Merge 4821 back to master (#4825)

* Merge 4821 into master

* Update to PRE3 snapshot

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4821-update-clinical-reasoning-version.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 4821
+title: "Update the clinical reasoning module version to the latest release of 3.0.0-PRE2"

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/BaseClinicalReasoningConfig.java

@@ -33,25 +33,20 @@
 import ca.uhn.fhir.cr.common.IDataProviderFactory;
 import ca.uhn.fhir.cr.common.IFhirDalFactory;
 import ca.uhn.fhir.cr.common.ILibraryLoaderFactory;
-import ca.uhn.fhir.cr.common.ILibraryManagerFactory;
 import ca.uhn.fhir.cr.common.ILibrarySourceProviderFactory;
 import ca.uhn.fhir.cr.common.ITerminologyProviderFactory;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
-import org.cqframework.cql.cql2elm.LibraryManager;
-import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.cql2elm.model.Model;
 import org.cqframework.cql.cql2elm.quick.FhirLibrarySourceProvider;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.cql.engine.data.CompositeDataProvider;
 import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
 import org.opencds.cqf.cql.engine.fhir.model.R4FhirModelResolver;
@@ -61,14 +56,14 @@
 import org.opencds.cqf.cql.evaluator.CqlOptions;
 import org.opencds.cqf.cql.evaluator.builder.DataProviderComponents;
 import org.opencds.cqf.cql.evaluator.builder.EndpointInfo;
-import org.opencds.cqf.cql.evaluator.cql2elm.model.CacheAwareModelManager;
 import org.opencds.cqf.cql.evaluator.cql2elm.util.LibraryVersionSelector;
 import org.opencds.cqf.cql.evaluator.engine.execution.CacheAwareLibraryLoaderDecorator;
 import org.opencds.cqf.cql.evaluator.engine.execution.TranslatingLibraryLoader;
 import org.opencds.cqf.cql.evaluator.engine.model.CachingModelResolverDecorator;
 import org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider;
 import org.opencds.cqf.cql.evaluator.fhir.Constants;
 import org.opencds.cqf.cql.evaluator.fhir.adapter.AdapterFactory;
+import org.opencds.cqf.cql.evaluator.library.EvaluationSettings;
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.cql.evaluator.spring.fhir.adapter.AdapterConfiguration;
 import org.slf4j.Logger;
@@ -87,13 +82,22 @@
 import java.util.concurrent.Executor;
 import java.util.concurrent.ForkJoinPool;
 
-@Import(AdapterConfiguration.class)
+
 @Configuration
-public abstract class BaseClinicalReasoningConfig extends BaseRepositoryConfig {
+@Import({AdapterConfiguration.class, BaseRepositoryConfig.class})
+public abstract class BaseClinicalReasoningConfig {
 
  private static final Logger ourLogger = LoggerFactory.getLogger(BaseClinicalReasoningConfig.class);
 
+ @Bean
+ EvaluationSettings evaluationSettings(CqlOptions theCqlOptions, Map<ModelIdentifier, Model> theGlobalModelCache, Map<org.cqframework.cql.elm.execution.VersionedIdentifier, org.cqframework.cql.elm.execution.Library> theGlobalLibraryCache) {
+ var evaluationSettings = new EvaluationSettings();
+ evaluationSettings.setCqlOptions(theCqlOptions);
+ evaluationSettings.setModelCache(theGlobalModelCache);
+ evaluationSettings.setLibraryCache(theGlobalLibraryCache);
 
+ return evaluationSettings;
+ }
  @Bean
  CrProviderFactory cqlProviderFactory() {
  return new CrProviderFactory();
@@ -153,7 +157,7 @@ public CqlTranslatorOptions cqlTranslatorOptions(FhirContext theFhirContext, CrP
  @Scope("prototype")
  public ModelManager modelManager(
  Map<ModelIdentifier, Model> theGlobalModelCache) {
- return new CacheAwareModelManager(theGlobalModelCache);
+ return new ModelManager(theGlobalModelCache);
  }
 
  @Bean
@@ -229,15 +233,7 @@ ILibraryLoaderFactory libraryLoaderFactory(
  lcp.add(new FhirLibrarySourceProvider());
  }
 
- return new CacheAwareLibraryLoaderDecorator(
- new TranslatingLibraryLoader(theModelManager, lcp, theCqlTranslatorOptions, null), theGlobalLibraryCache) {
- // TODO: This is due to a bug with the ELM annotations which prevent options
- // from matching the way they should
- @Override
- protected Boolean translatorOptionsMatch(org.cqframework.cql.elm.execution.Library library) {
- return true;
- }
- };
+ return new TranslatingLibraryLoader(theModelManager, lcp, theCqlTranslatorOptions, theGlobalLibraryCache);
  };
  }
 
@@ -296,7 +292,7 @@ public LibraryVersionSelector libraryVersionSelector(AdapterFactory theAdapterFa
  return new LibraryVersionSelector(theAdapterFactory);
  }
 
- @Bean(name = "cqlExecutor")
+ @Bean
  public Executor cqlExecutor() {
  CqlForkJoinWorkerThreadFactory factory = new CqlForkJoinWorkerThreadFactory();
  ForkJoinPool myCommonPool = new ForkJoinPool(Math.min(32767, Runtime.getRuntime().availableProcessors()),

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/BaseRepositoryConfig.java

@@ -28,7 +28,6 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 
-@Import(AdapterConfiguration.class)
 @Configuration
 public abstract class BaseRepositoryConfig {
  @Bean

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/CrDstu3Config.java

@@ -25,12 +25,14 @@
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Scope;
 
 import java.util.function.Function;
 
 @Configuration
-public class CrDstu3Config extends BaseClinicalReasoningConfig {
+@Import(BaseClinicalReasoningConfig.class)
+public class CrDstu3Config {
 
  @Bean
  public Function<RequestDetails, MeasureService> dstu3MeasureServiceFactory(ApplicationContext theApplicationContext) {

hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/CrR4Config.java

@@ -31,12 +31,15 @@
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Scope;
 
+import java.util.concurrent.Executor;
 import java.util.function.Function;
 
 @Configuration
-public class CrR4Config extends BaseClinicalReasoningConfig {
+@Import(BaseClinicalReasoningConfig.class)
+public class CrR4Config {
 
  @Bean
  public Function<RequestDetails, MeasureService> r4MeasureServiceFactory(ApplicationContext theApplicationContext) {
@@ -61,10 +64,10 @@ public MeasureOperationsProvider r4measureOperationsProvider() {
  @Bean
  public Function<RequestDetails, CareGapsService> r4CareGapsServiceFactory(Function<RequestDetails, MeasureService> theR4MeasureServiceFactory,
  CrProperties theCrProperties,
- DaoRegistry theDaoRegistry) {
+ DaoRegistry theDaoRegistry, Executor cqlExecutor) {
  return r -> {
  var ms = theR4MeasureServiceFactory.apply(r);
- var cs = new CareGapsService(theCrProperties, ms, theDaoRegistry, cqlExecutor(), r);
+ var cs = new CareGapsService(theCrProperties, ms, theDaoRegistry, cqlExecutor, r);
  return cs;
  };
  }