Merge branch 'master' into hapi3_refactor

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -334,6 +334,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 						continue;
 					}
 					nextId = nextValue.getReferenceElement();
+
+					/*
+					 * This can only really happen if the DAO is being called
+					 * programatically with a Bundle (not through the FHIR REST API)
+					 * but Smile does this 
+					 */
+					if (nextId.isEmpty() && nextValue.getResource() != null) {
+						nextId = nextValue.getResource().getIdElement();
+					}
+					
 					if (nextId.isEmpty() || nextId.getValue().startsWith("#")) {
 						// This is a blank or contained resource reference
 						continue;
@@ -2046,7 +2056,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return paramMap;
 	}
 
-	protected static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
+	public static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
 		List<NameValuePair> parameters;
 		String matchUrl = theMatchUrl;
 		int questionMarkIndex = matchUrl.indexOf('?');

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java

@@ -273,8 +273,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Notify interceptors
 			IdDt idToDelete = entity.getIdDt();
-			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+			if (theRequestDetails != null) {
-			notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+				notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
+			}
 			
 			// Perform delete
 			Date updateTime = new Date();
@@ -282,10 +284,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Notify JPA interceptors
 			T resourceToDelete = toResource(myResourceType, entity, false);
-			theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
+			if (theRequestDetails != null) {
-			for (IServerInterceptor next : getConfig().getInterceptors()) {
+				theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
-				if (next instanceof IJpaServerInterceptor) {
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
-					((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+				for (IServerInterceptor next : getConfig().getInterceptors()) {
+					if (next instanceof IJpaServerInterceptor) {
+						((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+					}
 				}
 			}
 			for (IServerInterceptor next : getConfig().getInterceptors()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java

@@ -247,7 +247,6 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 
 		QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
 
-		//@formatter:off
 		Query textQuery = qb
 				.phrase()
 				.withSlop(2)
@@ -261,7 +260,6 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 				.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(pid).createQuery())
 				.must(textQuery)
 				.createQuery();
-		//@formatter:on
 
 		FullTextQuery ftq = em.createFullTextQuery(query, ResourceTable.class);
 		ftq.setProjection("myContentText");
@@ -289,14 +287,6 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 				formatter.setAnalyzer("myContentTextEdgeNGram");
 				highlighter.getBestFragments(analyzer.tokenStream("myContentTextEdgeNGram", nextValue), nextValue, 10);
 
-				// formatter.setAnalyzer("myContentText");
-				// highlighter.getBestFragments(analyzer.tokenStream("myContentText", nextValue), nextValue, 10);
-				// formatter.setAnalyzer("myContentTextNGram");
-				// highlighter.getBestFragments(analyzer.tokenStream("myContentTextNGram", nextValue), nextValue, 10);
-				// formatter.setAnalyzer("myContentTextEdgeNGram");
-				// highlighter.getBestFragments(analyzer.tokenStream("myContentTextEdgeNGram", nextValue), nextValue, 10);
-				// formatter.setAnalyzer("myContentTextPhonetic");
-				// highlighter.getBestFragments(analyzer.tokenStream("myContentTextPhonetic", nextValue), nextValue, 10);
 			} catch (Exception e) {
 				throw new InternalErrorException(e);
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/RestHookSubscriptionDstu2Interceptor.java

@@ -29,9 +29,12 @@ import javax.annotation.PostConstruct;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.apache.http.NameValuePair;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.client.methods.HttpPut;
 import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.client.utils.URLEncodedUtils;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -63,6 +66,7 @@ import ca.uhn.fhir.rest.server.interceptor.*;
 
 public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterceptorAdapter {
 
+	private static final Integer MAX_SUBSCRIPTION_RESULTS = 10000;
 	private static volatile ExecutorService executor;
 	private final static int MAX_THREADS = 1;
 
@@ -71,13 +75,13 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
 	@Autowired
 	private FhirContext myFhirContext;
 
-	private boolean myNotifyOnDelete = false;
-	private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
-
 	@Autowired
 	@Qualifier("mySubscriptionDaoDstu2")
 	private IFhirResourceDao<Subscription> mySubscriptionDao;
 
+	private boolean myNotifyOnDelete = false;
+	private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
+
 	/**
 	 * Check subscriptions and send notifications or payload
 	 *
@@ -205,6 +209,7 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
 		req.setSubRequest(true);
 
 		IFhirResourceDao<? extends IBaseResource> responseDao = mySubscriptionDao.getDao(responseResourceDef.getImplementingClass());
+		responseCriteriaUrl.setCount(MAX_SUBSCRIPTION_RESULTS);
 		IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
 		return responseResults;
 	}
@@ -265,7 +270,12 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
 		RequestDetails req = new ServletSubRequestDetails();
 		req.setSubRequest(true);
 
+		map.setCount(MAX_SUBSCRIPTION_RESULTS);
 		IBundleProvider subscriptionBundleList = mySubscriptionDao.search(map, req);
+		if (subscriptionBundleList.size() >= MAX_SUBSCRIPTION_RESULTS) {
+			ourLog.error("Currently over "+MAX_SUBSCRIPTION_RESULTS+" subscriptions.  Some subscriptions have not been loaded.");
+		}
+
 		List<IBaseResource> resourceList = subscriptionBundleList.getResources(0, subscriptionBundleList.size());
 
 		for (IBaseResource resource : resourceList) {
@@ -398,4 +408,58 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
 	public void setSubscriptionDao(IFhirResourceDao<Subscription> theSubscriptionDao) {
 		mySubscriptionDao = theSubscriptionDao;
 	}
+
+	@Override
+	public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
+		//check the subscription criteria to see if its valid before creating or updating a subscription
+		if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
+			String resourceType = theDetails.getResourceType();
+			ourLog.info("prehandled resource type: " + resourceType);
+			if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
+				Subscription subscription = (Subscription) theDetails.getResource();
+				if (subscription != null) {
+					checkSubscriptionCriterias(subscription);
+				}
+			}
+		}
+		super.incomingRequestPreHandled(theOperation, theDetails);
+	}
+
+	private void checkSubscriptionCriterias(Subscription subscription){
+		try {
+			IBundleProvider results = executeSubscriptionCriteria(subscription, null);
+		}catch (Exception e){
+			throw new InvalidRequestException("Invalid criteria");
+		}
+	}
+
+	private IBundleProvider executeSubscriptionCriteria(Subscription subscription, IIdType idType){
+		//run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
+		String criteria = subscription.getCriteria();
+		if(idType != null) {
+			criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
+		}
+
+		IBundleProvider results = getBundleProvider(criteria);
+		return results;
+	}
+
+	/**
+	 * Get the encoding from the criteria or return JSON encoding if its not found
+	 *
+	 * @param criteria
+	 * @return
+	 */
+	private EncodingEnum getEncoding(String criteria) {
+		//check criteria
+		String params = criteria.substring(criteria.indexOf('?') + 1);
+		List<NameValuePair> paramValues = URLEncodedUtils.parse(params, Constants.CHARSET_UTF8, '&');
+		for (NameValuePair nameValuePair : paramValues) {
+			if (Constants.PARAM_FORMAT.equals(nameValuePair.getName())) {
+				return EncodingEnum.forContentType(nameValuePair.getValue());
+			}
+		}
+		return EncodingEnum.JSON;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/RestHookSubscriptionDstu3Interceptor.java

@@ -30,9 +30,12 @@ import javax.annotation.PostConstruct;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import org.apache.http.NameValuePair;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.client.methods.HttpPut;
 import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.client.utils.URLEncodedUtils;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.hl7.fhir.dstu3.model.Subscription;
@@ -61,6 +64,7 @@ import ca.uhn.fhir.rest.server.interceptor.*;
 
 public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterceptorAdapter {
 
+	private static final Integer MAX_SUBSCRIPTION_RESULTS = 10000;
 	private static volatile ExecutorService executor;
 	private final static int MAX_THREADS = 1;
 
@@ -69,20 +73,11 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
 	@Autowired
 	private FhirContext myFhirContext;
 
-	public void setFhirContext(FhirContext theFhirContext) {
-		myFhirContext = theFhirContext;
-	}
-
-	public void setSubscriptionDao(IFhirResourceDao<Subscription> theSubscriptionDao) {
-		mySubscriptionDao = theSubscriptionDao;
-	}
-
 	@Autowired
 	@Qualifier("mySubscriptionDaoDstu3")
 	private IFhirResourceDao<Subscription> mySubscriptionDao;
 	
 	private boolean notifyOnDelete = false;
-
 	private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
 
 	/**
@@ -205,6 +200,7 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
 		req.setSubRequest(true);
 
 		IFhirResourceDao<? extends IBaseResource> responseDao = mySubscriptionDao.getDao(responseResourceDef.getImplementingClass());
+		responseCriteriaUrl.setCount(MAX_SUBSCRIPTION_RESULTS);
 		IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
 		return responseResults;
 	}
@@ -254,7 +250,6 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
 		return entity;
 	}
 
-
 	/**
 	 * Read the existing subscriptions from the database
 	 */
@@ -266,7 +261,12 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
 		RequestDetails req = new ServletSubRequestDetails();
 		req.setSubRequest(true);
 
+		map.setCount(MAX_SUBSCRIPTION_RESULTS);
 		IBundleProvider subscriptionBundleList = mySubscriptionDao.search(map, req);
+		if (subscriptionBundleList.size() >= MAX_SUBSCRIPTION_RESULTS) {
+			ourLog.error("Currently over "+MAX_SUBSCRIPTION_RESULTS+" subscriptions.  Some subscriptions have not been loaded.");
+		}
+
 		List<IBaseResource> resourceList = subscriptionBundleList.getResources(0, subscriptionBundleList.size());
 
 		for (IBaseResource resource : resourceList) {
@@ -388,7 +388,69 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
 		}
 	}
 
+	public void setFhirContext(FhirContext theFhirContext) {
+		myFhirContext = theFhirContext;
+	}
+
 	public void setNotifyOnDelete(boolean notifyOnDelete) {
 		this.notifyOnDelete = notifyOnDelete;
 	}
+
+	public void setSubscriptionDao(IFhirResourceDao<Subscription> theSubscriptionDao) {
+		mySubscriptionDao = theSubscriptionDao;
+	}
+
+	@Override
+	public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
+		//check the subscription criteria to see if its valid before creating or updating a subscription
+		if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
+			String resourceType = theDetails.getResourceType();
+			ourLog.info("prehandled resource type: " + resourceType);
+			if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
+				Subscription subscription = (Subscription) theDetails.getResource();
+				if (subscription != null) {
+					checkSubscriptionCriterias(subscription);
+				}
+			}
+		}
+		super.incomingRequestPreHandled(theOperation, theDetails);
+	}
+
+	private void checkSubscriptionCriterias(Subscription subscription){
+		try {
+			IBundleProvider results = executeSubscriptionCriteria(subscription, null);
+		}catch (Exception e){
+			throw new InvalidRequestException("Invalid criteria");
+		}
+	}
+
+	private IBundleProvider executeSubscriptionCriteria(Subscription subscription, IIdType idType){
+		//run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
+		String criteria = subscription.getCriteria();
+		if(idType != null) {
+			criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
+		}
+
+		IBundleProvider results = getBundleProvider(criteria);
+		return results;
+	}
+
+	/**
+	 * Get the encoding from the criteria or return JSON encoding if its not found
+	 *
+	 * @param criteria
+	 * @return
+	 */
+	private EncodingEnum getEncoding(String criteria) {
+		//check criteria
+		String params = criteria.substring(criteria.indexOf('?') + 1);
+		List<NameValuePair> paramValues = URLEncodedUtils.parse(params, Constants.CHARSET_UTF8, '&');
+		for (NameValuePair nameValuePair : paramValues) {
+			if (Constants.PARAM_FORMAT.equals(nameValuePair.getName())) {
+				return EncodingEnum.forContentType(nameValuePair.getValue());
+			}
+		}
+		return EncodingEnum.JSON;
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -542,6 +542,60 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
+	@Test
+	public void testTransactionWithReferenceUuid() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference(p.getId());
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
+	@Test
+	public void testTransactionWithReferenceResource() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setResource(p);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu2.java

@@ -0,0 +1,125 @@
+package ca.uhn.fhir.jpa.demo;
+
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import org.apache.commons.dbcp2.BasicDataSource;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.springframework.beans.factory.annotation.Autowire;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+import java.util.Properties;
+
+/**
+ * This is the primary configuration file for the example server
+ */
+@Configuration
+@EnableTransactionManagement()
+public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
+
+	/**
+	 * Configure FHIR properties around the the JPA server via this bean
+	 */
+	@Bean()
+	public DaoConfig daoConfig() {
+		DaoConfig retVal = new DaoConfig();
+		retVal.setSubscriptionEnabled(true);
+		retVal.setSubscriptionPollDelay(5000);
+		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
+		retVal.setAllowMultipleDelete(true);
+		return retVal;
+	}
+
+	/**
+	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
+	 * directory called "jpaserver_derby_files".
+	 * 
+	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
+	 */
+	@Bean(destroyMethod = "close")
+	public DataSource dataSource() {
+		BasicDataSource retVal = new BasicDataSource();
+		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
+		retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
+		retVal.setUsername("");
+		retVal.setPassword("");
+		return retVal;
+	}
+
+	@Bean()
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		retVal.setPersistenceUnitName("HAPI_PU");
+		retVal.setDataSource(dataSource());
+		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
+		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
+		retVal.setJpaProperties(jpaProperties());
+		return retVal;
+	}
+
+	private Properties jpaProperties() {
+		Properties extraProperties = new Properties();
+		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.format_sql", "true");
+		extraProperties.put("hibernate.show_sql", "false");
+		extraProperties.put("hibernate.hbm2ddl.auto", "update");
+		extraProperties.put("hibernate.jdbc.batch_size", "20");
+		extraProperties.put("hibernate.cache.use_query_cache", "false");
+		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
+		extraProperties.put("hibernate.cache.use_structured_entries", "false");
+		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
+		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
+		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
+//		extraProperties.put("hibernate.search.default.worker.execution", "async");
+		return extraProperties;
+	}
+
+	/**
+	 * Do some fancy logging to create a nice access log that has details about each incoming request.
+	 */
+	public IServerInterceptor loggingInterceptor() {
+		LoggingInterceptor retVal = new LoggingInterceptor();
+		retVal.setLoggerName("fhirtest.access");
+		retVal.setMessageFormat(
+				"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
+		retVal.setLogExceptions(true);
+		retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
+		return retVal;
+	}
+
+	/**
+	 * This interceptor adds some pretty syntax highlighting in responses when a browser is detected
+	 */
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IServerInterceptor responseHighlighterInterceptor() {
+		ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
+		return retVal;
+	}
+
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IServerInterceptor subscriptionSecurityInterceptor() {
+		SubscriptionsRequireManualActivationInterceptorDstu2 retVal = new SubscriptionsRequireManualActivationInterceptorDstu2();
+		return retVal;
+	}
+
+	@Bean()
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+		JpaTransactionManager retVal = new JpaTransactionManager();
+		retVal.setEntityManagerFactory(entityManagerFactory);
+		return retVal;
+	}
+
+}

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirTesterConfigDstu2.java

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.demo;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.to.FhirTesterMvcConfig;
+import ca.uhn.fhir.to.TesterConfig;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+
+//@formatter:off
+
+/**
+ * This spring config file configures the web testing module. It serves two
+ * purposes:
+ * 1. It imports FhirTesterMvcConfig, which is the spring config for the
+ *    tester itself
+ * 2. It tells the tester which server(s) to talk to, via the testerConfig()
+ *    method below
+ */
+@Configuration
+@Import(FhirTesterMvcConfig.class)
+public class FhirTesterConfigDstu2 {
+
+	/**
+	 * This bean tells the testing webpage which servers it should configure itself
+	 * to communicate with. In this example we configure it to talk to the local
+	 * server, as well as one public server. If you are creating a project to
+	 * deploy somewhere else, you might choose to only put your own server's
+	 * address here.
+	 *
+	 * Note the use of the ${serverBase} variable below. This will be replaced with
+	 * the base URL as reported by the server itself. Often for a simple Tomcat
+	 * (or other container) installation, this will end up being something
+	 * like "http://localhost:8080/hapi-fhir-jpaserver-example". If you are
+	 * deploying your server to a place with a fully qualified domain name,
+	 * you might want to use that instead of using the variable.
+	 */
+	@Bean
+	public TesterConfig testerConfig() {
+		TesterConfig retVal = new TesterConfig();
+		retVal
+			.addServer()
+				.withId("home")
+				.withFhirVersion(FhirVersionEnum.DSTU2)
+				.withBaseUrl("${serverBase}/baseDstu2")
+				.withName("Local Tester")
+			.addServer()
+				.withId("hapi")
+				.withFhirVersion(FhirVersionEnum.DSTU2)
+				.withBaseUrl("http://fhirtest.uhn.ca/baseDstu2")
+				.withName("Public HAPI Test Server");
+		return retVal;
+	}
+
+}
+//@formatter:on

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemoDstu2.java

@@ -0,0 +1,169 @@
+
+package ca.uhn.fhir.jpa.demo;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
+import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
+import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.dstu2.composite.MetaDt;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.rest.server.ETagSupportEnum;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Meta;
+import org.springframework.web.context.ContextLoaderListener;
+import org.springframework.web.context.WebApplicationContext;
+
+import javax.servlet.ServletException;
+import java.util.Collection;
+import java.util.List;
+
+public class JpaServerDemoDstu2 extends RestfulServer {
+
+	private static final long serialVersionUID = 1L;
+
+	private WebApplicationContext myAppCtx;
+
+	@SuppressWarnings("unchecked")
+	@Override
+	protected void initialize() throws ServletException {
+		super.initialize();
+
+		/* 
+		 * We want to support FHIR DSTU2 format. This means that the server
+		 * will use the DSTU2 bundle format and other DSTU2 encoding changes.
+		 *
+		 * If you want to use DSTU1 instead, change the following line, and change the 2 occurrences of dstu2 in web.xml to dstu1
+		 */
+		FhirVersionEnum fhirVersion = FhirVersionEnum.DSTU2;
+		setFhirContext(new FhirContext(fhirVersion));
+
+		// Get the spring context from the web container (it's declared in web.xml)
+		myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
+
+		/* 
+		 * The BaseJavaConfigDstu2.java class is a spring configuration
+		 * file which is automatically generated as a part of hapi-fhir-jpaserver-base and
+		 * contains bean definitions for a resource provider for each resource type
+		 */
+		String resourceProviderBeanName;
+		if (fhirVersion == FhirVersionEnum.DSTU1) {
+			resourceProviderBeanName = "myResourceProvidersDstu1";
+		} else if (fhirVersion == FhirVersionEnum.DSTU2) {
+			resourceProviderBeanName = "myResourceProvidersDstu2";
+		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
+			resourceProviderBeanName = "myResourceProvidersDstu3";
+		} else {
+			throw new IllegalStateException();
+		}
+		List<IResourceProvider> beans = myAppCtx.getBean(resourceProviderBeanName, List.class);
+		setResourceProviders(beans);
+		
+		/* 
+		 * The system provider implements non-resource-type methods, such as
+		 * transaction, and global history.
+		 */
+		Object systemProvider;
+		if (fhirVersion == FhirVersionEnum.DSTU1) {
+			systemProvider = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
+		} else if (fhirVersion == FhirVersionEnum.DSTU2) {
+			systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
+		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
+			systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
+		} else {
+			throw new IllegalStateException();
+		}
+		setPlainProviders(systemProvider);
+
+		/*
+		 * The conformance provider exports the supported resources, search parameters, etc for
+		 * this server. The JPA version adds resource counts to the exported statement, so it
+		 * is a nice addition.
+		 */
+		if (fhirVersion == FhirVersionEnum.DSTU1) {
+			IFhirSystemDao<List<IResource>, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
+			JpaConformanceProviderDstu1 confProvider = new JpaConformanceProviderDstu1(this, systemDao);
+			confProvider.setImplementationDescription("Example Server");
+			setServerConformanceProvider(confProvider);
+		} else if (fhirVersion == FhirVersionEnum.DSTU2) {
+			IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+			JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
+					myAppCtx.getBean(DaoConfig.class));
+			confProvider.setImplementationDescription("Example Server");
+			setServerConformanceProvider(confProvider);
+		} else if (fhirVersion == FhirVersionEnum.DSTU3) {
+			IFhirSystemDao<Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
+			myAppCtx.getBean(DaoConfig.class));
+			confProvider.setImplementationDescription("Example Server");
+			setServerConformanceProvider(confProvider);
+		} else {
+			throw new IllegalStateException();
+		}
+
+		/*
+		 * Enable ETag Support (this is already the default)
+		 */
+		setETagSupport(ETagSupportEnum.ENABLED);
+
+		/*
+		 * This server tries to dynamically generate narratives
+		 */
+		FhirContext ctx = getFhirContext();
+		ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
+
+		/*
+		 * Default to JSON and pretty printing
+		 */
+		setDefaultPrettyPrint(true);
+		setDefaultResponseEncoding(EncodingEnum.JSON);
+
+		/*
+		 * -- New in HAPI FHIR 1.5 --
+		 * This configures the server to page search results to and from
+		 * the database, instead of only paging them to memory. This may mean
+		 * a performance hit when performing searches that return lots of results,
+		 * but makes the server much more scalable.
+		 */
+		setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
+
+		/*
+		 * Load interceptors for the server from Spring (these are defined in FhirServerConfig.java)
+		 */
+		Collection<IServerInterceptor> interceptorBeans = myAppCtx.getBeansOfType(IServerInterceptor.class).values();
+		for (IServerInterceptor interceptor : interceptorBeans) {
+			this.registerInterceptor(interceptor);
+		}
+
+		/*
+		 * If you are hosting this server at a specific DNS name, the server will try to 
+		 * figure out the FHIR base URL based on what the web container tells it, but
+		 * this doesn't always work. If you are setting links in your search bundles that
+		 * just refer to "localhost", you might want to use a server address strategy:
+		 */
+		//setServerAddressStrategy(new HardcodedServerAddressStrategy("http://mydomain.com/fhir/baseDstu2"));
+		
+		/*
+		 * If you are using DSTU3+, you may want to add a terminology uploader, which allows 
+		 * uploading of external terminologies such as Snomed CT. Note that this uploader
+		 * does not have any security attached (any anonymous user may use it by default)
+		 * so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
+		 * with this feature.
+		 */
+		//if (fhirVersion == FhirVersionEnum.DSTU3) {
+		//	 registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
+		//}
+	}
+
+}

hapi-fhir-jpaserver-example/src/main/webapp/WEB-INF/web-dstu2.xml

@@ -1,5 +1,5 @@
 <web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
+			xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
 
 	<listener>
 		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
@@ -13,7 +13,7 @@
 	<context-param>
 		<param-name>contextConfigLocation</param-name>
 		<param-value>
-			ca.uhn.fhir.jpa.demo.FhirServerConfigWSocket
+			ca.uhn.fhir.jpa.demo.FhirServerConfigDstu2
 		</param-value>
 	</context-param>
 
@@ -28,7 +28,7 @@
 		</init-param>
 		<init-param>
 			<param-name>contextConfigLocation</param-name>
-			<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
+			<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfigDstu2</param-value>
 		</init-param>
 		<load-on-startup>2</load-on-startup>
 	</servlet>
@@ -103,6 +103,4 @@
 		<filter-name>CORS Filter</filter-name>
 		<url-pattern>/*</url-pattern>
 	</filter-mapping>
-
-
 </web-app>

hapi-fhir-jpaserver-example/src/main/webapp/WEB-INF/web-non-polling-subscription-dstu3.xml

@@ -1,108 +0,0 @@
-<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
-
-	<listener>
-		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
-	</listener>
-	<context-param>
-		<param-name>contextClass</param-name>
-		<param-value>
-			org.springframework.web.context.support.AnnotationConfigWebApplicationContext
-		</param-value>
-	</context-param>
-	<context-param>
-		<param-name>contextConfigLocation</param-name>
-		<param-value>
-			ca.uhn.fhir.jpa.demo.FhirServerConfigDstu3WSocket
-		</param-value>
-	</context-param>
-
-	<!-- Servlets -->
-
-	<servlet>
-		<servlet-name>spring</servlet-name>
-		<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
-		<init-param>
-			<param-name>contextClass</param-name>
-			<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
-		</init-param>
-		<init-param>
-			<param-name>contextConfigLocation</param-name>
-			<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
-		</init-param>
-		<load-on-startup>2</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>fhirServlet</servlet-name>
-		<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemo</servlet-class>
-		<init-param>
-			<param-name>ImplementationDescription</param-name>
-			<param-value>FHIR JPA Server</param-value>
-		</init-param>
-		<init-param>
-			<param-name>FhirVersion</param-name>
-			<param-value>DSTU3</param-value>
-		</init-param>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet-mapping>
-		<servlet-name>fhirServlet</servlet-name>
-		<url-pattern>/baseDstu3/*</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>spring</servlet-name>
-		<url-pattern>/</url-pattern>
-	</servlet-mapping>
-
-
-
-	<!-- This filters provide support for Cross Origin Resource Sharing (CORS) -->
-	<filter>
-		<filter-name>CORS Filter</filter-name>
-		<filter-class>org.ebaysf.web.cors.CORSFilter</filter-class>
-		<init-param>
-			<description>A comma separated list of allowed origins. Note: An '*' cannot be used for an allowed origin when using credentials.</description>
-			<param-name>cors.allowed.origins</param-name>
-			<param-value>*</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list of HTTP verbs, using which a CORS request can be made.</description>
-			<param-name>cors.allowed.methods</param-name>
-			<param-value>GET,POST,PUT,DELETE,OPTIONS</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list of allowed headers when making a non simple CORS request.</description>
-			<param-name>cors.allowed.headers</param-name>
-			<param-value>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list non-standard response headers that will be exposed to XHR2 object.</description>
-			<param-name>cors.exposed.headers</param-name>
-			<param-value>Location,Content-Location</param-value>
-		</init-param>
-		<init-param>
-			<description>A flag that suggests if CORS is supported with cookies</description>
-			<param-name>cors.support.credentials</param-name>
-			<param-value>true</param-value>
-		</init-param>
-		<init-param>
-			<description>A flag to control logging</description>
-			<param-name>cors.logging.enabled</param-name>
-			<param-value>true</param-value>
-		</init-param>
-		<init-param>
-			<description>Indicates how long (in seconds) the results of a preflight request can be cached in a preflight result cache.</description>
-			<param-name>cors.preflight.maxage</param-name>
-			<param-value>300</param-value>
-		</init-param>
-	</filter>
-	<filter-mapping>
-		<filter-name>CORS Filter</filter-name>
-		<url-pattern>/*</url-pattern>
-	</filter-mapping>
-
-
-</web-app>

hapi-fhir-jpaserver-example/src/main/webapp/WEB-INF/web-polling-subscription-dstu2.xml

@@ -1,108 +0,0 @@
-<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
-
-	<listener>
-		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
-	</listener>
-	<context-param>
-		<param-name>contextClass</param-name>
-		<param-value>
-			org.springframework.web.context.support.AnnotationConfigWebApplicationContext
-		</param-value>
-	</context-param>
-	<context-param>
-		<param-name>contextConfigLocation</param-name>
-		<param-value>
-			ca.uhn.fhir.jpa.demo.FhirServerConfig
-		</param-value>
-	</context-param>
-
-	<!-- Servlets -->
-
-	<servlet>
-		<servlet-name>spring</servlet-name>
-		<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
-		<init-param>
-			<param-name>contextClass</param-name>
-			<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
-		</init-param>
-		<init-param>
-			<param-name>contextConfigLocation</param-name>
-			<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
-		</init-param>
-		<load-on-startup>2</load-on-startup>
-	</servlet>
-
-	<servlet>
-		<servlet-name>fhirServlet</servlet-name>
-		<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemo</servlet-class>
-		<init-param>
-			<param-name>ImplementationDescription</param-name>
-			<param-value>FHIR JPA Server</param-value>
-		</init-param>
-		<init-param>
-			<param-name>FhirVersion</param-name>
-			<param-value>DSTU2</param-value>
-		</init-param>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-
-	<servlet-mapping>
-		<servlet-name>fhirServlet</servlet-name>
-		<url-pattern>/baseDstu2/*</url-pattern>
-	</servlet-mapping>
-
-	<servlet-mapping>
-		<servlet-name>spring</servlet-name>
-		<url-pattern>/</url-pattern>
-	</servlet-mapping>
-
-
-
-	<!-- This filters provide support for Cross Origin Resource Sharing (CORS) -->
-	<filter>
-		<filter-name>CORS Filter</filter-name>
-		<filter-class>org.ebaysf.web.cors.CORSFilter</filter-class>
-		<init-param>
-			<description>A comma separated list of allowed origins. Note: An '*' cannot be used for an allowed origin when using credentials.</description>
-			<param-name>cors.allowed.origins</param-name>
-			<param-value>*</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list of HTTP verbs, using which a CORS request can be made.</description>
-			<param-name>cors.allowed.methods</param-name>
-			<param-value>GET,POST,PUT,DELETE,OPTIONS</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list of allowed headers when making a non simple CORS request.</description>
-			<param-name>cors.allowed.headers</param-name>
-			<param-value>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</param-value>
-		</init-param>
-		<init-param>
-			<description>A comma separated list non-standard response headers that will be exposed to XHR2 object.</description>
-			<param-name>cors.exposed.headers</param-name>
-			<param-value>Location,Content-Location</param-value>
-		</init-param>
-		<init-param>
-			<description>A flag that suggests if CORS is supported with cookies</description>
-			<param-name>cors.support.credentials</param-name>
-			<param-value>true</param-value>
-		</init-param>
-		<init-param>
-			<description>A flag to control logging</description>
-			<param-name>cors.logging.enabled</param-name>
-			<param-value>true</param-value>
-		</init-param>
-		<init-param>
-			<description>Indicates how long (in seconds) the results of a preflight request can be cached in a preflight result cache.</description>
-			<param-name>cors.preflight.maxage</param-name>
-			<param-value>300</param-value>
-		</init-param>
-	</filter>
-	<filter-mapping>
-		<filter-name>CORS Filter</filter-name>
-		<url-pattern>/*</url-pattern>
-	</filter-mapping>
-
-
-</web-app>

src/changes/changes.xml

@@ -66,6 +66,16 @@
 				Prevent duplicates in $everything query response in JPA server. Thanks to @vlad-ignatov 
 				for reporting!
 			</action>
+			<action type="fix">
+				Fix issue in calling JPA server transactions programmatically where resources
+				are linked by object reference and not by ID where indexes were not correctly
+				generated. This should not affect most users.
+			</action>
+			<action type="fix" issue="678">
+				FIx issue in SubscriptionInterceptor that caused interceptor to only
+				actually notify listeners of the first 10 subscriptions. Thanks to Jeff Chung
+				for the pull request!
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">