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@@ -1,7 +1,6 @@
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package ca.uhn.fhir.jpa.starter.common;
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import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
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import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
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import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
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import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
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import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
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@@ -10,6 +9,7 @@ import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.jpa.api.IDaoRegistry;
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import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
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@@ -18,6 +18,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
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import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
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import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
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import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
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import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
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import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
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@@ -60,7 +61,6 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
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import ca.uhn.fhir.validation.IValidatorModule;
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import ca.uhn.fhir.validation.ResultSeverityEnum;
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import com.google.common.base.Strings;
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import com.google.common.collect.ImmutableList;
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import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
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import org.springframework.beans.factory.NoSuchBeanDefinitionException;
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import org.springframework.beans.factory.annotation.Autowired;
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@@ -73,26 +73,23 @@ import org.springframework.http.HttpHeaders;
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import org.springframework.orm.jpa.JpaTransactionManager;
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import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
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import org.springframework.web.cors.CorsConfiguration;
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import javax.persistence.EntityManagerFactory;
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import javax.sql.DataSource;
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import java.util.*;
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import static ca.uhn.fhir.context.FhirVersionEnum.DSTU3;
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import static ca.uhn.fhir.context.FhirVersionEnum.R4;
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import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
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@Configuration
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// allow users to configure custom packages to scan for additional beans
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//allow users to configure custom packages to scan for additional beans
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@ComponentScan(basePackages = { "${hapi.fhir.custom-bean-packages:}" })
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@Import({ ThreadPoolFactoryConfig.class })
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@Import(
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ThreadPoolFactoryConfig.class
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)
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public class StarterJpaConfig {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
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public StarterJpaConfig() {
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}
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@Bean
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public IFulltextSearchSvc fullTextSearchSvc() {
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return new FulltextSearchSvcImpl();
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@@ -109,12 +106,14 @@ public class StarterJpaConfig {
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return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
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}
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@Autowired
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private ConfigurableEnvironment configurableEnvironment;
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/**
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* Customize the default/max page sizes for search results. You can set these
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* however
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* Customize the default/max page sizes for search results. You can set these however
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* you want, although very large page sizes will require a lot of RAM.
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*/
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@Bean
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@@ -125,6 +124,7 @@ public class StarterJpaConfig {
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return pagingProvider;
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}
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@Bean
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public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
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return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
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@@ -137,10 +137,8 @@ public class StarterJpaConfig {
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@Primary
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@Bean
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public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource,
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ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
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LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil
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.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
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public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource, ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
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LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
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retVal.setPersistenceUnitName("HAPI_PU");
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try {
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@@ -148,8 +146,7 @@ public class StarterJpaConfig {
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} catch (Exception e) {
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throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
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}
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retVal.setJpaProperties(
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EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
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retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
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return retVal;
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}
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@@ -166,10 +163,10 @@ public class StarterJpaConfig {
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return new HSearchSortHelperImpl(mySearchParamRegistry);
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}
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@Bean
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@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
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public RepositoryValidatingInterceptor repositoryValidatingInterceptor(
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IRepositoryValidationInterceptorFactory factory) {
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public RepositoryValidatingInterceptor repositoryValidatingInterceptor(IRepositoryValidationInterceptorFactory factory) {
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return factory.buildUsingStoredStructureDefinitions();
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}
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@@ -191,23 +188,20 @@ public class StarterJpaConfig {
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@Bean("packageInstaller")
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@Primary
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@Conditional(OnImplementationGuidesPresent.class)
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public IPackageInstallerSvc packageInstaller(AppProperties appProperties,
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JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
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JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc) {
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public IPackageInstallerSvc packageInstaller(AppProperties appProperties, JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition, JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc)
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{
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jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
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if (appProperties.getImplementationGuides() != null) {
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Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
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for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
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PackageInstallationSpec packageInstallationSpec = new PackageInstallationSpec()
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.setPackageUrl(guide.getValue().getUrl()).setName(guide.getValue().getName())
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.setVersion(guide.getValue().getVersion())
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.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
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packageInstallationSpec.setReloadExisting(appProperties.getReload_existing_implementationguides());
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Map<String, PackageInstallationSpec> guides = appProperties.getImplementationGuides();
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for (Map.Entry<String, PackageInstallationSpec> guidesEntry : guides.entrySet()) {
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PackageInstallationSpec packageInstallationSpec = guidesEntry.getValue();
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if (appProperties.getInstall_transitive_ig_dependencies()) {
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packageInstallationSpec.setFetchDependencies(true);
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packageInstallationSpec.setDependencyExcludes(
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ImmutableList.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
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packageInstallationSpec.addDependencyExclude("hl7.fhir.r2.core")
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.addDependencyExclude("hl7.fhir.r3.core")
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.addDependencyExclude("hl7.fhir.r4.core")
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.addDependencyExclude("hl7.fhir.r5.core");
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}
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packageInstallerSvc.install(packageInstallationSpec);
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}
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@@ -247,24 +241,7 @@ public class StarterJpaConfig {
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}
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@Bean
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public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties,
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DaoRegistry daoRegistry,
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Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider,
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ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings,
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ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport,
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DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor,
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Optional<TerminologyUploaderProvider> terminologyUploaderProvider,
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Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider,
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Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster,
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Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor,
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IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider,
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BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider,
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ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider,
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PartitionManagementProvider partitionManagementProvider,
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Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor,
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IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc,
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ApplicationContext appContext,
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Optional<IpsOperationProvider> theIpsOperationProvider) {
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public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider) {
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RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
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List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
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@@ -282,21 +259,18 @@ public class StarterJpaConfig {
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fhirSystemDao.getContext().setNarrativeGenerator(new NullNarrativeGenerator());
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}
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if (appProperties.getMdm_enabled()) {
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mdmProviderProvider.get().loadProvider();
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}
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if (appProperties.getMdm_enabled()) mdmProviderProvider.get().loadProvider();
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fhirServer.registerProviders(resourceProviderFactory.createProviders());
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fhirServer.registerProvider(jpaSystemProvider);
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fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer,
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jpaStorageSettings, searchParamRegistry, theValidationSupport));
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fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
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/*
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* ETag Support
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*/
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if (!appProperties.getEtag_support_enabled())
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fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
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if (!appProperties.getEtag_support_enabled()) fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
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/*
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* Default to JSON and pretty printing
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@@ -333,8 +307,7 @@ public class StarterJpaConfig {
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/*
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* If you are hosting this server at a specific DNS name, the server will try to
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* figure out the FHIR base URL based on what the web container tells it, but
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* this doesn't always work. If you are setting links in your search bundles
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* that
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* this doesn't always work. If you are setting links in your search bundles that
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* just refer to "localhost", you might want to use a server address strategy:
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*/
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String serverAddress = appProperties.getServer_address();
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@@ -342,24 +315,19 @@ public class StarterJpaConfig {
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fhirServer.setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
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} else if (appProperties.getUse_apache_address_strategy()) {
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boolean useHttps = appProperties.getUse_apache_address_strategy_https();
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fhirServer.setServerAddressStrategy(
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useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
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fhirServer.setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
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} else {
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fhirServer.setServerAddressStrategy(new IncomingRequestAddressStrategy());
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}
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/*
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* If you are using DSTU3+, you may want to add a terminology uploader, which
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* allows
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* uploading of external terminologies such as Snomed CT. Note that this
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* uploader
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* does not have any security attached (any anonymous user may use it by
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* default)
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* so it is a potential security vulnerability. Consider using an
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* AuthorizationInterceptor
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* If you are using DSTU3+, you may want to add a terminology uploader, which allows
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* uploading of external terminologies such as Snomed CT. Note that this uploader
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* does not have any security attached (any anonymous user may use it by default)
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* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
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* with this feature.
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*/
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if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(DSTU3)) { // <-- ENABLED RIGHT NOW
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if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
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fhirServer.registerProvider(terminologyUploaderProvider.get());
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}
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@@ -377,8 +345,7 @@ public class StarterJpaConfig {
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}
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if (appProperties.getAllow_cascading_deletes()) {
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CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
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fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
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CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
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fhirServer.registerInterceptor(cascadingDeleteInterceptor);
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}
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@@ -407,7 +374,7 @@ public class StarterJpaConfig {
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// GraphQL
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if (appProperties.getGraphql_enabled()) {
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if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(DSTU3)) {
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if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
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fhirServer.registerProvider(graphQLProvider.get());
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}
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}
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@@ -421,15 +388,16 @@ public class StarterJpaConfig {
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fhirServer.registerProvider(bulkDataExportProvider);
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}
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// Bulk Import
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//Bulk Import
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if (appProperties.getBulk_import_enabled()) {
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fhirServer.registerProvider(bulkDataImportProvider);
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}
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// valueSet Operations i.e $expand
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fhirServer.registerProvider(theValueSetOperationProvider);
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// reindex Provider $reindex
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//reindex Provider $reindex
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fhirServer.registerProvider(reindexProvider);
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// Partitioning
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@@ -443,7 +411,8 @@ public class StarterJpaConfig {
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// register custom interceptors
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registerCustomInterceptors(fhirServer, appContext, appProperties.getCustomInterceptorClasses());
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// register the IPS Provider
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//register the IPS Provider
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if (!theIpsOperationProvider.isEmpty()) {
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fhirServer.registerProvider(theIpsOperationProvider.get());
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}
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@@ -455,8 +424,7 @@ public class StarterJpaConfig {
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* check the properties for custom interceptor classes and registers them.
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*/
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@SuppressWarnings({ "unchecked", "rawtypes" })
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private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext,
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List<String> customInterceptorClasses) {
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private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
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if (customInterceptorClasses == null) {
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return;
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@@ -490,37 +458,30 @@ public class StarterJpaConfig {
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}
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}
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public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao,
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RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry,
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IValidationSupport theValidationSupport) {
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public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
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FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
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|
|
if (fhirVersion == FhirVersionEnum.DSTU2) {
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JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao,
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jpaStorageSettings);
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JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
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|
|
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
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|
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return confProvider;
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|
} else if (fhirVersion == DSTU3) {
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|
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
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|
|
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao,
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|
|
jpaStorageSettings, searchParamRegistry);
|
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|
|
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
|
|
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|
|
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
|
|
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|
|
return confProvider;
|
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|
|
} else if (fhirVersion == R4) {
|
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|
|
} else if (fhirVersion == FhirVersionEnum.R4) {
|
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|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
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|
|
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
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|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
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|
|
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
|
|
|
|
|
return confProvider;
|
|
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|
|
} else if (fhirVersion == FhirVersionEnum.R4B) {
|
|
|
|
|
|
|
|
|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
|
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|
|
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
|
|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
|
|
|
confProvider.setImplementationDescription("HAPI FHIR R4B Server");
|
|
|
|
|
return confProvider;
|
|
|
|
|
} else if (fhirVersion == FhirVersionEnum.R5) {
|
|
|
|
|
|
|
|
|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
|
|
|
|
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
|
|
|
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
|
|
|
|
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
|
|
|
|
|
return confProvider;
|
|
|
|
|
} else {
|
|
|
|
|
|
Justin McKelvy