Update Clinical Reasoning plugin (#692)
* Reproducing issues with CR/HAPI cds-hooks processing * Add new $questionnaire operation * Update StarterIpsConfig.java * Update pom.xml * Fixes for configuration properties * Update VS Code launch properties * Fixes for CQL logging * Update pom.xml * Remove unused threaded option * Update to 7.1.7 * Fix some CR defaults * Update to new snapshot * Update pom.xml * Fix test settings * Do not make prefetch calls if all items are present * Add alternative application.yaml for CDS settings. * Add CdsHook tests and documentation * Comment out custom prefetch until it is more mature * Removal of DataEndpoint parameter is not longer needed * Fix debug logging setting being overwritten * Revert change * Remove unused class * Adding Rec10 Test * Disable test until fixed * fix tests --------- Co-authored-by: c-schuler <hoofschu@gmail.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
This commit is contained in:
Brenin Rhodes
GitHub
File diff suppressed because one or more lines are too long
@@ -3,10 +3,6 @@ package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.fhir.jpa.starter.cr.CrProperties;
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public class ProviderConfiguration {
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public static final ProviderConfiguration DEFAULT_PROVIDER_CONFIGURATION =
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new ProviderConfiguration(false, "client_id");
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private final String clientIdHeaderName;
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private final boolean cqlLoggingEnabled;
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@@ -16,8 +12,7 @@ public class ProviderConfiguration {
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}
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public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
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this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
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this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
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this(crProperties.getCql().getRuntime().isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
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}
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public String getClientIdHeaderName() {
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@@ -1,11 +1,21 @@
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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
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import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
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import ca.uhn.fhir.jpa.starter.cr.CrProperties;
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import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
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import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
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import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchDaoSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchFhirClientSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsResolutionStrategySvc;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
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import org.springframework.boot.web.servlet.ServletRegistrationBean;
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@@ -16,8 +26,38 @@ import org.springframework.context.annotation.Import;
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@Configuration
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@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
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@Import(CdsHooksConfig.class)
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@Import({CdsHooksConfig.class, CrCommonConfig.class})
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public class StarterCdsHooksConfig {
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// @Bean
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// CdsPrefetchSvc cdsPrefetchSvc(
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// CdsResolutionStrategySvc theCdsResolutionStrategySvc,
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// CdsPrefetchDaoSvc theResourcePrefetchDao,
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// CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
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// ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
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// return new ModuleConfigurationPrefetchSvc(
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// theCdsResolutionStrategySvc,
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// theResourcePrefetchDao,
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// theResourcePrefetchFhirClient,
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// theCdsHooksDaoAuthorizationSvc);
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// }
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@Bean
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public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
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CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
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registry.unregister(FhirVersionEnum.R4);
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registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryServiceR4.class);
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return registry;
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}
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@Bean
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public ICdsCrServiceRegistry cdsCrServiceRegistry() {
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CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
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registry.unregister(FhirVersionEnum.R4);
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registry.register(FhirVersionEnum.R4, UpdatedCdsCrServiceR4.class);
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return registry;
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}
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@Bean
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public CdsHooksProperties cdsHooksProperties() {
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return new CdsHooksProperties();
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@@ -0,0 +1,30 @@
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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
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import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.Parameters;
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import org.opencds.cqf.fhir.api.Repository;
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import java.util.stream.Collectors;
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import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
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import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA_ENDPOINT;
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import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
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public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
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public UpdatedCdsCrServiceR4(RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
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super(theRequestDetails, theRepository, theCdsConfigService);
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}
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@Override
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public Parameters encodeParams(CdsServiceRequestJson theJson) {
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Parameters parameters = super.encodeParams(theJson);
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if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
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parameters.addParameter(part("useServerData", new BooleanType(false)));
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}
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return parameters;
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}
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}
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@@ -0,0 +1,12 @@
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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.opencds.cqf.fhir.api.Repository;
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public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
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public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
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super(thePlanDefinitionId, theRepository);
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myMaxUriLength = 6000;
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}
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}
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@@ -0,0 +1,22 @@
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package ca.uhn.fhir.jpa.starter.cr;
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public class CareGapsProperties {
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private String reporter = "default";
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private String section_author = "default";
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public String getReporter() {
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return reporter;
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}
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public void setReporter(String reporter) {
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this.reporter = reporter;
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}
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public String getSection_author() {
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return section_author;
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}
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public void setSection_author(String section_author) {
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this.section_author = section_author;
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}
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}
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@@ -0,0 +1,198 @@
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package ca.uhn.fhir.jpa.starter.cr;
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import org.cqframework.cql.cql2elm.CqlCompilerException;
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import org.cqframework.cql.cql2elm.CqlTranslator;
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import org.cqframework.cql.cql2elm.LibraryBuilder;
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public class CqlCompilerProperties {
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private Boolean validate_units = true;
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private Boolean verify_only = false;
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private String compatibility_level = "1.5";
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private CqlCompilerException.ErrorSeverity error_level = CqlCompilerException.ErrorSeverity.Info;
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private LibraryBuilder.SignatureLevel signature_level = LibraryBuilder.SignatureLevel.All;
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private Boolean analyze_data_requirements = false;
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private Boolean collapse_data_requirements = false;
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private CqlTranslator.Format translator_format = CqlTranslator.Format.JSON;
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private Boolean enable_date_range_optimization = true;
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private Boolean enable_annotations = true;
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private Boolean enable_locators = true;
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private Boolean enable_results_type = true;
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private Boolean enable_detailed_errors = true;
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private Boolean disable_list_traversal = false;
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private Boolean disable_list_demotion = false;
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private Boolean disable_list_promotion = false;
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private Boolean enable_interval_demotion = false;
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private Boolean enable_interval_promotion = false;
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private Boolean disable_method_invocation = false;
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private Boolean require_from_keyword = false;
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private Boolean disable_default_model_info_load = false;
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public boolean isValidateUnits() {
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return validate_units;
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}
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public void setValidateUnits(boolean validateUnits) {
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this.validate_units = validateUnits;
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}
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public boolean isVerifyOnly() {
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return verify_only;
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}
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public void setVerifyOnly(boolean verifyOnly) {
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this.verify_only = verifyOnly;
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}
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public String getCompatibilityLevel() {
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return compatibility_level;
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}
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public void setCompatibilityLevel(String compatibilityLevel) {
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this.compatibility_level = compatibilityLevel;
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}
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public CqlCompilerException.ErrorSeverity getErrorSeverityLevel() {
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return error_level;
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}
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public void setErrorSeverityLevel(CqlCompilerException.ErrorSeverity errorSeverityLevel) {
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this.error_level = errorSeverityLevel;
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}
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public LibraryBuilder.SignatureLevel getSignatureLevel() {
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return signature_level;
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}
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public void setSignatureLevel(LibraryBuilder.SignatureLevel signatureLevel) {
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this.signature_level = signatureLevel;
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}
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public boolean isAnalyzeDataRequirements() {
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return analyze_data_requirements;
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}
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public void setAnalyzeDataRequirements(boolean analyzeDataRequirements) {
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this.analyze_data_requirements = analyzeDataRequirements;
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}
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public boolean isCollapseDataRequirements() {
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return collapse_data_requirements;
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}
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public void setCollapseDataRequirements(boolean collapseDataRequirements) {
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this.collapse_data_requirements = collapseDataRequirements;
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}
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public boolean isEnableDateRangeOptimization() {
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return enable_date_range_optimization;
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}
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public void setEnableDateRangeOptimization(boolean enableDateRangeOptimization) {
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this.enable_date_range_optimization = enableDateRangeOptimization;
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}
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public boolean isEnableAnnotations() {
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return enable_annotations;
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}
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public void setEnableAnnotations(boolean enableAnnotations) {
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this.enable_annotations = enableAnnotations;
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}
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public boolean isEnableLocators() {
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return enable_locators;
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}
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public void setEnableLocators(boolean enableLocators) {
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this.enable_locators = enableLocators;
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}
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public boolean isEnableResultsType() {
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return enable_results_type;
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}
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public void setEnableResultsType(boolean enableResultsType) {
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this.enable_results_type = enableResultsType;
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}
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public boolean isEnableDetailedErrors() {
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return enable_detailed_errors;
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}
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public void setEnableDetailedErrors(boolean enableDetailedErrors) {
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this.enable_detailed_errors = enableDetailedErrors;
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}
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public boolean isDisableListTraversal() {
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return disable_list_traversal;
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}
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public void setDisableListTraversal(boolean disableListTraversal) {
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this.disable_list_traversal = disableListTraversal;
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}
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public boolean isDisableListDemotion() {
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return disable_list_demotion;
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}
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public void setDisableListDemotion(boolean disableListDemotion) {
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this.disable_list_demotion = disableListDemotion;
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}
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public boolean isDisableListPromotion() {
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return disable_list_promotion;
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}
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public void setDisableListPromotion(boolean disableListPromotion) {
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this.disable_list_promotion = disableListPromotion;
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}
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public boolean isEnableIntervalPromotion() {
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return enable_interval_promotion;
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}
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public void setEnableIntervalPromotion(boolean enableIntervalPromotion) {
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this.enable_interval_promotion = enableIntervalPromotion;
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}
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public boolean isEnableIntervalDemotion() {
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return enable_interval_demotion;
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}
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public void setEnableIntervalDemotion(boolean enableIntervalDemotion) {
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this.enable_interval_demotion = enableIntervalDemotion;
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}
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public boolean isDisableMethodInvocation() {
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return disable_method_invocation;
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}
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public void setDisableMethodInvocation(boolean disableMethodInvocation) {
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this.disable_method_invocation = disableMethodInvocation;
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}
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public boolean isRequireFromKeyword() {
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return require_from_keyword;
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}
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public void setRequireFromKeyword(boolean requireFromKeyword) {
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this.require_from_keyword = requireFromKeyword;
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}
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public boolean isDisableDefaultModelInfoLoad() {
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return disable_default_model_info_load;
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}
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public void setDisableDefaultModelInfoLoad(boolean disableDefaultModelInfoLoad) {
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this.disable_default_model_info_load = disableDefaultModelInfoLoad;
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}
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public CqlTranslator.Format getTranslatorFormat() {
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return translator_format;
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}
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public void setTranslatorFormat(CqlTranslator.Format translatorFormat) {
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this.translator_format = translatorFormat;
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}
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}
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53
src/main/java/ca/uhn/fhir/jpa/starter/cr/CqlProperties.java
Normal file
53
src/main/java/ca/uhn/fhir/jpa/starter/cr/CqlProperties.java
Normal file
@@ -0,0 +1,53 @@
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package ca.uhn.fhir.jpa.starter.cr;
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import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
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import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
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public class CqlProperties {
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private Boolean use_embedded_libraries = true;
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private CqlCompilerProperties compiler = new CqlCompilerProperties();
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private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
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private TerminologySettings terminology = new TerminologySettings();
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private RetrieveSettings data = new RetrieveSettings();
|
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|
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public Boolean getUse_embedded_libraries() {
|
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return use_embedded_libraries;
|
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}
|
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|
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public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
|
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this.use_embedded_libraries = use_embedded_libraries;
|
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}
|
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|
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public CqlCompilerProperties getCompiler() {
|
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return compiler;
|
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}
|
||||
|
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public void setCompiler(CqlCompilerProperties compiler) {
|
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this.compiler = compiler;
|
||||
}
|
||||
|
||||
public CqlRuntimeProperties getRuntime() {
|
||||
return runtime;
|
||||
}
|
||||
|
||||
public void setRuntime(CqlRuntimeProperties runtime) {
|
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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;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,35 @@
|
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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;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
228
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrCommonConfig.java
Normal file
228
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrCommonConfig.java
Normal file
@@ -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();
|
||||
}
|
||||
}
|
||||
@@ -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;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -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();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -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();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -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;
|
||||
|
||||
|
||||
@@ -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)
|
||||
|
||||
294
src/main/resources/cds.application.yaml
Normal file
294
src/main/resources/cds.application.yaml
Normal file
@@ -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
|
||||
@@ -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>
|
||||
|
||||
Reference in New Issue
Block a user