Update ruler to HAPI 6.1.1 and add Batch2 beans

.vscode/launch.json

@@ -12,7 +12,6 @@
 			"projectName": "cqf-ruler-core",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Dspring.main.lazy-initialization=true",
 				"-Ddebug=true",
 				"-Dloader.debug=true",
 				"-Dhapi.fhir.bulk_export_enabled=false",
@@ -38,7 +37,6 @@
 			"projectName": "cqf-ruler-server",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Dspring.main.lazy-initialization=true",
 				"-Ddebug=true",
 				"-Dloader.debug=true",
 				"-Dhapi.fhir.bulk_export_enabled=false",
@@ -99,7 +97,6 @@
 			"projectName": "cqf-ruler-server",
 			"vmArgs": [
 				"-XX:TieredStopAtLevel=1",
-				"-Dspring.main.lazy-initialization=true",
 				"-Ddebug=true",
 				"-Dloader.debug=true",
 				"-Dhapi.fhir.fhir_version=DSTU3",

.vscode/settings.json

@@ -5,8 +5,7 @@
 		{
 			"name": "test-config",
 			"vmArgs": [
-				"-XX:TieredStopAtLevel=1",
-				"-Dspring.main.lazy-initialization=true"
+				"-XX:TieredStopAtLevel=1"
 			]
 		},
 	],
@@ -81,5 +80,5 @@
 	"files.eol": "\r\n",
 	"editor.formatOnSave": true,
 	"thunder-client.saveToWorkspace": true,
-	"java.jdt.ls.vmargs": "-noverify -Xmx2G -XX:+UseG1GC -XX:+UseStringDeduplication"
+	"java.jdt.ls.vmargs": "-Xmx2G -XX:+UseG1GC -XX:+UseStringDeduplication"
 }

core/src/main/java/org/opencds/cqf/ruler/Application.java

@@ -1,12 +1,11 @@
 package org.opencds.cqf.ruler;
 
+import org.opencds.cqf.external.annotations.OnEitherVersion;
+import org.opencds.cqf.external.mdm.MdmConfig;
 import org.opencds.cqf.ruler.config.BeanFinderConfig;
+import org.opencds.cqf.ruler.config.RulerConfig;
+import org.opencds.cqf.ruler.config.ServerProperties;
 import org.opencds.cqf.ruler.config.TesterUIConfig;
-import org.opencds.cqf.ruler.external.FhirTesterConfig;
-import org.opencds.cqf.ruler.external.annotations.OnEitherVersion;
-import org.opencds.cqf.ruler.external.cql.StarterCqlDstu3Config;
-import org.opencds.cqf.ruler.external.cql.StarterCqlR4Config;
-import org.opencds.cqf.ruler.external.mdm.MdmConfig;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.SpringApplication;
@@ -18,27 +17,20 @@
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Conditional;
-import org.springframework.context.annotation.FilterType;
 import org.springframework.context.annotation.Import;
 
-import ca.uhn.fhir.cql.config.BaseCqlConfig;
-import ca.uhn.fhir.cql.config.CqlDstu3Config;
-import ca.uhn.fhir.cql.config.CqlR4Config;
-import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
-import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
-import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 
 @ServletComponentScan(basePackageClasses = Application.class)
-@ComponentScan(basePackageClasses = { org.opencds.cqf.ruler.external.Application.class,
-		Application.class }, excludeFilters = @ComponentScan.Filter(type = FilterType.ASSIGNABLE_TYPE, value = {
-				FhirTesterConfig.class, org.opencds.cqf.ruler.external.Application.class, StarterCqlR4Config.class,
-				StarterCqlDstu3Config.class, CqlR4Config.class, CqlDstu3Config.class, BaseCqlConfig.class }))
 @SpringBootApplication(exclude = { ElasticsearchRestClientAutoConfiguration.class, QuartzAutoConfiguration.class })
-@Import({ SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class,
-		WebsocketDispatcherConfig.class, MdmConfig.class, TesterUIConfig.class, BeanFinderConfig.class })
+@Import({
+		RulerConfig.class,
+		ServerProperties.class,
+		WebsocketDispatcherConfig.class,
+		MdmConfig.class,
+		TesterUIConfig.class,
+		BeanFinderConfig.class, })
 public class Application extends SpringBootServletInitializer {
 
 	public static void main(String[] args) {

core/src/main/java/org/opencds/cqf/ruler/Server.java

@@ -10,28 +10,48 @@
 
 import org.hl7.fhir.dstu3.model.CapabilityStatement;
 import org.hl7.fhir.instance.model.api.IBaseConformance;
+import org.opencds.cqf.external.AppProperties;
+import org.opencds.cqf.external.BaseJpaRestfulServer;
+import org.opencds.cqf.external.mdm.MdmConfig;
 import org.opencds.cqf.ruler.api.Interceptor;
 import org.opencds.cqf.ruler.api.MetadataExtender;
 import org.opencds.cqf.ruler.api.OperationProvider;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaCapabilityStatementProvider;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu2;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu3;
+import org.opencds.cqf.ruler.config.BeanFinderConfig;
 import org.opencds.cqf.ruler.config.ServerProperties;
-import org.opencds.cqf.ruler.external.AppProperties;
-import org.opencds.cqf.ruler.external.BaseJpaRestfulServer;
+import org.opencds.cqf.ruler.config.TesterUIConfig;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.Import;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
+import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
+import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
+import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
+import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 import ca.uhn.fhir.model.dstu2.resource.Conformance;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 
+@Import({
+		ServerProperties.class,
+		SubscriptionSubmitterConfig.class,
+		SubscriptionProcessorConfig.class,
+		SubscriptionChannelConfig.class,
+		WebsocketDispatcherConfig.class,
+		MdmConfig.class,
+		JpaBatch2Config.class,
+		Batch2JobsConfig.class,
+		TesterUIConfig.class,
+		BeanFinderConfig.class })
 public class Server extends BaseJpaRestfulServer {
 	private static final long serialVersionUID = 1L;
 
@@ -59,9 +79,6 @@ public class Server extends BaseJpaRestfulServer {
 	@Autowired
 	ServerProperties myServerProperties;
 
-	@Autowired
-	ValueSetOperationProvider valueSetOperationProvider;
-
 	public Server() {
 		super();
 	}
@@ -71,10 +88,6 @@ public Server() {
 	protected void initialize() throws ServletException {
 		super.initialize();
 
-		// TODO: This is needed due to a version mismatch with HAPI. Once we upgrade to
-		// >=5.7.0 we need to remove this
-		this.registerProvider(valueSetOperationProvider);
-
 		log.info("Loading operation providers from plugins");
 		Map<String, OperationProvider> providers = applicationContext.getBeansOfType(OperationProvider.class);
 		for (OperationProvider o : providers.values()) {
@@ -88,7 +101,7 @@ protected void initialize() throws ServletException {
 			log.info("Registering {} interceptor", o.getClass().getName());
 			this.registerInterceptor(o);
 		}
-		
+
 		log.info("Loading metadata extenders from plugins");
 		Map<String, MetadataExtender> extenders = applicationContext.getBeansOfType(MetadataExtender.class);
 		for (MetadataExtender o : extenders.values()) {

core/src/main/java/org/opencds/cqf/ruler/config/FhirServerConfigDstu2.java

@@ -0,0 +1,16 @@
+package org.opencds.cqf.ruler.config;
+
+import org.opencds.cqf.external.annotations.OnDSTU2Condition;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+import ca.uhn.fhir.jpa.config.JpaDstu2Config;
+
+@Configuration
+@Conditional(OnDSTU2Condition.class)
+@Import({
+		JpaDstu2Config.class
+})
+public class FhirServerConfigDstu2 {
+}

core/src/main/java/org/opencds/cqf/ruler/config/FhirServerConfigDstu3.java

@@ -0,0 +1,17 @@
+package org.opencds.cqf.ruler.config;
+
+import org.opencds.cqf.external.ElasticsearchConfig;
+import org.opencds.cqf.external.annotations.OnDSTU3Condition;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
+
+@Configuration
+@Conditional(OnDSTU3Condition.class)
+@Import({
+		JpaDstu3Config.class,
+		ElasticsearchConfig.class })
+public class FhirServerConfigDstu3 {
+}

core/src/main/java/org/opencds/cqf/ruler/config/FhirServerConfigR4.java

@@ -0,0 +1,18 @@
+package org.opencds.cqf.ruler.config;
+
+import org.opencds.cqf.external.ElasticsearchConfig;
+import org.opencds.cqf.external.annotations.OnR4Condition;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
+
+@Configuration
+@Conditional(OnR4Condition.class)
+@Import({
+		JpaR4Config.class,
+		ElasticsearchConfig.class
+})
+public class FhirServerConfigR4 {
+}

core/src/main/java/org/opencds/cqf/ruler/config/FhirServerConfigR5.java

@@ -0,0 +1,18 @@
+package org.opencds.cqf.ruler.config;
+
+import org.opencds.cqf.external.ElasticsearchConfig;
+import org.opencds.cqf.external.annotations.OnR5Condition;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
+
+@Configuration
+@Conditional(OnR5Condition.class)
+@Import({
+		JpaR5Config.class,
+		ElasticsearchConfig.class
+})
+public class FhirServerConfigR5 {
+}

core/src/main/java/org/opencds/cqf/ruler/config/JpaConfigCommon.java

@@ -0,0 +1,125 @@
+package org.opencds.cqf.ruler.config;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
+import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
+import org.opencds.cqf.external.AppProperties;
+import org.opencds.cqf.external.EnvironmentHelper;
+import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
+import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
+import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
+import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
+import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
+import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
+import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
+import ca.uhn.fhir.jpa.entity.MdmLink;
+import ca.uhn.fhir.jpa.provider.DaoRegistryResourceSupportedSvc;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
+import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
+import ca.uhn.fhir.jpa.util.ResourceCountCache;
+import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
+import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
+import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
+
+@Configuration
+public class JpaConfigCommon {
+	@Bean
+	public IFulltextSearchSvc fullTextSearchSvc() {
+		return new FulltextSearchSvcImpl();
+	}
+
+	@Bean
+	public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
+		return new StaleSearchDeletingSvcImpl();
+	}
+
+	@Primary
+	@Bean
+	public CachingValidationSupport validationSupportChain(JpaValidationSupportChain theJpaValidationSupportChain) {
+		return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
+	}
+
+	@Bean
+	public BatchConfigurer batchConfigurer() {
+		return new NonPersistedBatchConfigurer();
+	}
+
+	/**
+	 * Customize the default/max page sizes for search results. You can set these
+	 * however
+	 * you want, although very large page sizes will require a lot of RAM.
+	 */
+	@Bean
+	public DatabaseBackedPagingProvider databaseBackedPagingProvider(AppProperties appProperties) {
+		DatabaseBackedPagingProvider pagingProvider = new DatabaseBackedPagingProvider();
+		pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
+		pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
+		return pagingProvider;
+	}
+
+	@Bean
+	public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
+		return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
+	}
+
+	@Bean(name = "myResourceCountsCache")
+	public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
+		return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
+	}
+
+	@Primary
+	@Bean
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+			ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext,
+			DataSource myDataSource,
+			ConfigurableEnvironment configurableEnvironment) {
+		LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil
+				.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
+		retVal.setPersistenceUnitName("HAPI_PU");
+
+		try {
+			retVal.setDataSource(myDataSource);
+		} catch (Exception e) {
+			throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
+		}
+		retVal.setJpaProperties(
+				EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
+		return retVal;
+	}
+
+	@Bean
+	@Primary
+	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+		JpaTransactionManager retVal = new JpaTransactionManager();
+		retVal.setEntityManagerFactory(entityManagerFactory);
+		return retVal;
+	}
+
+	@Bean
+	public IHSearchSortHelper hSearchSortHelper(ISearchParamRegistry mySearchParamRegistry) {
+		return new HSearchSortHelperImpl(mySearchParamRegistry);
+	}
+
+	@Bean
+	public IMdmLinkDao<MdmLink> mdmLinkDao() {
+		return new MdmLinkDaoJpaImpl();
+	}
+}