Update to HAPI 7.6.0 (#731)

* Bump to HAPI 7.5.0-SNAPSHOT

* Bump to latest HAPI version + fix config

* Bump to latest HAPI version + fix CR config + spotless

* Bump parent version to 7.5.4-SNAPSHOT

* Update to HAPI Release 7.6.0

---------

Co-authored-by: Brenin Rhodes <brenin@alphora.com>

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>7.4.0</version>
+        <version>7.6.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.starter.common;
 
+import ca.uhn.fhir.batch2.config.Batch2JobRegisterer;
 import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
 import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
@@ -46,7 +47,6 @@ import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
 import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
 import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
 import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
-import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -66,6 +66,8 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Strings;
 import jakarta.persistence.EntityManagerFactory;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.NoSuchBeanDefinitionException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@@ -89,7 +91,7 @@ import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInt
 @Import(ThreadPoolFactoryConfig.class)
 public class StarterJpaConfig {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(StarterJpaConfig.class);
 
 	@Bean
 	public IFulltextSearchSvc fullTextSearchSvc() {
@@ -191,11 +193,11 @@ public class StarterJpaConfig {
 	@Primary
 	@Conditional(OnImplementationGuidesPresent.class)
 	public IPackageInstallerSvc packageInstaller(
-			AppProperties appProperties,
+		AppProperties appProperties,
-			JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
+		IPackageInstallerSvc packageInstallerSvc,
-			JobDefinitionRegistry jobDefinitionRegistry,
+		Batch2JobRegisterer batch2JobRegisterer) {
-			IPackageInstallerSvc packageInstallerSvc) {
+
-		jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
+		batch2JobRegisterer.start();
 
 		if (appProperties.getImplementationGuides() != null) {
 			Map<String, PackageInstallationSpec> guides = appProperties.getImplementationGuides();

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

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

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

@@ -5,7 +5,7 @@ import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 
 public class CqlCompilerProperties {
-    private Boolean validate_units = true;
+	private Boolean validate_units = true;
 	private Boolean verify_only = false;
 	private String compatibility_level = "1.5";
 	private CqlCompilerException.ErrorSeverity error_level = CqlCompilerException.ErrorSeverity.Info;
@@ -27,7 +27,6 @@ public class CqlCompilerProperties {
 	private Boolean require_from_keyword = false;
 	private Boolean disable_default_model_info_load = false;
 
-
 	public boolean isValidateUnits() {
 		return validate_units;
 	}
@@ -194,5 +193,5 @@ public class CqlCompilerProperties {
 
 	public void setTranslatorFormat(CqlTranslator.Format translatorFormat) {
 		this.translator_format = translatorFormat;
-	}  
+	}
 }

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

@@ -5,49 +5,49 @@ import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
 
 public class CqlProperties {
 
-    private Boolean use_embedded_libraries = true;
+	private Boolean use_embedded_libraries = true;
-    private CqlCompilerProperties compiler = new CqlCompilerProperties();
+	private CqlCompilerProperties compiler = new CqlCompilerProperties();
-    private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
+	private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
-    private TerminologySettings terminology = new TerminologySettings();
+	private TerminologySettings terminology = new TerminologySettings();
-    private RetrieveSettings data = new RetrieveSettings();
+	private RetrieveSettings data = new RetrieveSettings();
-    
-    public Boolean getUse_embedded_libraries() {
-        return use_embedded_libraries;
-    }
 
-    public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
+	public Boolean getUse_embedded_libraries() {
-        this.use_embedded_libraries = use_embedded_libraries;
+		return use_embedded_libraries;
-    }
+	}
 
-    public CqlCompilerProperties getCompiler() {
+	public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
-        return compiler;
+		this.use_embedded_libraries = use_embedded_libraries;
-    }
+	}
 
-    public void setCompiler(CqlCompilerProperties compiler) {
+	public CqlCompilerProperties getCompiler() {
-        this.compiler = compiler;
+		return compiler;
-    }
+	}
 
-    public CqlRuntimeProperties getRuntime() {
+	public void setCompiler(CqlCompilerProperties compiler) {
-        return runtime;
+		this.compiler = compiler;
-    }
+	}
-    
-    public void setRuntime(CqlRuntimeProperties runtime) {
-        this.runtime = runtime;
-    }
 
-    public TerminologySettings getTerminology() {
+	public CqlRuntimeProperties getRuntime() {
-        return terminology;
+		return runtime;
-    }
+	}
 
-    public void setTerminology(TerminologySettings terminology) {
+	public void setRuntime(CqlRuntimeProperties runtime) {
-        this.terminology = terminology;
+		this.runtime = runtime;
-    }
+	}
 
-    public RetrieveSettings getData() {
+	public TerminologySettings getTerminology() {
-        return data;
+		return terminology;
-    }
+	}
 
-    public void setData(RetrieveSettings data) {
+	public void setTerminology(TerminologySettings terminology) {
-        this.data = data;
+		this.terminology = terminology;
-    }
+	}
+
+	public RetrieveSettings getData() {
+		return data;
+	}
+
+	public void setData(RetrieveSettings data) {
+		this.data = data;
+	}
 }

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

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.starter.cr;
 
 public class CqlRuntimeProperties {
 
-    private Boolean debug_logging_enabled = false;
+	private Boolean debug_logging_enabled = false;
 	private Boolean enable_validation = false;
 	private Boolean enable_expression_caching = true;
 
@@ -14,7 +14,6 @@ public class CqlRuntimeProperties {
 		this.debug_logging_enabled = debug_logging_enabled;
 	}
 
-
 	public boolean isEnableExpressionCaching() {
 		return enable_expression_caching;
 	}
@@ -30,6 +29,4 @@ public class CqlRuntimeProperties {
 	public void EnableValidation(boolean enable_validation) {
 		this.enable_validation = enable_validation;
 	}
-
-    
 }

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

@@ -1,13 +1,14 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import java.util.EnumSet;
+import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
-import java.util.List;
+import ca.uhn.fhir.cr.common.CqlThreadFactory;
-import java.util.Map;
+import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
-import java.util.Set;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import java.util.concurrent.ConcurrentHashMap;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
-import java.util.concurrent.ExecutorService;
+import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
-import java.util.concurrent.Executors;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-
+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;
@@ -28,15 +29,13 @@ 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 java.util.EnumSet;
-import ca.uhn.fhir.cr.common.CqlThreadFactory;
+import java.util.List;
-import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
+import java.util.Map;
-import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import java.util.Set;
-import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
+import java.util.concurrent.ConcurrentHashMap;
-import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
+import java.util.concurrent.ExecutorService;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import java.util.concurrent.Executors;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 
 @Configuration
 @Conditional({CrConfigCondition.class})
@@ -157,8 +156,12 @@ public class CrCommonConfig {
 	@Bean
 	CareGapsProperties careGapsProperties(CrProperties theCrProperties) {
 		var careGapsProperties = new CareGapsProperties();
-		careGapsProperties.setCareGapsReporter(theCrProperties.getCareGaps().getReporter());
+		// This check for the resource type really should be happening down in CR where the setting is actually used but
-		careGapsProperties.setCareGapsCompositionSectionAuthor(theCrProperties.getCareGaps().getSection_author());
+		// that will have to wait for a future CR release
+		careGapsProperties.setCareGapsReporter(
+				theCrProperties.getCareGaps().getReporter().replace("Organization/", ""));
+		careGapsProperties.setCareGapsCompositionSectionAuthor(
+				theCrProperties.getCareGaps().getSection_author().replace("Organization/", ""));
 		return careGapsProperties;
 	}
 
@@ -224,5 +227,5 @@ public class CrCommonConfig {
 	@Bean
 	public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
 		return new ResourceChangeListenerRegistryInterceptor();
-	}   
+	}
 }

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

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
-import org.cqframework.cql.cql2elm.CqlCompilerException;
-import org.cqframework.cql.cql2elm.CqlTranslator;
-import org.cqframework.cql.cql2elm.LibraryBuilder;
-
 public class CrProperties {
 	private Boolean enabled;
 

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

@@ -2,10 +2,9 @@ package ca.uhn.fhir.jpa.starter.cr;
 
 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.DataRequirementsOperationConfig;
+import ca.uhn.fhir.cr.config.dstu3.EvaluateOperationConfig;
 import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
-import ca.uhn.fhir.cr.config.dstu3.PopulateOperationConfig;
-import ca.uhn.fhir.cr.config.dstu3.QuestionnaireOperationConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
 import org.springframework.context.annotation.*;
 
@@ -15,11 +14,8 @@ import org.springframework.context.annotation.*;
 	CrCommonConfig.class,
 	CrDstu3Config.class,
 	ApplyOperationConfig.class,
-	ExtractOperationConfig.class,
+	DataRequirementsOperationConfig.class,
-	PackageOperationConfig.class,
+	EvaluateOperationConfig.class,
-	PopulateOperationConfig.class,
+	PackageOperationConfig.class
-	QuestionnaireOperationConfig.class
 })
-public class StarterCrDstu3Config {
+public class StarterCrDstu3Config {}
-	
-}

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

@@ -2,6 +2,8 @@ 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.DataRequirementsOperationConfig;
+import ca.uhn.fhir.cr.config.r4.EvaluateOperationConfig;
 import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
 import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
 import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
@@ -17,11 +19,11 @@ import org.springframework.context.annotation.Import;
 	CrCommonConfig.class,
 	CrR4Config.class,
 	ApplyOperationConfig.class,
+	DataRequirementsOperationConfig.class,
+	EvaluateOperationConfig.class,
 	ExtractOperationConfig.class,
 	PackageOperationConfig.class,
 	PopulateOperationConfig.class,
 	QuestionnaireOperationConfig.class
 })
-public class StarterCrR4Config {
+public class StarterCrR4Config {}
-	
-}

src/main/resources/application.yaml

@@ -121,7 +121,7 @@ hapi:
           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
+          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: DECLARED # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
 

src/main/resources/cds.application.yaml

@@ -177,7 +177,7 @@ hapi:
     #    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_external_references: true
     #    allow_multiple_delete: true
     #    allow_override_default_search_params: true
     #    auto_create_placeholder_reference_targets: false

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

@@ -16,6 +16,7 @@ import java.util.GregorianCalendar;
 import java.util.List;
 
 import co.elastic.clients.elasticsearch.ElasticsearchClient;
+import co.elastic.clients.elasticsearch.indices.IndexSettings;
 import co.elastic.clients.json.JsonData;
 import jakarta.annotation.PreDestroy;
 import org.elasticsearch.client.RequestOptions;
@@ -91,7 +92,7 @@ public class ElasticsearchLastNR4IT {
 	  elasticsearchHighLevelRestClient.indices().putTemplate(t->{
 		  t.name("hapi_fhir_template");
 		  t.indexPatterns("*");
-		  t.settings("index.max_result_window", JsonData.of(50000));
+		  t.settings(new IndexSettings.Builder().maxResultWindow(50000).build());
 		  return t;
 	  });
 

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

@@ -69,6 +69,7 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 	"hapi.fhir.cr.enabled=true",
 	"hapi.fhir.cr.caregaps.section_author=Organization/alphora-author",
 	"hapi.fhir.cr.caregaps.reporter=Organization/alphora",
+	"hapi.fhir.cr.cql.data.search_parameter_mode=USE_SEARCH_PARAMETERS",
 	"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
 	"hapi.fhir.implementationguides.dk-core.version=1.1.0",
 	"hapi.fhir.auto_create_placeholder_reference_targets=true",