Test fixes
This commit is contained in:
2
pom.xml
2
pom.xml
@@ -11,7 +11,7 @@
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir</artifactId>
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<version>5.0.0-SNAPSHOT</version>
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<version>5.0.0</version>
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</parent>
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<artifactId>hapi-fhir-jpaserver-starter</artifactId>
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@@ -1,28 +1,40 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
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import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
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import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
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import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
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import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
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public class ApplicationContext extends AnnotationConfigWebApplicationContext {
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public ApplicationContext() {
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FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
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if (fhirVersion == FhirVersionEnum.DSTU2) {
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register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.DSTU3) {
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register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.R4) {
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register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.R5) {
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register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
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} else {
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throw new IllegalStateException();
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}
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if (HapiProperties.getSubscriptionWebsocketEnabled()) {
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register(ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig.class);
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}
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public ApplicationContext() {
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FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
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if (fhirVersion == FhirVersionEnum.DSTU2) {
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register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.DSTU3) {
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register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.R4) {
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register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
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} else if (fhirVersion == FhirVersionEnum.R5) {
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register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
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} else {
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throw new IllegalStateException();
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}
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if (HapiProperties.getSubscriptionWebsocketEnabled()) {
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register(WebsocketDispatcherConfig.class);
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}
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if (HapiProperties.getSubscriptionEmailEnabled()
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|| HapiProperties.getSubscriptionRestHookEnabled()
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|| HapiProperties.getSubscriptionWebsocketEnabled()) {
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register(SubscriptionSubmitterConfig.class);
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register(SubscriptionProcessorConfig.class);
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register(SubscriptionChannelConfig.class);
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}
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}
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}
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@@ -1,14 +1,16 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
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import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.model.config.PartitionSettings;
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import ca.uhn.fhir.jpa.model.entity.ModelConfig;
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import ca.uhn.fhir.jpa.subscription.module.channel.SubscriptionDeliveryHandlerFactory;
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import ca.uhn.fhir.jpa.subscription.module.subscriber.email.IEmailSender;
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import ca.uhn.fhir.jpa.subscription.module.subscriber.email.JavaMailEmailSender;
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import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
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import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
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import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
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import org.apache.commons.dbcp2.BasicDataSource;
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import org.hl7.fhir.dstu2.model.Subscription;
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import org.springframework.beans.factory.BeanFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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@@ -50,9 +52,8 @@ public class FhirServerConfigCommon {
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private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
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private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
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private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
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@Autowired
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private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
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private ApplicationContext myAppCtx;
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public FhirServerConfigCommon() {
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ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
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@@ -116,15 +117,15 @@ public class FhirServerConfigCommon {
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// Subscriptions are enabled by channel type
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if (HapiProperties.getSubscriptionRestHookEnabled()) {
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ourLog.info("Enabling REST-hook subscriptions");
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retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
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retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
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}
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if (HapiProperties.getSubscriptionEmailEnabled()) {
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ourLog.info("Enabling email subscriptions");
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retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
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retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
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}
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if (HapiProperties.getSubscriptionWebsocketEnabled()) {
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ourLog.info("Enabling websocket subscriptions");
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retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
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retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
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}
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retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
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@@ -132,6 +133,12 @@ public class FhirServerConfigCommon {
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return retVal;
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}
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@Bean
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public PartitionSettings partitionSettings() {
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return new PartitionSettings();
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}
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@Bean
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public ModelConfig modelConfig() {
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ModelConfig modelConfig = new ModelConfig();
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@@ -197,8 +204,9 @@ public class FhirServerConfigCommon {
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// retVal.setStartTlsRequired(this.emailStartTlsRequired);
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// retVal.setQuitWait(this.emailQuitWait);
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Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
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mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
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SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
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Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");
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subscriptionDeliveryHandlerFactory.setEmailSender(retVal);
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return retVal;
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@@ -485,5 +485,9 @@ public class HapiProperties {
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public static boolean getBulkExportEnabled() {
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return HapiProperties.getBooleanProperty(BULK_EXPORT_ENABLED, true);
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}
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public static boolean isFhirPathFilterInterceptorEnabled() {
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return HapiProperties.getBooleanProperty("fhirpath_interceptor.enabled", false);
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}
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}
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@@ -4,11 +4,12 @@ import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.interceptor.api.IInterceptorService;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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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.api.rp.ResourceProviderFactory;
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import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
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import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
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import ca.uhn.fhir.jpa.provider.GraphQLProvider;
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import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
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@@ -22,25 +23,23 @@ import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
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import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
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import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
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import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
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import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
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import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
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import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
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import ca.uhn.fhir.model.dstu2.composite.MetaDt;
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import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
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import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
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import ca.uhn.fhir.rest.server.RestfulServer;
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import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
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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 java.util.HashSet;
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import java.util.TreeSet;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.r4.model.Bundle.BundleType;
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import org.hl7.fhir.dstu3.model.Meta;
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import org.hl7.fhir.r4.model.Bundle.BundleType;
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import org.springframework.context.ApplicationContext;
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import org.springframework.http.HttpHeaders;
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import org.springframework.web.cors.CorsConfiguration;
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@@ -48,7 +47,9 @@ import org.springframework.web.cors.CorsConfiguration;
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import javax.servlet.ServletException;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.Set;
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import java.util.TreeSet;
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public class JpaRestfulServer extends RestfulServer {
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@@ -64,12 +65,12 @@ public class JpaRestfulServer extends RestfulServer {
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* specified in the properties file.
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*/
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ApplicationContext appCtx = (ApplicationContext) getServletContext()
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.getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
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.getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
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// Customize supported resource types
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Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
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if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
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supportedResourceTypes.add("SearchParameter");
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supportedResourceTypes.add("SearchParameter");
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}
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if (!supportedResourceTypes.isEmpty()) {
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@@ -112,36 +113,32 @@ public class JpaRestfulServer extends RestfulServer {
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* You can also create your own subclass of the conformance provider if you need to
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* provide further customization of your server's CapabilityStatement
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*/
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DaoConfig daoConfig = appCtx.getBean(DaoConfig.class);
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ISearchParamRegistry searchParamRegistry = appCtx.getBean(ISearchParamRegistry.class);
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if (fhirVersion == FhirVersionEnum.DSTU2) {
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IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx
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.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
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JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
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appCtx.getBean(DaoConfig.class));
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IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
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JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, daoConfig);
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confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
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setServerConformanceProvider(confProvider);
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} else if (fhirVersion == FhirVersionEnum.DSTU3) {
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IFhirSystemDao<Bundle, Meta> systemDao = appCtx
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.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
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JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
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appCtx.getBean(DaoConfig.class));
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confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
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setServerConformanceProvider(confProvider);
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} else if (fhirVersion == FhirVersionEnum.R4) {
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IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx
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.getBean("mySystemDaoR4", IFhirSystemDao.class);
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JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
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appCtx.getBean(DaoConfig.class));
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confProvider.setImplementationDescription("HAPI FHIR R4 Server");
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setServerConformanceProvider(confProvider);
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} else if (fhirVersion == FhirVersionEnum.R5) {
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IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx
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.getBean("mySystemDaoR5", IFhirSystemDao.class);
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JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
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appCtx.getBean(DaoConfig.class));
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confProvider.setImplementationDescription("HAPI FHIR R5 Server");
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setServerConformanceProvider(confProvider);
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} else {
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throw new IllegalStateException();
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if (fhirVersion == FhirVersionEnum.DSTU3) {
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IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
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JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, daoConfig, searchParamRegistry);
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confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
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setServerConformanceProvider(confProvider);
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} else if (fhirVersion == FhirVersionEnum.R4) {
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IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
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JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, daoConfig, searchParamRegistry);
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confProvider.setImplementationDescription("HAPI FHIR R4 Server");
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setServerConformanceProvider(confProvider);
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} else if (fhirVersion == FhirVersionEnum.R5) {
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IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
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JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, daoConfig, searchParamRegistry);
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confProvider.setImplementationDescription("HAPI FHIR R5 Server");
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setServerConformanceProvider(confProvider);
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} else {
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throw new IllegalStateException();
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}
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}
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/*
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@@ -179,9 +176,12 @@ public class JpaRestfulServer extends RestfulServer {
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* browser.
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*/
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ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
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;
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this.registerInterceptor(responseHighlighterInterceptor);
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if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
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registerInterceptor(new FhirPathFilterInterceptor());
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}
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/*
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* Add some logging for each request
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*/
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@@ -218,7 +218,7 @@ public class JpaRestfulServer extends RestfulServer {
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// manual triggering of a subscription delivery, enable this provider
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if (false) { // <-- DISABLED RIGHT NOW
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SubscriptionTriggeringProvider retriggeringProvider = appCtx
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.getBean(SubscriptionTriggeringProvider.class);
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.getBean(SubscriptionTriggeringProvider.class);
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registerProvider(retriggeringProvider);
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}
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@@ -244,7 +244,7 @@ public class JpaRestfulServer extends RestfulServer {
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config.addExposedHeader("Location");
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config.addExposedHeader("Content-Location");
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config.setAllowedMethods(
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Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
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Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
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config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
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// Create the interceptor and register it
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@@ -255,14 +255,8 @@ public class JpaRestfulServer extends RestfulServer {
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// If subscriptions are enabled, we want to register the interceptor that
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// will activate them and match results against them
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if (HapiProperties.getSubscriptionWebsocketEnabled() ||
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HapiProperties.getSubscriptionEmailEnabled() ||
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HapiProperties.getSubscriptionRestHookEnabled()) {
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// Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
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// with activation of scheduled subscription
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SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx
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.getBean(SubscriptionInterceptorLoader.class);
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subscriptionInterceptorLoader.registerInterceptors();
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HapiProperties.getSubscriptionEmailEnabled() ||
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HapiProperties.getSubscriptionRestHookEnabled()) {
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// Subscription debug logging
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IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
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interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
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@@ -272,15 +266,14 @@ public class JpaRestfulServer extends RestfulServer {
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DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
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IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
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if (HapiProperties.getAllowCascadingDeletes()) {
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CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
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daoRegistry, interceptorBroadcaster);
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CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
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getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
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}
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// Binary Storage
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if (HapiProperties.isBinaryStorageEnabled()) {
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BinaryStorageInterceptor binaryStorageInterceptor = appCtx
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.getBean(BinaryStorageInterceptor.class);
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.getBean(BinaryStorageInterceptor.class);
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getInterceptorService().registerInterceptor(binaryStorageInterceptor);
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}
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@@ -315,16 +308,16 @@ public class JpaRestfulServer extends RestfulServer {
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BundleType type = BundleType.valueOf(o);
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allowedBundleTypes.add(type.toCode());
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});
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DaoConfig config = appCtx.getBean(DaoConfig.class);
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||||
DaoConfig config = (DaoConfig) daoConfig;
|
||||
config.setBundleTypesAllowedForStorage(
|
||||
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
|
||||
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
|
||||
}
|
||||
|
||||
// Bulk Export
|
||||
if (HapiProperties.getBulkExportEnabled()) {
|
||||
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
|
||||
}
|
||||
|
||||
// Bulk Export
|
||||
if (HapiProperties.getBulkExportEnabled()) {
|
||||
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -61,6 +61,8 @@ validation.responses.enabled=false
|
||||
###################################################
|
||||
filter_search.enabled=true
|
||||
graphql.enabled=true
|
||||
# See FhirPathFilterInterceptor
|
||||
fhirpath_interceptor.enabled=false
|
||||
|
||||
###################################################
|
||||
# Supported Resources
|
||||
|
||||
@@ -14,7 +14,12 @@ import org.eclipse.jetty.websocket.api.Session;
|
||||
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
|
||||
import org.eclipse.jetty.websocket.client.WebSocketClient;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r5.model.*;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.Enumerations;
|
||||
import org.hl7.fhir.r5.model.Observation;
|
||||
import org.hl7.fhir.r5.model.Patient;
|
||||
import org.hl7.fhir.r5.model.Subscription;
|
||||
import org.hl7.fhir.r5.model.SubscriptionTopic;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
@@ -62,7 +67,7 @@ public class ExampleServerR5IT {
|
||||
/*
|
||||
* Create topic
|
||||
*/
|
||||
Topic topic = new Topic();
|
||||
SubscriptionTopic topic = new SubscriptionTopic();
|
||||
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
|
||||
|
||||
/*
|
||||
@@ -71,14 +76,11 @@ public class ExampleServerR5IT {
|
||||
Subscription subscription = new Subscription();
|
||||
subscription.getTopic().setResource(topic);
|
||||
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
|
||||
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
|
||||
|
||||
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
|
||||
channel.getType().addCoding()
|
||||
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
|
||||
subscription.getChannelType()
|
||||
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
|
||||
.setCode("websocket");
|
||||
channel.getPayload().setContentType("application/json");
|
||||
subscription.setChannel(channel);
|
||||
subscription.setContentType("application/json");
|
||||
|
||||
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
|
||||
IIdType mySubscriptionId = methodOutcome.getId();
|
||||
|
||||
Reference in New Issue
Block a user