.concurrent.DelegatingSecurityContextExecutorService;
+
+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.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.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+
+@Configuration
+@Conditional({CrConfigCondition.class})
+public class CrCommonConfig {
+
+	@Bean
+	@ConfigurationProperties(prefix = "hapi.fhir.cr")
+	CrProperties crProperties() {
+		return new CrProperties();
+	}
+
+	@Bean
+	RetrieveSettings retrieveSettings(CrProperties theCrProperties) {
+		return theCrProperties.getCql().getData();
+	}
+
+	@Bean
+	TerminologySettings terminologySettings(CrProperties theCrProperties) {
+		return theCrProperties.getCql().getTerminology();
+	}
+
+	@Bean
+	public EvaluationSettings evaluationSettings(
+			CrProperties theCrProperties,
+			RetrieveSettings theRetrieveSettings,
+			TerminologySettings theTerminologySettings,
+			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);
+		var cqlRuntimeProperties = theCrProperties.getCql().getRuntime();
+		if (cqlRuntimeProperties.isEnableExpressionCaching()) {
+			options.add(CqlEngine.Options.EnableExpressionCaching);
+		}
+		if (cqlRuntimeProperties.isEnableValidation()) {
+			options.add(CqlEngine.Options.EnableValidation);
+		}
+		cqlEngineOptions.setOptions(options);
+		if (cqlRuntimeProperties.isDebugLoggingEnabled()) {
+			cqlEngineOptions.setDebugLoggingEnabled(true);
+		}
+		cqlOptions.setCqlEngineOptions(cqlEngineOptions);
+
+		var cqlCompilerOptions = new CqlCompilerOptions();
+
+		var cqlCompilerProperties = theCrProperties.getCql().getCompiler();
+
+		if (cqlCompilerProperties.isEnableDateRangeOptimization()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
+		}
+		if (cqlCompilerProperties.isEnableAnnotations()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
+		}
+		if (cqlCompilerProperties.isEnableLocators()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
+		}
+		if (cqlCompilerProperties.isEnableResultsType()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
+		}
+		cqlCompilerOptions.setVerifyOnly(cqlCompilerProperties.isVerifyOnly());
+		if (cqlCompilerProperties.isEnableDetailedErrors()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
+		}
+		cqlCompilerOptions.setErrorLevel(cqlCompilerProperties.getErrorSeverityLevel());
+		if (cqlCompilerProperties.isDisableListTraversal()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
+		}
+		if (cqlCompilerProperties.isDisableListDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
+		}
+		if (cqlCompilerProperties.isDisableListPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
+		}
+		if (cqlCompilerProperties.isEnableIntervalDemotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
+		}
+		if (cqlCompilerProperties.isEnableIntervalPromotion()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
+		}
+		if (cqlCompilerProperties.isDisableMethodInvocation()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
+		}
+		if (cqlCompilerProperties.isRequireFromKeyword()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
+		}
+		cqlCompilerOptions.setValidateUnits(cqlCompilerProperties.isValidateUnits());
+		if (cqlCompilerProperties.isDisableDefaultModelInfoLoad()) {
+			cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
+		}
+		cqlCompilerOptions.setSignatureLevel(cqlCompilerProperties.getSignatureLevel());
+		cqlCompilerOptions.setCompatibilityLevel(cqlCompilerProperties.getCompatibilityLevel());
+		cqlCompilerOptions.setAnalyzeDataRequirements(cqlCompilerProperties.isAnalyzeDataRequirements());
+		cqlCompilerOptions.setCollapseDataRequirements(cqlCompilerProperties.isCollapseDataRequirements());
+
+		cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
+		evaluationSettings.setLibraryCache(theGlobalLibraryCache);
+		evaluationSettings.setModelCache(theGlobalModelCache);
+		evaluationSettings.setValueSetCache(theGlobalValueSetCache);
+		evaluationSettings.setRetrieveSettings(theRetrieveSettings);
+		evaluationSettings.setTerminologySettings(theTerminologySettings);
+		return evaluationSettings;
+	}
+
+	@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.setCareGapsReporter(theCrProperties.getCareGaps().getReporter());
+		careGapsProperties.setCareGapsCompositionSectionAuthor(theCrProperties.getCareGaps().getSection_author());
+		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 PostInitProviderRegisterer postInitProviderRegisterer(
+			RestfulServer theRestfulServer, ResourceProviderFactory theResourceProviderFactory) {
+		return new PostInitProviderRegisterer(theRestfulServer, theResourceProviderFactory);
+	}
+
+	@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/CrProperties.java

@@ -3,40 +3,12 @@ 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";
+
+	private CareGapsProperties careGaps = new CareGapsProperties();
+	private CqlProperties cql = new CqlProperties();
 
 	public Boolean getEnabled() {
 		return enabled;
@@ -46,219 +18,19 @@ public class CrProperties {
 		this.enabled = enabled;
 	}
 
-	public boolean isCqlUseEmbeddedLibraries() {
-		return cql_use_embedded_libraries;
+	public CareGapsProperties getCareGaps() {
+		return careGaps;
 	}
 
-	public void setCqlUseEmbeddedLibraries(boolean cql_use_embedded_libraries) {
-		this.cql_use_embedded_libraries = cql_use_embedded_libraries;
+	public void setCareGaps(CareGapsProperties careGaps) {
+		this.careGaps = careGaps;
 	}
 
-	public boolean isCqlRuntimeDebugLoggingEnabled() {
-		return cql_runtime_debug_logging_enabled;
+	public CqlProperties getCql() {
+		return cql;
 	}
 
-	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;
+	public void setCql(CqlProperties cql) {
+		this.cql = cql;
 	}
 }

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

@@ -1,195 +1,25 @@
 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.cr.config.dstu3.QuestionnaireOperationConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
-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({
-	// BaseCrConfig.class,
+	CrCommonConfig.class,
 	CrDstu3Config.class,
 	ApplyOperationConfig.class,
 	ExtractOperationConfig.class,
 	PackageOperationConfig.class,
-	PopulateOperationConfig.class
+	PopulateOperationConfig.class,
+	QuestionnaireOperationConfig.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

@@ -1,220 +1,27 @@
 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.cr.config.r4.QuestionnaireOperationConfig;
 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({
+	CrCommonConfig.class,
 	CrR4Config.class,
 	ApplyOperationConfig.class,
 	ExtractOperationConfig.class,
 	PackageOperationConfig.class,
-	PopulateOperationConfig.class
+	PopulateOperationConfig.class,
+	QuestionnaireOperationConfig.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.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/ips/StarterIpsConfig.java

@@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
 import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
 import ca.uhn.fhir.jpa.ips.jpa.DefaultJpaIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
-
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Conditional;
 

src/main/resources/application.yaml

@@ -29,7 +29,6 @@ management:
 spring:
   main:
     allow-circular-references: true
-    #allow-bean-definition-overriding: true
   flyway:
     enabled: false
     baselineOnMigrate: true
@@ -78,9 +77,50 @@ hapi:
     ### Flag is false by default, can be passed as command line argument to override.
     cr:
       enabled: false
+      caregaps:
+        reporter: "default"
+        section_author: "default"
+      cql:
+        use_embedded_libraries: true
+        compiler:
+          ### These are low-level compiler options.
+          ### They are not typically needed by most users.
+          # validate_units: true
+          # verify_only: false
+          # compatibility_level: "1.5"
+          error_level: Info
+          signature_level: All
+          # analyze_data_requirements: false
+          # collapse_data_requirements: false
+          # translator_format: JSON
+          # enable_date_range_optimization: true
+          enable_annotations: true
+          enable_locators: true
+          enable_results_type: true
+          enable_detailed_errors: true
+          # disable_list_traversal: false
+          # disable_list_demotion: false
+          # enable_interval_demotion: false
+          # enable_interval_promotion: false
+          # disable_method_invocation: false
+          # require_from_keyword: false
+          # disable_default_model_info_load: false
+        runtime:
+          debug_logging_enabled: false
+          # enable_validation: false
+          # enable_expression_caching: true
+        terminology:
+          valueset_preexpansion_mode: REQUIRE # USE_IF_PRESENT, REQUIRE, IGNORE
+          valueset_expansion_mode: PERFORM_NAIVE_EXPANSION # AUTO, USE_EXPANSION_OPERATION, PERFORM_NAIVE_EXPANSION
+          valueset_membership_mode: USE_EXPANSION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_EXPANSION
+          code_lookup_mode: USE_VALIDATE_CODE_OPERATION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_CODESYSTEM_URL
+        data:
+          search_parameter_mode: FILTER_IN_MEMORY # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
+          terminology_parameter_mode: FILTER_IN_MEMORY #  AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY
+          profile_mode: DECLARED # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
 
     cdshooks:
-      enabled: true
+      enabled: false
       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)

src/main/resources/cds.application.yaml

@@ -0,0 +1,294 @@
+#Uncomment the "servlet" and "context-path" lines below to make the fhir endpoint available at /example/path/fhir instead of the default value of /fhir
+server:
+#  servlet:
+#    context-path: /example/path
+  port: 8080
+#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
+#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
+management:
+  endpoints:
+    web:
+      exposure:
+        include: "health,prometheus"
+spring:
+  main:
+    allow-circular-references: true
+    allow-bean-definition-overriding: true
+  flyway:
+    enabled: false
+    baselineOnMigrate: true
+    fail-on-missing-locations: false
+  datasource:
+    #url: 'jdbc:h2:file:./target/database/h2'
+    url: jdbc:h2:mem:test_mem
+    username: sa
+    password: null
+    driverClassName: org.h2.Driver
+    max-active: 15
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
+  jpa:
+    properties:
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+
+      #Hibernate dialect is automatically detected except Postgres and H2.
+      #If using H2, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
+      #If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
+  #      hibernate.hbm2ddl.auto: update
+  #      hibernate.jdbc.batch_size: 20
+  #      hibernate.cache.use_query_cache: false
+  #      hibernate.cache.use_second_level_cache: false
+  #      hibernate.cache.use_structured_entries: false
+  #      hibernate.cache.use_minimal_puts: false
+
+  ###    These settings will enable fulltext search with lucene or elastic
+      hibernate.search.enabled: true
+  ### lucene parameters
+#      hibernate.search.backend.type: lucene
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
+#      hibernate.search.backend.directory.type: local-filesystem
+#      hibernate.search.backend.directory.root: target/lucenefiles
+#      hibernate.search.backend.lucene_version: lucene_current
+  ### elastic parameters ===> see also elasticsearch section below <===
+#      hibernate.search.backend.type: elasticsearch
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$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: true
+      caregaps:
+        reporter: "default"
+        section_author: "default"
+      cql:
+        use_embedded_libraries: true
+        compiler:
+          ### These are low-level compiler options.
+          ### They are not typically needed by most users.
+          # validate_units: true
+          # verify_only: false
+          # compatibility_level: "1.5"
+          error_level: Info
+          signature_level: All
+          # analyze_data_requirements: false
+          # collapse_data_requirements: false
+          # translator_format: JSON
+          # enable_date_range_optimization: true
+          enable_annotations: true
+          enable_locators: true
+          enable_results_type: true
+          enable_detailed_errors: true
+          # disable_list_traversal: false
+          # disable_list_demotion: false
+          # enable_interval_demotion: false
+          # enable_interval_promotion: false
+          # disable_method_invocation: false
+          # require_from_keyword: false
+          # disable_default_model_info_load: false
+        runtime:
+          debug_logging_enabled: false
+          # enable_validation: false
+          # enable_expression_caching: true
+        terminology:
+          valueset_preexpansion_mode: REQUIRE # USE_IF_PRESENT, REQUIRE, IGNORE
+          valueset_expansion_mode: PERFORM_NAIVE_EXPANSION # AUTO, USE_EXPANSION_OPERATION, PERFORM_NAIVE_EXPANSION
+          valueset_membership_mode: USE_EXPANSION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_EXPANSION
+          code_lookup_mode: USE_CODESYSTEM_URL # AUTO, USE_VALIDATE_CODE_OPERATION, USE_CODESYSTEM_URL
+        data:
+          search_parameter_mode: USE_SEARCH_PARAMETERS # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
+          terminology_parameter_mode: FILTER_IN_MEMORY #  AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY
+          profile_mode: OFF # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
+
+    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
+    ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
+    fhir_version: R4
+    ### 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.
+
+    ### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
+    ### to determine the FHIR server address
+    #   use_apache_address_strategy: false
+    ### forces the use of the https:// protocol for the returned server address.
+    ### alternatively, it may be set using the X-Forwarded-Proto header.
+    #   use_apache_address_strategy_https: false
+    ### enables the server to overwrite defaults on HTML, css, etc. under the url pattern of eg. /content/custom **
+    ### Folder with custom content MUST be named custom. If omitted then default content applies
+    #custom_content_path: ./custom
+    ### enables the server host custom content. If e.g. the value ./configs/app is supplied then the content
+    ### will be served under /web/app
+    #app_content_path: ./configs/app
+    ### enable to set the Server URL
+    #    server_address: http://hapi.fhir.org/baseR4
+    #    defer_indexing_for_codesystems_of_size: 101
+    #    install_transitive_ig_dependencies: true
+    #implementationguides:
+    ###    example from registry (packages.fhir.org)
+    #  swiss:
+    #    name: swiss.mednet.fhir
+    #    version: 0.8.0
+    #    reloadExisting: false
+    #    installMode: STORE_AND_INSTALL
+    #      example not from registry
+    #      ips_1_0_0:
+    #        packageUrl: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
+    #        name: hl7.fhir.uv.ips
+    #        version: 1.0.0
+    #    supported_resource_types:
+    #      - Patient
+    #      - Observation
+    ##################################################
+    # Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
+    ##################################################
+    #    allowed_bundle_types: COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
+    #    allow_cascading_deletes: true
+    #    allow_contains_searches: true
+    #    allow_external_references: true
+    #    allow_multiple_delete: true
+    #    allow_override_default_search_params: true
+    #    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
+    #    ips_enabled: false
+    #    default_encoding: JSON
+    #    default_pretty_print: true
+    #    default_page_size: 20
+    #    delete_expunge_enabled: true
+    #    enable_repository_validating_interceptor: true
+    #    enable_index_missing_fields: false
+    #    enable_index_of_type: true
+    #    enable_index_contained_resource: false
+    #    resource_dbhistory_enabled: false
+    ###  !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
+    ###  more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
+    advanced_lucene_indexing: false
+    bulk_export_enabled: false
+    bulk_import_enabled: false
+    #    language_search_parameter_enabled: true
+    #    enforce_referential_integrity_on_delete: false
+    # This is an experimental feature, and does not fully support _total and other FHIR features.
+    #    enforce_referential_integrity_on_delete: false
+    #    enforce_referential_integrity_on_write: false
+    #    etag_support_enabled: true
+    #    expunge_enabled: true
+    #    client_id_strategy: ALPHANUMERIC
+    #    server_id_strategy: SEQUENTIAL_NUMERIC
+    #    fhirpath_interceptor_enabled: false
+    #    filter_search_enabled: true
+    #    graphql_enabled: true
+    narrative_enabled: false
+    mdm_enabled: false
+    mdm_rules_json_location: "mdm-rules.json"
+    #    local_base_urls:
+    #      - https://hapi.fhir.org/baseR4
+    logical_urls:
+      - http://terminology.hl7.org/*
+      - https://terminology.hl7.org/*
+      - http://snomed.info/*
+      - https://snomed.info/*
+      - http://unitsofmeasure.org/*
+      - https://unitsofmeasure.org/*
+      - http://loinc.org/*
+      - https://loinc.org/*
+    #    partitioning:
+    #      allow_references_across_partitions: false
+    #      partitioning_include_in_search_hashes: false
+    cors:
+      allow_Credentials: true
+      # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
+      allowed_origin:
+        - '*'
+
+    # Search coordinator thread pool sizes
+    search-coord-core-pool-size: 20
+    search-coord-max-pool-size: 100
+    search-coord-queue-capacity: 200
+    
+    # comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans
+    #custom-bean-packages:
+    
+    # comma-separated list of fully qualified interceptor classes. 
+    # classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages', 
+    # or will be instantiated via reflection using an no-arg contructor; then registered with the server  
+    #custom-interceptor-classes:  
+
+    # comma-separated list of fully qualified provider classes. 
+    # classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages', 
+    # or will be instantiated via reflection using an no-arg contructor; then registered with the server  
+    #custom-provider-classes:  
+    
+    # Threadpool size for BATCH'ed GETs in a bundle.
+    #    bundle_batch_pool_size: 10
+    #    bundle_batch_pool_max_size: 50
+
+    #    logger:
+    #      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
+    #      format: >-
+    #        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
+    #        Operation[${operationType} ${operationName} ${idOrResourceName}]
+    #        UA[${requestHeader.user-agent}] Params[${requestParameters}]
+    #        ResponseEncoding[${responseEncodingNoDefault}]
+    #      log_exceptions: true
+    #      name: fhirtest.access
+    #    max_binary_size: 104857600
+    #    max_page_size: 200
+    #    retain_cached_searches_mins: 60
+    #    reuse_cached_search_results_millis: 60000
+    tester:
+      home:
+        name: Local Tester
+        server_address: 'http://localhost:8080/fhir'
+        refuse_to_fetch_third_party_urls: false
+        fhir_version: R4
+      global:
+        name: Global Tester
+        server_address: "http://hapi.fhir.org/baseR4"
+        refuse_to_fetch_third_party_urls: false
+        fhir_version: R4
+    #    validation:
+    #      requests_enabled: true
+    #      responses_enabled: true
+    #    binary_storage_enabled: true
+    inline_resource_storage_below_size: 4000
+#    bulk_export_enabled: true
+#    subscription:
+#      resthook_enabled: true
+#      websocket_enabled: false
+#      email:
+#        from: some@test.com
+#        host: google.com
+#        port:
+#        username:
+#        password:
+#        auth:
+#        startTlsEnable:
+#        startTlsRequired:
+#        quitWait:
+#    lastn_enabled: true
+#    store_resource_in_lucene_index_enabled: true
+###  This is configuration for normalized quantity search level default is 0
+###   0: NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED - default
+###   1: NORMALIZED_QUANTITY_STORAGE_SUPPORTED
+###   2: NORMALIZED_QUANTITY_SEARCH_SUPPORTED
+#    normalized_quantity_search_level: 2
+#elasticsearch:
+#  debug:
+#    pretty_print_json_log: false
+#    refresh_after_write: false
+#  enabled: false
+#  password: SomePassword
+#  required_index_status: YELLOW
+#  rest_url: 'localhost:9200'
+#  protocol: 'http'
+#  schema_management_strategy: CREATE
+#  username: SomeUsername

src/main/resources/logback.xml

@@ -1,23 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <configuration scan="true" scanPeriod="30 seconds">
-
-	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
-			<level>INFO</level>
-		</filter>
-		<encoder>
-			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
-		</encoder>
-	</appender>
-
-	<logger name="org.springframework.beans" level="INFO">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.springframework.core" level="INFO">
-		<appender-ref ref="STDOUT" />
-	</logger>
-
+	<include resource="org/springframework/boot/logging/logback/defaults.xml"/>
+	<include resource="org/springframework/boot/logging/logback/console-appender.xml" />
 	<root level="INFO">
-		<appender-ref ref="STDOUT" />
+		<appender-ref ref="CONSOLE" />
 	</root>
-
+	<logger name = "org.opencds.cqf.cql.engine.debug" level="DEBUG"/>
 </configuration>

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

@@ -0,0 +1,242 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.config.RepositoryConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
+import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.util.EntityUtils;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.web.server.LocalServerPort;
+
+import java.io.IOException;
+import java.util.concurrent.TimeUnit;
+
+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.fail;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+	classes = {
+		Application.class,
+		NicknameServiceConfig.class,
+		RepositoryConfig.class,
+		CdsHooksConfig.class,
+		StarterCdsHooksConfig.class
+	}, properties = {
+	"spring.profiles.include=storageSettingsTest",
+	"spring.datasource.url=jdbc:h2:mem:dbr4",
+	"hapi.fhir.enable_repository_validating_interceptor=true",
+	"hapi.fhir.fhir_version=r4",
+	"hapi.fhir.cr.enabled=true",
+	"hapi.fhir.cr.caregaps.section_author=Organization/alphora-author",
+	"hapi.fhir.cr.caregaps.reporter=Organization/alphora",
+	"hapi.fhir.cdshooks.enabled=true",
+	"spring.main.allow-bean-definition-overriding=true"})
+class CdsHooksServletIT implements IServerSupport {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CdsHooksServletIT.class);
+	private final FhirContext ourCtx = FhirContext.forR4Cached();
+	private final IParser ourParser = ourCtx.newJsonParser();
+	private IGenericClient ourClient;
+	private String ourCdsBase;
+
+	@Autowired
+	DaoRegistry myDaoRegistry;
+
+	@Autowired
+	ICdsServiceRegistry myCdsServiceRegistry;
+
+	@LocalServerPort
+	private int port;
+
+	private String ourServerBase;
+
+	@BeforeEach
+	void beforeEach() {
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+		ourServerBase = "http://localhost:" + port + "/fhir/";
+		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+		ourCdsBase = "http://localhost:" + port + "/cds-services";
+
+		var cdsServicesJson = myCdsServiceRegistry.getCdsServicesJson();
+		if (cdsServicesJson != null && cdsServicesJson.getServices() != null && !cdsServicesJson.getServices().isEmpty()) {
+			var services = cdsServicesJson.getServices();
+			for (int i = 0; i < services.size(); i++) {
+				myCdsServiceRegistry.unregisterService(services.get(i).getId(), "CR");
+			}
+		}
+	}
+
+	private Boolean hasCdsServices() throws IOException {
+		var response = callCdsServicesDiscovery();
+		return response.getEntity().getContentLength() > 21 || response.getEntity().isChunked();
+	}
+
+	private CloseableHttpResponse callCdsServicesDiscovery() {
+		try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+			HttpGet request = new HttpGet(ourCdsBase);
+			request.addHeader("Content-Type", "application/json");
+			return httpClient.execute(request);
+		} catch (IOException ioe) {
+			fail(ioe.getMessage());
+			return null;
+		}
+	}
+
+	@Test
+	void testGetCdsServices() {
+		var response = callCdsServicesDiscovery();
+		assertEquals(200, response.getStatusLine().getStatusCode());
+	}
+
+	@Test
+	void testCdsHooks() throws IOException, InterruptedException {
+		loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
+		await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
+		var cdsRequest = "{\n" +
+			"  \"hookInstance\": \"12345\",\n" +
+			"  \"hook\": \"patient-view\",\n" +
+			"  \"context\": {\n" +
+			"    \"userId\": \"Practitioner/example\",\n" +
+			"    \"patientId\": \"Patient/example-hello-world\"\n" +
+			"  },\n" +
+			"  \"prefetch\": {\n" +
+			"    \"item1\": {\n" +
+			"      \"resourceType\": \"Patient\",\n" +
+			"      \"id\": \"example-hello-world\",\n" +
+			"      \"gender\": \"male\",\n" +
+			"      \"birthDate\": \"2000-01-01\"\n" +
+			"    }\n" +
+			"  }\n" +
+			"}";
+		try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+			HttpPost request = new HttpPost(ourCdsBase + "/hello-world");
+			request.setEntity(new StringEntity(cdsRequest));
+			request.addHeader("Content-Type", "application/json");
+
+			CloseableHttpResponse httpResponse = httpClient.execute(request);
+			String result = EntityUtils.toString(httpResponse.getEntity());
+			Gson gsonResponse = new Gson();
+			JsonObject response = gsonResponse.fromJson(result, JsonObject.class);
+			assertNotNull(response);
+			JsonArray cards = response.getAsJsonArray("cards");
+			assertEquals(1, cards.size());
+			assertEquals("\"Hello World!\"", cards.get(0).getAsJsonObject().get("summary").toString());
+		} catch (IOException ioe) {
+			fail(ioe.getMessage());
+		}
+	}
+
+	@Test
+	void testRec10() throws IOException {
+		loadBundle("r4/opioidcds-10-order-sign-bundle.json", ourCtx, ourClient);
+		await().atMost(20000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
+		var fhirServer = "  \"fhirServer\": " + "\"" + ourServerBase + "\"" + ",\n";
+		var cdsRequest = "{\n" +
+			"  \"hookInstance\": \"055b009c-4a7d-4db4-a35e-0e5198918ed1\",\n" +
+			"  \"hook\": \"order-sign\",\n" +
+			fhirServer +
+			"  \"context\": {\n" +
+			"    \"patientId\": \"example-rec-10-order-sign-illicit-POS-Cocaine-drugs\",\n" +
+			"    \"userId\": \"COREPRACTITIONER1\",\n" +
+			"    \"draftOrders\": {\n" +
+			"      \"resourceType\": \"Bundle\",\n" +
+			"      \"entry\": [\n" +
+			"        {\n" +
+			"          \"resource\": {\n" +
+			"            \"resourceType\": \"MedicationRequest\",\n" +
+			"            \"id\": \"request-123\",\n" +
+			"            \"status\": \"draft\",\n" +
+			"            \"subject\": {\n" +
+			"              \"reference\": \"Patient/example-rec-10-order-sign-illicit-POS-Cocaine-drugs\"\n" +
+			"            },\n" +
+			"            \"authoredOn\": \"2024-03-27\",\n" +
+			"            \"dosageInstruction\": [\n" +
+			"              {\n" +
+			"                \"timing\": {\n" +
+			"                  \"repeat\": {\n" +
+			"                    \"frequency\": 1,\n" +
+			"                    \"period\": 1,\n" +
+			"                    \"periodUnit\": \"d\"\n" +
+			"                  }\n" +
+			"                },\n" +
+			"                \"doseAndRate\": [\n" +
+			"                  {\n" +
+			"                    \"doseQuantity\": {\n" +
+			"                      \"value\": 1,\n" +
+			"                      \"system\": \"http://unitsofmeasure.org\",\n" +
+			"                      \"code\": \"{pill}\"\n" +
+			"                    }\n" +
+			"                  }\n" +
+			"                ]\n" +
+			"              }\n" +
+			"            ],\n" +
+			"            \"dispenseRequest\": {\n" +
+			"              \"expectedSupplyDuration\": {\n" +
+			"                \"value\": 90,\n" +
+			"                \"unit\": \"days\",\n" +
+			"                \"system\": \"http://unitsofmeasure.org\",\n" +
+			"                \"code\": \"d\"\n" +
+			"              }\n" +
+			"            },\n" +
+			"            \"intent\": \"order\",\n" +
+			"            \"category\": {\n" +
+			"              \"coding\": [\n" +
+			"                {\n" +
+			"                  \"system\": \"http://terminology.hl7.org/CodeSystem/medicationrequest-category\",\n" +
+			"                  \"code\": \"community\"\n" +
+			"                }\n" +
+			"              ]\n" +
+			"            },\n" +
+			"            \"medicationCodeableConcept\": {\n" +
+			"              \"coding\": [\n" +
+			"                {\n" +
+			"                  \"system\": \"http://www.nlm.nih.gov/research/umls/rxnorm\",\n" +
+			"                  \"code\": \"1049502\",\n" +
+			"                  \"display\": \"12 HR oxycodone hydrochloride 10 MG Extended Release Oral Tablet\"\n" +
+			"                }\n" +
+			"              ]\n" +
+			"            }\n" +
+			"          }\n" +
+			"        }\n" +
+			"      ]\n" +
+			"    }\n" +
+			"  }\n" +
+			"}";
+		try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
+			HttpPost request = new HttpPost(ourCdsBase + "/opioidcds-10-order-sign");
+			request.setEntity(new StringEntity(cdsRequest));
+			request.addHeader("Content-Type", "application/json");
+
+			CloseableHttpResponse httpResponse = httpClient.execute(request);
+			String result = EntityUtils.toString(httpResponse.getEntity());
+			Gson gsonResponse = new Gson();
+			JsonObject response = gsonResponse.fromJson(result, JsonObject.class);
+			assertNotNull(response);
+			JsonArray cards = response.getAsJsonArray("cards");
+			assertEquals(0, cards.size());
+//			assertEquals("\"Hello World!\"", cards.get(0).getAsJsonObject().get("summary").toString());
+		} catch (IOException ioe) {
+			fail(ioe.getMessage());
+		}
+	}
+}

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

@@ -151,13 +151,6 @@ class ExampleServerDstu3IT implements IServerSupport {
     return count;
   }
 
-  private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
-    String json = stringFromResource(theLocation);
-    Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json);
-    Bundle result = theClient.transaction().withBundle(bundle).execute();
-    return result;
-  }
-
   @Test
   void testWebsocketSubscription() throws Exception {
     /*

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

@@ -61,8 +61,8 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 	"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.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",
@@ -130,13 +130,6 @@ class ExampleServerR4IT implements IServerSupport {
 		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()
@@ -274,8 +267,8 @@ class ExampleServerR4IT implements IServerSupport {
 	@Test
 	void testCareGaps() throws IOException {
 
-		var reporter = crProperties.getCareGapsReporter();
-		var author = crProperties.getCareGapsSectionAuthor();
+		var reporter = crProperties.getCareGaps().getReporter();
+		var author = crProperties.getCareGaps().getSection_author();
 
 		assertTrue(reporter.equals("Organization/alphora"));
 		assertTrue(author.equals("Organization/alphora-author"));

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

@@ -3,8 +3,10 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
@@ -28,6 +30,12 @@ public interface  IServerSupport {
     }
   }
 
+  default IBaseBundle loadBundle(String theLocation, FhirContext theFhirContext, IGenericClient theClient) throws IOException {
+	  String json = stringFromResource(theLocation);
+	  IBaseBundle bundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(json);
+	  return theClient.transaction().withBundle(bundle).execute();
+  }
+
   default String stringFromResource(String theLocation) throws IOException {
     InputStream is = null;
     if (theLocation.startsWith(File.separator)) {