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Add settings for CDS Hooks and use latest hapi-fhir-cr configs

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This commit is contained in:
Brenin Rhodes
2023-10-19 06:50:29 -06:00
parent 6d10c0bade
commit 408da72cf4
15 changed files with 474 additions and 538 deletions
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250
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -26,36 +26,6 @@ import java.util.Set;
@EnableConfigurationProperties @EnableConfigurationProperties
public class AppProperties { public class AppProperties {
private Boolean cr_enabled = false;
//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 Boolean ips_enabled = false; private Boolean ips_enabled = false;
private Boolean openapi_enabled = false; private Boolean openapi_enabled = false;
private Boolean mdm_enabled = false; private Boolean mdm_enabled = false;
@@ -197,226 +167,6 @@ public class AppProperties {
this.partitioning = partitioning; this.partitioning = partitioning;
} }
public Boolean getCr_enabled() {
return cr_enabled;
}
public void setCr_enabled(Boolean cr_enabled) {
this.cr_enabled = cr_enabled;
}
public boolean isCqlUseEmbeddedLibraries() {
return cql_use_embedded_libraries;
}
public void setCqlUseEmbeddedLibraries(boolean cql_use_embedded_libraries) {
this.cql_use_embedded_libraries = cql_use_embedded_libraries;
}
public boolean isCqlRuntimeDebugLoggingEnabled() {
return cql_runtime_debug_logging_enabled;
}
public void setCqlRuntimeDebugLoggingEnabled(boolean cqlRuntimeDebugLoggingEnabled) {
this.cql_runtime_debug_logging_enabled = cqlRuntimeDebugLoggingEnabled;
}
public boolean isCqlCompilerValidateUnits() {
return cql_compiler_validate_units;
}
public void setCqlCompilerValidateUnits(boolean cqlCompilerValidateUnits) {
this.cql_compiler_validate_units = cqlCompilerValidateUnits;
}
public boolean isCqlCompilerVerifyOnly() {
return cql_compiler_verify_only;
}
public void setCqlCompilerVerifyOnly(boolean cqlCompilerVerifyOnly) {
this.cql_compiler_verify_only = cqlCompilerVerifyOnly;
}
public String getCqlCompilerCompatibilityLevel() {
return cql_compiler_compatibility_level;
}
public void setCqlCompilerCompatibilityLevel(String cqlCompilerCompatibilityLevel) {
this.cql_compiler_compatibility_level = cqlCompilerCompatibilityLevel;
}
public CqlCompilerException.ErrorSeverity getCqlCompilerErrorSeverityLevel() {
return cql_compiler_error_level;
}
public void setCqlCompilerErrorSeverityLevel(CqlCompilerException.ErrorSeverity cqlCompilerErrorSeverityLevel) {
this.cql_compiler_error_level = cqlCompilerErrorSeverityLevel;
}
public LibraryBuilder.SignatureLevel getCqlCompilerSignatureLevel() {
return cql_compiler_signature_level;
}
public void setCqlCompilerSignatureLevel(LibraryBuilder.SignatureLevel cqlCompilerSignatureLevel) {
this.cql_compiler_signature_level = cqlCompilerSignatureLevel;
}
public boolean isCqlCompilerAnalyzeDataRequirements() {
return cql_compiler_analyze_data_requirements;
}
public void setCqlCompilerAnalyzeDataRequirements(boolean cqlCompilerAnalyzeDataRequirements) {
this.cql_compiler_analyze_data_requirements = cqlCompilerAnalyzeDataRequirements;
}
public boolean isCqlCompilerCollapseDataRequirements() {
return cql_compiler_collapse_data_requirements;
}
public void setCqlCompilerCollapseDataRequirements(boolean cqlCompilerCollapseDataRequirements) {
this.cql_compiler_collapse_data_requirements = cqlCompilerCollapseDataRequirements;
}
public boolean isEnableDateRangeOptimization() {
return cql_compiler_enable_date_range_optimization;
}
public void setEnableDateRangeOptimization(boolean enableDateRangeOptimization) {
this.cql_compiler_enable_date_range_optimization = enableDateRangeOptimization;
}
public boolean isEnableAnnotations() {
return cql_compiler_enable_annotations;
}
public void setEnableAnnotations(boolean enableAnnotations) {
this.cql_compiler_enable_annotations = enableAnnotations;
}
public boolean isEnableLocators() {
return cql_compiler_enable_locators;
}
public void setEnableLocators(boolean enableLocators) {
this.cql_compiler_enable_locators = enableLocators;
}
public boolean isEnableResultsType() {
return cql_compiler_enable_results_type;
}
public void setEnableResultsType(boolean enableResultsType) {
this.cql_compiler_enable_results_type = enableResultsType;
}
public boolean isEnableDetailedErrors() {
return cql_compiler_enable_detailed_errors;
}
public void setEnableDetailedErrors(boolean enableDetailedErrors) {
this.cql_compiler_enable_detailed_errors = enableDetailedErrors;
}
public boolean isDisableListTraversal() {
return cql_compiler_disable_list_traversal;
}
public void setDisableListTraversal(boolean disableListTraversal) {
this.cql_compiler_disable_list_traversal = disableListTraversal;
}
public boolean isDisableListDemotion() {
return cql_compiler_disable_list_demotion;
}
public void setDisableListDemotion(boolean disableListDemotion) {
this.cql_compiler_disable_list_demotion = disableListDemotion;
}
public boolean isDisableListPromotion() {
return cql_compiler_disable_list_promotion;
}
public void setDisableListPromotion(boolean disableListPromotion) {
this.cql_compiler_disable_list_promotion = disableListPromotion;
}
public boolean isEnableIntervalPromotion() {
return cql_compiler_enable_interval_promotion;
}
public void setEnableIntervalPromotion(boolean enableIntervalPromotion) {
this.cql_compiler_enable_interval_promotion = enableIntervalPromotion;
}
public boolean isEnableIntervalDemotion() {
return cql_compiler_enable_interval_demotion;
}
public void setEnableIntervalDemotion(boolean enableIntervalDemotion) {
this.cql_compiler_enable_interval_demotion = enableIntervalDemotion;
}
public boolean isDisableMethodInvocation() {
return cql_compiler_disable_method_invocation;
}
public void setDisableMethodInvocation(boolean disableMethodInvocation) {
this.cql_compiler_disable_method_invocation = disableMethodInvocation;
}
public boolean isRequireFromKeyword() {
return cql_compiler_require_from_keyword;
}
public void setRequireFromKeyword(boolean requireFromKeyword) {
this.cql_compiler_require_from_keyword = requireFromKeyword;
}
public boolean isDisableDefaultModelInfoLoad() {
return cql_compiler_disable_default_model_info_load;
}
public void setDisableDefaultModelInfoLoad(boolean disableDefaultModelInfoLoad) {
this.cql_compiler_disable_default_model_info_load = disableDefaultModelInfoLoad;
}
public boolean isCqlRuntimeEnableExpressionCaching() {
return cql_runtime_enable_expression_caching;
}
public void setCqlRuntimeEnableExpressionCaching(boolean cqlRuntimeEnableExpressionCaching) {
this.cql_runtime_enable_expression_caching = cqlRuntimeEnableExpressionCaching;
}
public boolean isCqlRuntimeEnableValidation() {
return cql_runtime_enable_validation;
}
public void setCqlRuntimeEnableValidation(boolean cqlRuntimeEnableValidation) {
this.cql_runtime_enable_validation = cqlRuntimeEnableValidation;
}
public CqlTranslator.Format getCqlTranslatorFormat() {
return cql_compiler_translator_format;
}
public void setCqlTranslatorFormat(CqlTranslator.Format cqlTranslatorFormat) {
this.cql_compiler_translator_format = cqlTranslatorFormat;
}
public String getCareGapsReporter() {
return caregaps_reporter;
}
public String getCareGapsSectionAuthor() {
return caregaps_section_author;
}
public void setCareGapsSectionAuthor(String theCareGapsSectionAuthor) {this.caregaps_section_author = theCareGapsSectionAuthor;}
public void setCareGapsReporter(String theCareGapsReporter) {
this.caregaps_reporter = theCareGapsReporter;
}
public Boolean getIps_enabled() { public Boolean getIps_enabled() {
return ips_enabled; return ips_enabled;
} }

8
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -96,8 +96,8 @@ public class Application extends SpringBootServletInitializer {
} }
@Bean // @Bean
IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) { // IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer); // return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
} // }
} }

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

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

22
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java
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@@ -37,6 +37,8 @@ public class CdsHooksServlet extends HttpServlet {
@Autowired @Autowired
private AppProperties appProperties; private AppProperties appProperties;
@Autowired @Autowired
private ProviderConfiguration providerConfiguration;
@Autowired
ICdsServiceRegistry cdsServiceRegistry; ICdsServiceRegistry cdsServiceRegistry;
@Autowired @Autowired
RestfulServer restfulServer; RestfulServer restfulServer;
@@ -44,6 +46,10 @@ public class CdsHooksServlet extends HttpServlet {
@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY) @Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY)
ObjectMapper objectMapper; ObjectMapper objectMapper;
protected ProviderConfiguration getProviderConfiguration() {
return this.providerConfiguration;
}
// CORS Pre-flight // CORS Pre-flight
@Override @Override
protected void doOptions(HttpServletRequest req, HttpServletResponse resp) { protected void doOptions(HttpServletRequest req, HttpServletResponse resp) {
@@ -103,26 +109,12 @@ public class CdsHooksServlet extends HttpServlet {
private void logRequestInfo(CdsServiceRequestJson request, String jsonRequest) { private void logRequestInfo(CdsServiceRequestJson request, String jsonRequest) {
logger.info(jsonRequest); logger.info(jsonRequest);
logger.info("cds-hooks hook instance: {}", request.getHookInstance()); logger.info("cds-hooks hook instance: {}", request.getHookInstance());
// logger.info("cds-hooks maxCodesPerQuery: {}", this.getProviderConfiguration().getMaxCodesPerQuery());
// logger.info("cds-hooks expandValueSets: {}", this.getProviderConfiguration().getExpandValueSets());
// logger.info("cds-hooks queryBatchThreshold: {}", this.getProviderConfiguration().getQueryBatchThreshold());
// logger.info("cds-hooks searchStyle: {}", this.getProviderConfiguration().getSearchStyle());
// logger.info("cds-hooks prefetch maxUriLength: {}", this.getProviderConfiguration().getMaxUriLength());
logger.info("cds-hooks local server address: {}", appProperties.getServer_address()); logger.info("cds-hooks local server address: {}", appProperties.getServer_address());
logger.info("cds-hooks fhir server address: {}", request.getFhirServer()); logger.info("cds-hooks fhir server address: {}", request.getFhirServer());
// logger.info("cds-hooks cql_logging_enabled: {}", this.getProviderConfiguration().getCqlLoggingEnabled()); logger.info("cds-hooks cql_logging_enabled: {}", this.getProviderConfiguration().getCqlLoggingEnabled());
} }
private CdsServicesJson getServices() { private CdsServicesJson getServices() {
return cdsServiceRegistry.getCdsServicesJson(); return cdsServiceRegistry.getCdsServicesJson();
} }
// public DebugMap getDebugMap() {
// DebugMap debugMap = new DebugMap();
// if (cqlProperties.getCqlRuntimeOptions().isDebugLoggingEnabled()) {
// // getOptions().getCqlEngineOptions().isDebugLoggingEnabled()) {
// debugMap.setIsLoggingEnabled(true);
// }
// return debugMap;
// }
} }

29
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ProviderConfiguration.java Normal file
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@@ -0,0 +1,29 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.jpa.starter.cr.CrProperties;
public class ProviderConfiguration {
public static final ProviderConfiguration DEFAULT_PROVIDER_CONFIGURATION = new ProviderConfiguration(false, "client_id");
private final String clientIdHeaderName;
private final boolean cqlLoggingEnabled;
public ProviderConfiguration(boolean cqlLoggingEnabled, String clientIdHeaderName) {
this.cqlLoggingEnabled = cqlLoggingEnabled;
this.clientIdHeaderName = clientIdHeaderName;
}
public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
}
public String getClientIdHeaderName() {
return this.clientIdHeaderName;
}
public boolean getCqlLoggingEnabled() {
return this.cqlLoggingEnabled;
}
}

22
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java
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@@ -4,16 +4,33 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.config.AutowireCapableBeanFactory; import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
import org.springframework.boot.web.servlet.ServletRegistrationBean; import org.springframework.boot.web.servlet.ServletRegistrationBean;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import; import org.springframework.context.annotation.Import;
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.api.ICdsHooksDaoAuthorizationSvc;
import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig; import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter; import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
@Configuration @Configuration
@Conditional({ CdsHooksConfigCondition.class, CrConfigCondition.class })
@Import(CdsHooksConfig.class) @Import(CdsHooksConfig.class)
public class StarterCdsHooksConfig { public class StarterCdsHooksConfig {
@Bean
public CdsHooksProperties cdsHooksProperties() {
return new CdsHooksProperties();
}
@Bean
public CdsCrSettings cdsCrSettings(CdsHooksProperties cdsHooksProperties) {
CdsCrSettings settings = CdsCrSettings.getDefault();
settings.setClientIdHeaderName(cdsHooksProperties.getClientIdHeaderName());
return settings;
}
@Bean @Bean
public CdsHooksContextBooter cdsHooksContextBooter() { public CdsHooksContextBooter cdsHooksContextBooter() {
// ourLog.info("No Spring Context provided. Assuming all CDS Services will be registered dynamically."); // ourLog.info("No Spring Context provided. Assuming all CDS Services will be registered dynamically.");
@@ -25,6 +42,11 @@ public class StarterCdsHooksConfig {
public void authorizePreShow(IBaseResource theResource) {} public void authorizePreShow(IBaseResource theResource) {}
} }
@Bean
public ProviderConfiguration providerConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
return new ProviderConfiguration(cdsProperties, crProperties);
}
@Bean @Bean
ICdsHooksDaoAuthorizationSvc cdsHooksDaoAuthorizationSvc() { ICdsHooksDaoAuthorizationSvc cdsHooksDaoAuthorizationSvc() {
return new CdsHooksDaoAuthorizationSvc(); return new CdsHooksDaoAuthorizationSvc();

30
src/main/java/ca/uhn/fhir/jpa/starter/cr/BaseCrConfig.java
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@@ -1,17 +1,11 @@
package ca.uhn.fhir.jpa.starter.cr; package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener; import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener; import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerCacheRefresher;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry; import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheFactory;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor; import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import org.cqframework.cql.cql2elm.model.CompiledLibrary; import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model; import org.cqframework.cql.cql2elm.model.Model;
import org.hl7.cql.model.ModelIdentifier; import org.hl7.cql.model.ModelIdentifier;
@@ -27,6 +21,11 @@ import java.util.concurrent.ConcurrentHashMap;
@Configuration @Configuration
public class BaseCrConfig { public class BaseCrConfig {
@Bean
public CrProperties crProperties() {
return new CrProperties();
}
@Bean @Bean
public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() { public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() {
return new ConcurrentHashMap<>(); return new ConcurrentHashMap<>();
@@ -42,7 +41,6 @@ public class BaseCrConfig {
return new ConcurrentHashMap<>(); return new ConcurrentHashMap<>();
} }
@Bean @Bean
public ElmCacheResourceChangeListener elmCacheResourceChangeListener( public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
IResourceChangeListenerRegistry theResourceChangeListenerRegistry, IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
@@ -69,15 +67,17 @@ public class BaseCrConfig {
return listener; return listener;
} }
@Bean // These beans were being duplicated
public IResourceChangeListenerRegistry resourceChangeListenerRegistry(InMemoryResourceMatcher theInMemoryResourceMatcher, FhirContext theFhirContext, ResourceChangeListenerCacheFactory theResourceChangeListenerCacheFactory) { // @Bean
return new ResourceChangeListenerRegistryImpl(theFhirContext, theResourceChangeListenerCacheFactory, theInMemoryResourceMatcher); // public IResourceChangeListenerRegistry resourceChangeListenerRegistry(InMemoryResourceMatcher theInMemoryResourceMatcher, FhirContext theFhirContext, ResourceChangeListenerCacheFactory theResourceChangeListenerCacheFactory) {
} // return new ResourceChangeListenerRegistryImpl(theFhirContext, theResourceChangeListenerCacheFactory, theInMemoryResourceMatcher);
// }
// @Bean
// IResourceChangeListenerCacheRefresher resourceChangeListenerCacheRefresher() {
// return new ResourceChangeListenerCacheRefresherImpl();
// }
@Bean
IResourceChangeListenerCacheRefresher resourceChangeListenerCacheRefresher() {
return new ResourceChangeListenerCacheRefresherImpl();
}
@Bean @Bean
public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() { public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
return new ResourceChangeListenerRegistryInterceptor(); return new ResourceChangeListenerRegistryInterceptor();

8
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrConfigCondition.java
View File

@@ -6,9 +6,9 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
public class CrConfigCondition implements Condition { public class CrConfigCondition implements Condition {
@Override @Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) { public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr_enabled"); String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr.enabled");
return Boolean.parseBoolean(property); return Boolean.parseBoolean(property);
} }
} }

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

182
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrR4Config.java
View File

@@ -1,182 +0,0 @@
package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.cr.common.IRepositoryFactory;
import ca.uhn.fhir.cr.config.ProviderLoader;
import ca.uhn.fhir.cr.config.ProviderSelector;
import ca.uhn.fhir.cr.r4.IActivityDefinitionProcessorFactory;
import ca.uhn.fhir.cr.r4.ICareGapsServiceFactory;
import ca.uhn.fhir.cr.r4.ICqlExecutionServiceFactory;
import ca.uhn.fhir.cr.r4.IMeasureServiceFactory;
import ca.uhn.fhir.cr.r4.IPlanDefinitionProcessorFactory;
import ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory;
import ca.uhn.fhir.cr.r4.IQuestionnaireResponseProcessorFactory;
import ca.uhn.fhir.cr.r4.ISubmitDataProcessorFactory;
import ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionApplyProvider;
import ca.uhn.fhir.cr.r4.cqlexecution.CqlExecutionOperationProvider;
import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider;
import ca.uhn.fhir.cr.r4.measure.SubmitDataProvider;
import ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionApplyProvider;
import ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionPackageProvider;
import ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePackageProvider;
import ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePopulateProvider;
import ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseExtractProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cr.activitydefinition.r4.ActivityDefinitionProcessor;
import org.opencds.cqf.fhir.cr.cql.r4.R4CqlExecutionService;
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
import org.opencds.cqf.fhir.cr.measure.r4.R4CareGapsService;
import org.opencds.cqf.fhir.cr.measure.r4.R4MeasureService;
import org.opencds.cqf.fhir.cr.measure.r4.R4SubmitDataService;
import org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor;
import org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor;
import org.opencds.cqf.fhir.cr.questionnaireresponse.r4.QuestionnaireResponseProcessor;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import java.util.Arrays;
import java.util.Map;
import java.util.concurrent.Executor;
@Configuration
public class CrR4Config {
@Bean
IMeasureServiceFactory r4MeasureServiceFactory(
IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
return rd -> new R4MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
}
@Bean
ISubmitDataProcessorFactory r4SubmitDataProcessorFactory(IRepositoryFactory theRepositoryFactory) {
return rd -> new R4SubmitDataService(theRepositoryFactory.create(rd));
}
@Bean
ICqlExecutionServiceFactory r4CqlExecutionServiceFactory(
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
return rd -> new R4CqlExecutionService(theRepositoryFactory.create(rd), theEvaluationSettings);
}
@Bean
CqlExecutionOperationProvider r4CqlExecutionOperationProvider() {
return new CqlExecutionOperationProvider();
}
@Bean
ICareGapsServiceFactory careGapsServiceFactory(
IRepositoryFactory theRepositoryFactory,
CareGapsProperties theCareGapsProperties,
MeasureEvaluationOptions theMeasureEvaluationOptions,
@Qualifier("cqlExecutor") Executor theExecutor) {
return rd -> new R4CareGapsService(
theCareGapsProperties,
theRepositoryFactory.create(rd),
theMeasureEvaluationOptions,
theExecutor,
rd.getFhirServerBase());
}
@Bean
CareGapsOperationProvider r4CareGapsOperationProvider() {
return new CareGapsOperationProvider();
}
@Bean
SubmitDataProvider r4SubmitDataProvider() {
return new SubmitDataProvider();
}
@Bean
MeasureOperationsProvider r4MeasureOperationsProvider() {
return new MeasureOperationsProvider();
}
@Bean
IActivityDefinitionProcessorFactory r4ActivityDefinitionProcessorFactory(
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
return rd -> new ActivityDefinitionProcessor(
theRepositoryFactory.create(rd), theEvaluationSettings);
}
@Bean
IPlanDefinitionProcessorFactory r4PlanDefinitionProcessorFactory(
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
return rd -> new PlanDefinitionProcessor(
theRepositoryFactory.create(rd), theEvaluationSettings);
}
@Bean
IQuestionnaireProcessorFactory r4QuestionnaireProcessorFactory(
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
return rd -> new QuestionnaireProcessor(
theRepositoryFactory.create(rd), theEvaluationSettings);
}
@Bean
IQuestionnaireResponseProcessorFactory r4QuestionnaireResponseProcessorFactory(
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
return rd -> new QuestionnaireResponseProcessor(
theRepositoryFactory.create(rd), theEvaluationSettings);
}
@Bean
ActivityDefinitionApplyProvider r4ActivityDefinitionApplyProvider() {
return new ActivityDefinitionApplyProvider();
}
@Bean
PlanDefinitionApplyProvider r4PlanDefinitionApplyProvider() {
return new PlanDefinitionApplyProvider();
}
@Bean
QuestionnaireResponseExtractProvider
r4QuestionnaireResponseExtractProvider() {
return new QuestionnaireResponseExtractProvider();
}
@Bean
PlanDefinitionPackageProvider r4PlanDefinitionPackageProvider() {
return new PlanDefinitionPackageProvider();
}
@Bean
QuestionnairePackageProvider r4QuestionnairePackageProvider() {
return new QuestionnairePackageProvider();
}
@Bean
QuestionnairePopulateProvider r4QuestionnairePopulateProvider() {
return new QuestionnairePopulateProvider();
}
@Bean
public ProviderLoader r4PdLoader(
ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
var selector = new ProviderSelector(
theFhirContext,
Map.of(
FhirVersionEnum.R4,
Arrays.asList(
MeasureOperationsProvider.class,
SubmitDataProvider.class,
CareGapsOperationProvider.class,
CqlExecutionOperationProvider.class,
ActivityDefinitionApplyProvider.class,
PlanDefinitionApplyProvider.class,
QuestionnaireResponseExtractProvider.class,
QuestionnairePackageProvider.class,
PlanDefinitionPackageProvider.class,
QuestionnairePopulateProvider.class)));
return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
}
}

56
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java
View File

@@ -5,7 +5,6 @@ import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
import ca.uhn.fhir.cr.config.dstu3.ExtractOperationConfig; import ca.uhn.fhir.cr.config.dstu3.ExtractOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig; import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.PopulateOperationConfig; import ca.uhn.fhir.cr.config.dstu3.PopulateOperationConfig;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
import ca.uhn.fhir.rest.server.RestfulServer; import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory; import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
@@ -27,15 +26,17 @@ import java.util.EnumSet;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Set; import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
@Configuration @Configuration
@Conditional({ OnDSTU3Condition.class, CrConfigCondition.class }) @Conditional({ OnDSTU3Condition.class, CrConfigCondition.class })
@Import({ CrDstu3Config.class, @Import({
BaseCrConfig.class,
CrDstu3Config.class,
ApplyOperationConfig.class, ApplyOperationConfig.class,
ExtractOperationConfig.class, ExtractOperationConfig.class,
PackageOperationConfig.class, PackageOperationConfig.class,
PopulateOperationConfig.class, BaseCrConfig.class}) PopulateOperationConfig.class
})
public class StarterCrDstu3Config { public class StarterCrDstu3Config {
private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrDstu3Config.class); private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrDstu3Config.class);
@@ -52,7 +53,7 @@ public class StarterCrDstu3Config {
@Bean @Bean
public EvaluationSettings evaluationSettings( public EvaluationSettings evaluationSettings(
AppProperties theAppProperties, CrProperties theCrProperties,
Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache, Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
Map<ModelIdentifier, Model> theGlobalModelCache, Map<ModelIdentifier, Model> theGlobalModelCache,
Map<String, List<Code>> theGlobalValueSetCache) { Map<String, List<Code>> theGlobalValueSetCache) {
@@ -61,10 +62,10 @@ public class StarterCrDstu3Config {
var cqlEngineOptions = cqlOptions.getCqlEngineOptions(); var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class); Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
if (theAppProperties.isCqlRuntimeEnableExpressionCaching()) { if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
options.add(CqlEngine.Options.EnableExpressionCaching); options.add(CqlEngine.Options.EnableExpressionCaching);
} }
if (theAppProperties.isCqlRuntimeEnableValidation()) { if (theCrProperties.isCqlRuntimeEnableValidation()) {
options.add(CqlEngine.Options.EnableValidation); options.add(CqlEngine.Options.EnableValidation);
} }
cqlEngineOptions.setOptions(options); cqlEngineOptions.setOptions(options);
@@ -72,53 +73,52 @@ public class StarterCrDstu3Config {
var cqlCompilerOptions = new CqlCompilerOptions(); var cqlCompilerOptions = new CqlCompilerOptions();
if (theAppProperties.isEnableDateRangeOptimization() if (theCrProperties.isEnableDateRangeOptimization()) {
) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
} }
if (theAppProperties.isEnableAnnotations()) { if (theCrProperties.isEnableAnnotations()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
} }
if (theAppProperties.isEnableLocators()) { if (theCrProperties.isEnableLocators()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
} }
if (theAppProperties.isEnableResultsType()) { if (theCrProperties.isEnableResultsType()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
} }
cqlCompilerOptions.setVerifyOnly(theAppProperties.isCqlCompilerVerifyOnly()); cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
if (theAppProperties.isEnableDetailedErrors()) { if (theCrProperties.isEnableDetailedErrors()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
} }
cqlCompilerOptions.setErrorLevel(theAppProperties.getCqlCompilerErrorSeverityLevel()); cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
if (theAppProperties.isDisableListTraversal()) { if (theCrProperties.isDisableListTraversal()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
} }
if (theAppProperties.isDisableListDemotion()) { if (theCrProperties.isDisableListDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
} }
if (theAppProperties.isDisableListPromotion()) { if (theCrProperties.isDisableListPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
} }
if (theAppProperties.isEnableIntervalDemotion()) { if (theCrProperties.isEnableIntervalDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
} }
if (theAppProperties.isEnableIntervalPromotion()) { if (theCrProperties.isEnableIntervalPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
} }
if (theAppProperties.isDisableMethodInvocation()) { if (theCrProperties.isDisableMethodInvocation()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
} }
if (theAppProperties.isRequireFromKeyword()) { if (theCrProperties.isRequireFromKeyword()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
} }
cqlCompilerOptions.setValidateUnits(theAppProperties.isCqlCompilerValidateUnits()); cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
if (theAppProperties.isDisableDefaultModelInfoLoad()) { if (theCrProperties.isDisableDefaultModelInfoLoad()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
} }
cqlCompilerOptions.setSignatureLevel(theAppProperties.getCqlCompilerSignatureLevel()); cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
cqlCompilerOptions.setCompatibilityLevel(theAppProperties.getCqlCompilerCompatibilityLevel()); cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
cqlCompilerOptions.setAnalyzeDataRequirements(theAppProperties.isCqlCompilerAnalyzeDataRequirements()); cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
cqlCompilerOptions.setCollapseDataRequirements(theAppProperties.isCqlCompilerCollapseDataRequirements()); cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions); cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
evaluationSettings.setLibraryCache(theGlobalLibraryCache); evaluationSettings.setLibraryCache(theGlobalLibraryCache);

75
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java
View File

@@ -1,10 +1,15 @@
package ca.uhn.fhir.jpa.starter.cr; package ca.uhn.fhir.jpa.starter.cr;
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.starter.annotations.OnR4Condition; import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import ca.uhn.fhir.rest.server.RestfulServer; import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory; import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.cr.common.CqlThreadFactory; import ca.uhn.fhir.cr.common.CqlThreadFactory;
import ca.uhn.fhir.jpa.starter.AppProperties;
import org.cqframework.cql.cql2elm.CqlCompilerOptions; import org.cqframework.cql.cql2elm.CqlCompilerOptions;
import org.cqframework.cql.cql2elm.model.CompiledLibrary; import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model; import org.cqframework.cql.cql2elm.model.Model;
@@ -18,7 +23,11 @@ import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
import org.opencds.cqf.fhir.utility.ValidationProfile; import org.opencds.cqf.fhir.utility.ValidationProfile;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.*; 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 org.springframework.security.concurrent.DelegatingSecurityContextExecutorService;
import java.util.EnumSet; import java.util.EnumSet;
@@ -30,7 +39,14 @@ import java.util.concurrent.Executors;
@Configuration @Configuration
@Conditional({ OnR4Condition.class, CrConfigCondition.class }) @Conditional({ OnR4Condition.class, CrConfigCondition.class })
@Import({BaseCrConfig.class, CrR4Config.class}) @Import({
BaseCrConfig.class,
CrR4Config.class,
ApplyOperationConfig.class,
ExtractOperationConfig.class,
PackageOperationConfig.class,
PopulateOperationConfig.class
})
public class StarterCrR4Config { public class StarterCrR4Config {
private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrR4Config.class); private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrR4Config.class);
@@ -47,11 +63,11 @@ public class StarterCrR4Config {
} }
@Bean @Bean
CareGapsProperties careGapsProperties(AppProperties theAppProperties) { CareGapsProperties careGapsProperties(CrProperties theCrProperties) {
var careGapsProperties = new CareGapsProperties(); var careGapsProperties = new CareGapsProperties();
careGapsProperties.setThreadedCareGapsEnabled(false); careGapsProperties.setThreadedCareGapsEnabled(false);
careGapsProperties.setCareGapsReporter(theAppProperties.getCareGapsReporter()); careGapsProperties.setCareGapsReporter(theCrProperties.getCareGapsReporter());
careGapsProperties.setCareGapsCompositionSectionAuthor(theAppProperties.getCareGapsSectionAuthor()); careGapsProperties.setCareGapsCompositionSectionAuthor(theCrProperties.getCareGapsSectionAuthor());
return careGapsProperties; return careGapsProperties;
} }
@@ -67,7 +83,7 @@ public class StarterCrR4Config {
@Bean @Bean
public EvaluationSettings evaluationSettings( public EvaluationSettings evaluationSettings(
AppProperties theAppProperties, CrProperties theCrProperties,
Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache, Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
Map<ModelIdentifier, Model> theGlobalModelCache, Map<ModelIdentifier, Model> theGlobalModelCache,
Map<String, List<Code>> theGlobalValueSetCache) { Map<String, List<Code>> theGlobalValueSetCache) {
@@ -76,10 +92,10 @@ public class StarterCrR4Config {
var cqlEngineOptions = cqlOptions.getCqlEngineOptions(); var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class); Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
if (theAppProperties.isCqlRuntimeEnableExpressionCaching()) { if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
options.add(CqlEngine.Options.EnableExpressionCaching); options.add(CqlEngine.Options.EnableExpressionCaching);
} }
if (theAppProperties.isCqlRuntimeEnableValidation()) { if (theCrProperties.isCqlRuntimeEnableValidation()) {
options.add(CqlEngine.Options.EnableValidation); options.add(CqlEngine.Options.EnableValidation);
} }
cqlEngineOptions.setOptions(options); cqlEngineOptions.setOptions(options);
@@ -87,53 +103,52 @@ public class StarterCrR4Config {
var cqlCompilerOptions = new CqlCompilerOptions(); var cqlCompilerOptions = new CqlCompilerOptions();
if (theAppProperties.isEnableDateRangeOptimization() if (theCrProperties.isEnableDateRangeOptimization()) {
) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
} }
if (theAppProperties.isEnableAnnotations()) { if (theCrProperties.isEnableAnnotations()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
} }
if (theAppProperties.isEnableLocators()) { if (theCrProperties.isEnableLocators()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
} }
if (theAppProperties.isEnableResultsType()) { if (theCrProperties.isEnableResultsType()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
} }
cqlCompilerOptions.setVerifyOnly(theAppProperties.isCqlCompilerVerifyOnly()); cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
if (theAppProperties.isEnableDetailedErrors()) { if (theCrProperties.isEnableDetailedErrors()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
} }
cqlCompilerOptions.setErrorLevel(theAppProperties.getCqlCompilerErrorSeverityLevel()); cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
if (theAppProperties.isDisableListTraversal()) { if (theCrProperties.isDisableListTraversal()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
} }
if (theAppProperties.isDisableListDemotion()) { if (theCrProperties.isDisableListDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
} }
if (theAppProperties.isDisableListPromotion()) { if (theCrProperties.isDisableListPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
} }
if (theAppProperties.isEnableIntervalDemotion()) { if (theCrProperties.isEnableIntervalDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
} }
if (theAppProperties.isEnableIntervalPromotion()) { if (theCrProperties.isEnableIntervalPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
} }
if (theAppProperties.isDisableMethodInvocation()) { if (theCrProperties.isDisableMethodInvocation()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
} }
if (theAppProperties.isRequireFromKeyword()) { if (theCrProperties.isRequireFromKeyword()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
} }
cqlCompilerOptions.setValidateUnits(theAppProperties.isCqlCompilerValidateUnits()); cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
if (theAppProperties.isDisableDefaultModelInfoLoad()) { if (theCrProperties.isDisableDefaultModelInfoLoad()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad); cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
} }
cqlCompilerOptions.setSignatureLevel(theAppProperties.getCqlCompilerSignatureLevel()); cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
cqlCompilerOptions.setCompatibilityLevel(theAppProperties.getCqlCompilerCompatibilityLevel()); cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
cqlCompilerOptions.setAnalyzeDataRequirements(theAppProperties.isCqlCompilerAnalyzeDataRequirements()); cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
cqlCompilerOptions.setCollapseDataRequirements(theAppProperties.isCqlCompilerCollapseDataRequirements()); cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions); cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
evaluationSettings.setLibraryCache(theGlobalLibraryCache); evaluationSettings.setLibraryCache(theGlobalLibraryCache);

12
src/main/resources/application.yaml
View File

@@ -53,14 +53,19 @@ spring:
# hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer # hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
hapi: hapi:
fhir: 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
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) ### 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 openapi_enabled: true
### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5 ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
fhir_version: R4 fhir_version: R4
### 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
### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers ### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
### to determine the FHIR server address ### to determine the FHIR server address
@@ -104,7 +109,6 @@ hapi:
# auto_create_placeholder_reference_targets: false # auto_create_placeholder_reference_targets: false
### tells the server to automatically append the current version of the target resource to references at these paths ### 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 # auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
# cr_enabled: true
# ips_enabled: false # ips_enabled: false
# default_encoding: JSON # default_encoding: JSON
# default_pretty_print: true # default_pretty_print: true

13
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig; import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.fhir.rest.api.CacheControlDirective; import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum; import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome; import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -42,9 +43,9 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
"hapi.fhir.fhir_version=r4", "hapi.fhir.fhir_version=r4",
//"hapi.fhir.subscription.websocket_enabled=true", //"hapi.fhir.subscription.websocket_enabled=true",
//"hapi.fhir.mdm_enabled=true", //"hapi.fhir.mdm_enabled=true",
"hapi.fhir.cr_enabled=true", "hapi.fhir.cr.enabled=true",
"hapi.fhir.caregaps_section_author=Organization/alphora-author", "hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
"hapi.fhir.caregaps_reporter=Organization/alphora", "hapi.fhir.cr.caregaps_reporter=Organization/alphora",
"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core", "hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
"hapi.fhir.implementationguides.dk-core.version=1.1.0", "hapi.fhir.implementationguides.dk-core.version=1.1.0",
"hapi.fhir.auto_create_placeholder_reference_targets=true", "hapi.fhir.auto_create_placeholder_reference_targets=true",
@@ -57,7 +58,7 @@ class ExampleServerR4IT implements IServerSupport{
private IGenericClient ourClient; private IGenericClient ourClient;
private FhirContext ourCtx; private FhirContext ourCtx;
@Autowired private AppProperties appProperties; @Autowired private CrProperties crProperties;
@LocalServerPort @LocalServerPort
private int port; private int port;
@@ -253,8 +254,8 @@ class ExampleServerR4IT implements IServerSupport{
@Test @Test
void testCareGaps() throws IOException { void testCareGaps() throws IOException {
var reporter = appProperties.getCareGapsReporter(); var reporter = crProperties.getCareGapsReporter();
var author = appProperties.getCareGapsSectionAuthor(); var author = crProperties.getCareGapsSectionAuthor();
assertTrue(reporter.equals("Organization/alphora")); assertTrue(reporter.equals("Organization/alphora"));
assertTrue(author.equals("Organization/alphora-author")); assertTrue(author.equals("Organization/alphora-author"));