Keep the complete resource history in the history table, including the

current version

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao;
 
+import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -27,7 +28,6 @@ import java.text.Normalizer;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -35,6 +35,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.UUID;
 
 import javax.persistence.EntityManager;
 import javax.persistence.NoResultException;
@@ -66,14 +67,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.TransactionCallback;
-import org.springframework.transaction.support.TransactionTemplate;
 
-import com.google.common.base.Function;
 import com.google.common.collect.ArrayListMultimap;
-import com.google.common.collect.Collections2;
-import com.google.common.collect.Lists;
 
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.ConfigurationException;
@@ -83,6 +78,9 @@ import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
@@ -101,10 +99,12 @@ import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
 import ca.uhn.fhir.jpa.entity.ResourceLink;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.ResourceTag;
+import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
-import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
@@ -151,10 +151,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
 	public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
 	public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
-
 	public static final String OO_SEVERITY_ERROR = "error";
 	public static final String OO_SEVERITY_INFO = "information";
-
 	public static final String OO_SEVERITY_WARN = "warning";
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirDao.class);
@@ -204,10 +202,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@Autowired
 	private List<IFhirResourceDao<?>> myResourceDaos;
 
+	@Autowired
+	private IResourceHistoryTableDao myResourceHistoryTableDao;
+
 	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
 
+	@Autowired
+	private ISearchDao mySearchDao;
+
 	private ISearchParamExtractor mySearchParamExtractor;
 
+	@Autowired
+	private ISearchResultDao mySearchResultDao;
+
 	protected void createForcedIdIfNeeded(ResourceTable entity, IIdType id) {
 		if (id.isEmpty() == false && id.hasIdPart()) {
 			if (isValidPid(id)) {
@@ -269,19 +276,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 						String typeString = nextValue.getReferenceElement().getResourceType();
 						if (isBlank(typeString)) {
-							throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource type - " + nextValue.getReferenceElement().getValue());
+							throw new InvalidRequestException(
+									"Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource type - " + nextValue.getReferenceElement().getValue());
 						}
 						RuntimeResourceDefinition resourceDefinition;
 						try {
 							resourceDefinition = getContext().getResourceDefinition(typeString);
 						} catch (DataFormatException e) {
-							throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Resource type is unknown or not supported on this server - " + nextValue.getReferenceElement().getValue());
+							throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Resource type is unknown or not supported on this server - "
+									+ nextValue.getReferenceElement().getValue());
 						}
 
 						Class<? extends IBaseResource> type = resourceDefinition.getImplementingClass();
 						String id = nextValue.getReferenceElement().getIdPart();
 						if (StringUtils.isBlank(id)) {
-							throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource ID - " + nextValue.getReferenceElement().getValue());
+							throw new InvalidRequestException(
+									"Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource ID - " + nextValue.getReferenceElement().getValue());
 						}
 
 						IFhirResourceDao<?> dao = getDao(type);
@@ -311,7 +321,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 						}
 
 						if (!typeString.equals(target.getResourceType())) {
-							throw new UnprocessableEntityException("Resource contains reference to " + nextValue.getReferenceElement().getValue() + " but resource with ID " + nextValue.getReferenceElement().getIdPart() + " is actually of type " + target.getResourceType());
+							throw new UnprocessableEntityException("Resource contains reference to " + nextValue.getReferenceElement().getValue() + " but resource with ID "
+									+ nextValue.getReferenceElement().getIdPart() + " is actually of type " + target.getResourceType());
 						}
 
 						/*
@@ -364,15 +375,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return retVal;
 	}
 
-	protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
-		return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
-	}
-
 	// @Override
 	// public void setResourceDaos(List<IFhirResourceDao<?>> theResourceDaos) {
 	// myResourceDaos = theResourceDaos;
 	// }
 
+	protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
+		return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
+	}
+
 	protected Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
 		return mySearchParamExtractor.extractSearchParamDates(theEntity, theResource);
 	}
@@ -501,6 +512,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return myConfig;
 	}
 
+	@Override
 	public FhirContext getContext() {
 		return myContext;
 	}
@@ -608,90 +620,48 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	protected IBundleProvider history(String theResourceName, Long theId, Date theSince) {
-		final List<HistoryTuple> tuples = new ArrayList<HistoryTuple>();
 
-		final InstantDt end = createHistoryToTimestamp();
+		String resourceName = defaultIfBlank(theResourceName, null);
 
-		StopWatch timer = new StopWatch();
+		Search search = new Search();
+		search.setCreated(new Date());
+		search.setLastUpdated(null, theSince);
+		search.setUuid(UUID.randomUUID().toString());
+		search.setResourceType(resourceName);
+		search.setResourceId(theId);
+		search.setSearchType(SearchTypeEnum.HISTORY);
 
-		int limit = 10000;
+		if (theSince != null) {
-
+			if (resourceName == null) {
-		// Get list of IDs
+				search.setTotalCount(myResourceHistoryTableDao.countForAllResourceTypes(theSince));
-		searchHistoryCurrentVersion(theResourceName, theId, theSince, end.getValue(), limit, tuples);
+			} else if (theId == null) {
-		ourLog.info("Retrieved {} history IDs from current versions in {} ms", tuples.size(), timer.getMillisAndRestart());
+				search.setTotalCount(myResourceHistoryTableDao.countForResourceType(resourceName, theSince));
-
+			} else {
-		searchHistoryHistory(theResourceName, theId, theSince, end.getValue(), limit, tuples);
+				search.setTotalCount(myResourceHistoryTableDao.countForResourceInstance(theId, theSince));
-		ourLog.info("Retrieved {} history IDs from previous versions in {} ms", tuples.size(), timer.getMillisAndRestart());
-
-		// Sort merged list
-		Collections.sort(tuples, Collections.reverseOrder());
-		assert tuples.size() < 2 || !tuples.get(tuples.size() - 2).getUpdated().before(tuples.get(tuples.size() - 1).getUpdated()) : tuples.toString();
-
-		return new IBundleProvider() {
-
-			@Override
-			public InstantDt getPublished() {
-				return end;
 			}
-
+		} else {
-			@Override
+			if (resourceName == null) {
-			public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
+				search.setTotalCount(myResourceHistoryTableDao.countForAllResourceTypes());
-				final StopWatch grTimer = new StopWatch();
+			} else if (theId == null) {
-				TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+				search.setTotalCount(myResourceHistoryTableDao.countForResourceType(resourceName));
-				return template.execute(new TransactionCallback<List<IBaseResource>>() {
+			} else {
-					@Override
+				search.setTotalCount(myResourceHistoryTableDao.countForResourceInstance(theId));
-					public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
-						List<BaseHasResource> resEntities = Lists.newArrayList();
-
-						List<HistoryTuple> tupleSubList = tuples.subList(theFromIndex, theToIndex);
-						searchHistoryCurrentVersion(tupleSubList, resEntities);
-						ourLog.info("Loaded history from current versions in {} ms", grTimer.getMillisAndRestart());
-
-						searchHistoryHistory(tupleSubList, resEntities);
-						ourLog.info("Loaded history from previous versions in {} ms", grTimer.getMillisAndRestart());
-
-						Collections.sort(resEntities, new Comparator<BaseHasResource>() {
-							@Override
-							public int compare(BaseHasResource theO1, BaseHasResource theO2) {
-								return theO2.getUpdated().getValue().compareTo(theO1.getUpdated().getValue());
-							}
-						});
-
-						int grLimit = theToIndex - theFromIndex;
-						if (resEntities.size() > grLimit) {
-							resEntities = resEntities.subList(0, grLimit);
-						}
-
-						ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
-						for (BaseHasResource next : resEntities) {
-							RuntimeResourceDefinition type;
-							try {
-								type = myContext.getResourceDefinition(next.getResourceType());
-							} catch (DataFormatException e) {
-								if (next.getFhirVersion() != getContext().getVersion().getVersion()) {
-									ourLog.info("Ignoring history resource of type[{}] because it is not compatible with version[{}]", next.getResourceType(), getContext().getVersion().getVersion());
-									continue;
-								}
-								throw e;
-							}
-							IBaseResource resource = toResource(type.getImplementingClass(), next, true);
-							retVal.add(resource);
-						}
-						return retVal;
-					}
-				});
 			}
+		}
 		
-			@Override
+		search = mySearchDao.save(search);
-			public Integer preferredPageSize() {
-				return null;
-			}
 
-			@Override
+		return new PersistedJpaBundleProvider(search.getUuid(), this);
-			public int size() {
+	}
-				return tuples.size();
+
-			}
+	@Override
-		};
+	public void injectDependenciesIntoBundleProvider(PersistedJpaBundleProvider theProvider) {
+		theProvider.setContext(getContext());
+		theProvider.setEntityManager(myEntityManager);
+		theProvider.setPlatformTransactionManager(myPlatformTransactionManager);
+		theProvider.setResourceHistoryTableDao(myResourceHistoryTableDao);
+		theProvider.setSearchDao(mySearchDao);
+		theProvider.setSearchResultDao(mySearchResultDao);
 	}
 
 	protected void notifyInterceptors(RestOperationTypeEnum operationType, ActionRequestDetails requestDetails) {
@@ -808,8 +778,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 		} else if (theForHistoryOperation) {
 			/*
-			 * If the create and update times match, this was when the resource was created so we should mark it as a POST.
+			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
-			 * Otherwise, it's a PUT.
 			 */
 			Date published = theEntity.getPublished().getValue();
 			Date updated = theEntity.getUpdated().getValue();
@@ -879,8 +848,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 		} else if (theForHistoryOperation) {
 			/*
-			 * If the create and update times match, this was when the resource was created so we should mark it as a POST.
+			 * If the create and update times match, this was when the resource was created so we should mark it as a POST. Otherwise, it's a PUT.
-			 * Otherwise, it's a PUT.
 			 */
 			Date published = theEntity.getPublished().getValue();
 			Date updated = theEntity.getUpdated().getValue();
@@ -903,6 +871,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		IDao.RESOURCE_PID.put(res, theEntity.getId());
 
 		Collection<? extends BaseTag> tags = theEntity.getTags();
+		
 		if (theEntity.isHasTags()) {
 			for (BaseTag next : tags) {
 				switch (next.getTag().getTagType()) {
@@ -928,8 +897,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the
+	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the first time.
-	 * first time.
 	 * 
 	 * @param theEntity
 	 *           The entity being updated (Do not modify the entity! Undefined behaviour will occur!)
@@ -943,8 +911,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the
+	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the first time.
-	 * first time.
 	 * 
 	 * @param theEntity
 	 *           The resource
@@ -977,146 +944,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		throw new NotImplementedException("");
 	}
 
-	private void searchHistoryCurrentVersion(List<HistoryTuple> theTuples, List<BaseHasResource> theRetVal) {
-		Collection<HistoryTuple> tuples = Collections2.filter(theTuples, new com.google.common.base.Predicate<HistoryTuple>() {
-			@Override
-			public boolean apply(HistoryTuple theInput) {
-				return theInput.isHistory() == false;
-			}
-		});
-		Collection<Long> ids = Collections2.transform(tuples, new Function<HistoryTuple, Long>() {
-			@Override
-			public Long apply(HistoryTuple theInput) {
-				return theInput.getId();
-			}
-		});
-		if (ids.isEmpty()) {
-			return;
-		}
-
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
-		Root<ResourceTable> from = cq.from(ResourceTable.class);
-		cq.where(from.get("myId").in(ids));
-
-		cq.orderBy(builder.desc(from.get("myUpdated")));
-		TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
-		for (ResourceTable next : q.getResultList()) {
-			theRetVal.add(next);
-		}
-	}
-
-	private void searchHistoryCurrentVersion(String theResourceName, Long theId, Date theSince, Date theEnd, Integer theLimit, List<HistoryTuple> tuples) {
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<Tuple> cq = builder.createTupleQuery();
-		Root<?> from = cq.from(ResourceTable.class);
-		cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
-
-		List<Predicate> predicates = new ArrayList<Predicate>();
-		if (theSince != null) {
-			Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
-			predicates.add(low);
-		}
-
-		Predicate high = builder.lessThan(from.<Date> get("myUpdated"), theEnd);
-		predicates.add(high);
-
-		if (theResourceName != null) {
-			predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
-		}
-		if (theId != null) {
-			predicates.add(builder.equal(from.get("myId"), theId));
-		}
-
-		cq.where(builder.and(predicates.toArray(new Predicate[0])));
-
-		cq.orderBy(builder.desc(from.get("myUpdated")));
-		TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
-		if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
-			q.setMaxResults(theLimit);
-		} else {
-			q.setMaxResults(myConfig.getHardSearchLimit());
-		}
-		for (Tuple next : q.getResultList()) {
-			long id = next.get(0, Long.class);
-			Date updated = next.get(1, Date.class);
-			tuples.add(new HistoryTuple(false, updated, id));
-		}
-	}
-
-	private void searchHistoryHistory(List<HistoryTuple> theTuples, List<BaseHasResource> theRetVal) {
-		Collection<HistoryTuple> tuples = Collections2.filter(theTuples, new com.google.common.base.Predicate<HistoryTuple>() {
-			@Override
-			public boolean apply(HistoryTuple theInput) {
-				return theInput.isHistory() == true;
-			}
-		});
-		Collection<Long> ids = Collections2.transform(tuples, new Function<HistoryTuple, Long>() {
-			@Override
-			public Long apply(HistoryTuple theInput) {
-				return (Long) theInput.getId();
-			}
-		});
-		if (ids.isEmpty()) {
-			return;
-		}
-
-		ourLog.info("Retrieving {} history elements from ResourceHistoryTable", ids.size());
-
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<ResourceHistoryTable> cq = builder.createQuery(ResourceHistoryTable.class);
-		Root<ResourceHistoryTable> from = cq.from(ResourceHistoryTable.class);
-		cq.where(from.get("myId").in(ids));
-
-		cq.orderBy(builder.desc(from.get("myUpdated")));
-		TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(cq);
-		for (ResourceHistoryTable next : q.getResultList()) {
-			theRetVal.add(next);
-		}
-	}
-
-	private void searchHistoryHistory(String theResourceName, Long theResourceId, Date theSince, Date theEnd, Integer theLimit, List<HistoryTuple> tuples) {
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<Tuple> cq = builder.createTupleQuery();
-		Root<?> from = cq.from(ResourceHistoryTable.class);
-		cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
-
-		List<Predicate> predicates = new ArrayList<Predicate>();
-		if (theSince != null) {
-			Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
-			predicates.add(low);
-		}
-
-		Predicate high = builder.lessThan(from.<Date> get("myUpdated"), theEnd);
-		predicates.add(high);
-
-		if (theResourceName != null) {
-			predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
-		}
-		if (theResourceId != null) {
-			predicates.add(builder.equal(from.get("myResourceId"), theResourceId));
-		}
-
-		cq.where(builder.and(predicates.toArray(new Predicate[0])));
-
-		cq.orderBy(builder.desc(from.get("myUpdated")));
-		TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
-		if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
-			q.setMaxResults(theLimit);
-		} else {
-			q.setMaxResults(myConfig.getHardSearchLimit());
-		}
-		for (Tuple next : q.getResultList()) {
-			Long id = next.get(0, Long.class);
-			Date updated = (Date) next.get(1);
-			tuples.add(new HistoryTuple(true, updated, id));
-		}
-	}
-
-	public void setConfig(DaoConfig theConfig) {
-		myConfig = theConfig;
-	}
-
 	// protected MetaDt toMetaDt(Collection<TagDefinition> tagDefinitions) {
 	// MetaDt retVal = new MetaDt();
 	// for (TagDefinition next : tagDefinitions) {
@@ -1135,6 +962,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	// return retVal;
 	// }
 
+	public void setConfig(DaoConfig theConfig) {
+		myConfig = theConfig;
+	}
+
 	@Autowired
 	public void setContext(FhirContext theContext) {
 		myContext = theContext;
@@ -1162,15 +993,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * This method is called when an update to an existing resource detects that the resource supplied for update is
+	 * This method is called when an update to an existing resource detects that the resource supplied for update is missing a tag/profile/security label that the currently persisted resource holds.
-	 * missing a tag/profile/security label that the currently persisted resource holds.
 	 * <p>
-	 * The default implementation removes any profile declarations, but leaves tags and security labels in place.
+	 * The default implementation removes any profile declarations, but leaves tags and security labels in place. Subclasses may choose to override and change this behaviour.
-	 * Subclasses may choose to override and change this behaviour.
 	 * </p>
 	 * <p>
-	 * See <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security
+	 * See <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security Labels</a> for a description of the logic that the default behaviour folows.
-	 *      Labels</a> for a description of the logic that the default behaviour folows.
 	 * </p>
 	 * 
 	 * @param theEntity
@@ -1200,53 +1028,53 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return toResource(type.getImplementingClass(), theEntity, theForHistoryOperation);
 	}
 
-		@Override
+	@Override
-		public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
+	public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
-			String resourceText = null;
+		String resourceText = null;
-			switch (theEntity.getEncoding()) {
+		switch (theEntity.getEncoding()) {
-			case JSON:
+		case JSON:
-				try {
-					resourceText = new String(theEntity.getResource(), "UTF-8");
-				} catch (UnsupportedEncodingException e) {
-					throw new Error("Should not happen", e);
-				}
-				break;
-			case JSONC:
-				resourceText = GZipUtil.decompress(theEntity.getResource());
-				break;
-			}
-
-			IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
-			R retVal;
 			try {
-				retVal = parser.parseResource(theResourceType, resourceText);
+				resourceText = new String(theEntity.getResource(), "UTF-8");
-			} catch (Exception e) {
+			} catch (UnsupportedEncodingException e) {
-				StringBuilder b = new StringBuilder();
+				throw new Error("Should not happen", e);
-				b.append("Failed to parse database resource[");
-				b.append(theResourceType);
-				b.append("/");
-				b.append(theEntity.getIdDt().getIdPart());
-				b.append(" (pid ");
-				b.append(theEntity.getId());
-				b.append(", version ");
-				b.append(myContext.getVersion().getVersion());
-				b.append("): ");
-				b.append(e.getMessage());
-				String msg = b.toString();
-				ourLog.error(msg, e);
-				throw new DataFormatException(msg, e);
 			}
-
+			break;
-			if (retVal instanceof IResource) {
+		case JSONC:
-				IResource res = (IResource) retVal;
+			resourceText = GZipUtil.decompress(theEntity.getResource());
-				retVal = populateResourceMetadataHapi(theResourceType, theEntity, theForHistoryOperation, res);
+			break;
-			} else {
-				IAnyResource res = (IAnyResource) retVal;
-				retVal = populateResourceMetadataRi(theResourceType, theEntity, theForHistoryOperation, res);
-			}
-			return retVal;
 		}
 
+		IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
+		R retVal;
+		try {
+			retVal = parser.parseResource(theResourceType, resourceText);
+		} catch (Exception e) {
+			StringBuilder b = new StringBuilder();
+			b.append("Failed to parse database resource[");
+			b.append(theResourceType);
+			b.append("/");
+			b.append(theEntity.getIdDt().getIdPart());
+			b.append(" (pid ");
+			b.append(theEntity.getId());
+			b.append(", version ");
+			b.append(myContext.getVersion().getVersion());
+			b.append("): ");
+			b.append(e.getMessage());
+			String msg = b.toString();
+			ourLog.error(msg, e);
+			throw new DataFormatException(msg, e);
+		}
+
+		if (retVal instanceof IResource) {
+			IResource res = (IResource) retVal;
+			retVal = populateResourceMetadataHapi(theResourceType, theEntity, theForHistoryOperation, res);
+		} else {
+			IAnyResource res = (IAnyResource) retVal;
+			retVal = populateResourceMetadataRi(theResourceType, theEntity, theForHistoryOperation, res);
+		}
+		return retVal;
+	}
+
 	protected String toResourceName(Class<? extends IBaseResource> theResourceType) {
 		return myContext.getResourceDefinition(theResourceType).getName();
 	}
@@ -1268,12 +1096,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 	}
 
-	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, Date theUpdateTime, RequestDetails theRequestDetails) {
-		return updateEntity(theResource, entity, theUpdateHistory, theDeletedTimestampOrNull, true, true, theUpdateTime, theRequestDetails);
-	}
-
 	@SuppressWarnings("unchecked")
-	protected ResourceTable updateEntity(final IBaseResource theResource, ResourceTable theEntity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion, Date theUpdateTime, RequestDetails theRequestDetails) {
+	protected ResourceTable updateEntity(final IBaseResource theResource, ResourceTable theEntity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
+			boolean theUpdateVersion, Date theUpdateTime, RequestDetails theRequestDetails) {
+		ourLog.info("Starting entity update");
 
 		/*
 		 * This should be the very first thing..
@@ -1284,7 +1110,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 			String resourceType = myContext.getResourceDefinition(theResource).getName();
 			if (isNotBlank(theEntity.getResourceType()) && !theEntity.getResourceType().equals(resourceType)) {
-				throw new UnprocessableEntityException("Existing resource ID[" + theEntity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + theEntity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
+				throw new UnprocessableEntityException(
+						"Existing resource ID[" + theEntity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + theEntity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
 			}
 		}
 
@@ -1292,10 +1119,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			theEntity.setPublished(theUpdateTime);
 		}
 
-		if (theUpdateHistory) {
+//		if (theUpdateHistory) {
-			final ResourceHistoryTable historyEntry = theEntity.toHistory();
+//			Long existingId = theEntity.getId();
-			myEntityManager.persist(historyEntry);
+//			ResourceHistoryTable existingHistory = existingId != null ? myResourceHistoryTableDao.findForIdAndVersion(existingId, theEntity.getVersion()) : null;
-		}
+//			final ResourceHistoryTable historyEntry = theEntity.toHistory(existingHistory);
+//
+//			ourLog.info("Saving history entry for update {}", historyEntry.getIdDt());
+//			myResourceHistoryTableDao.save(historyEntry);
+//
+//		}
 
 		if (theUpdateVersion) {
 			theEntity.setVersion(theEntity.getVersion() + 1);
@@ -1384,9 +1216,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				}
 
 				/*
-				 *	Handle references within the resource that are match URLs, for example
+				 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the matching
-				 * references like "Patient?identifier=foo". These match URLs are resolved
+				 * resource.
-				 * and replaced with the ID of the matching resource. 
 				 */
 				if (myConfig.isAllowInlineMatchUrlReferences()) {
 					FhirTerser terser = getContext().newTerser();
@@ -1429,8 +1260,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				links = extractResourceLinks(theEntity, theResource);
 
 				/*
-				 * If the existing resource already has links and those match links we still want, use them instead of
+				 * If the existing resource already has links and those match links we still want, use them instead of removing them and re adding them
-				 * removing them and re adding them
 				 */
 				for (Iterator<ResourceLink> existingLinkIter = existingResourceLinks.iterator(); existingLinkIter.hasNext();) {
 					ResourceLink nextExisting = existingLinkIter.next();
@@ -1479,6 +1309,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 		}
 
+		/*
+		 * Save the resource itself
+		 */
 		if (theEntity.getId() == null) {
 			myEntityManager.persist(theEntity);
 
@@ -1494,6 +1327,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			postUpdate(theEntity, (T) theResource);
 		}
 
+		/*
+		 * Create history entry
+		 */
+		if (theUpdateVersion) {
+			final ResourceHistoryTable historyEntry = theEntity.toHistory(null);
+
+			ourLog.info("Saving history entry {}", historyEntry.getIdDt());
+			myResourceHistoryTableDao.save(historyEntry);
+		}
+
+		/*
+		 * Indexing
+		 */
 		if (thePerformIndexing) {
 
 			for (ResourceIndexedSearchParamString next : paramsString) {
@@ -1569,6 +1415,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return theEntity;
 	}
 
+	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, Date theUpdateTime,
+			RequestDetails theRequestDetails) {
+		return updateEntity(theResource, entity, theUpdateHistory, theDeletedTimestampOrNull, true, true, theUpdateTime, theRequestDetails);
+	}
+
 	protected void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
 		if (theDeleteConflicts.isEmpty()) {
 			return;
@@ -1576,7 +1427,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
 		for (DeleteConflict next : theDeleteConflicts) {
-			String msg = "Unable to delete " + next.getTargetId().toUnqualifiedVersionless().getValue() + " because at least one resource has a reference to this resource. First reference found was resource " + next.getTargetId().toUnqualifiedVersionless().getValue() + " in path "
+			String msg = "Unable to delete " + next.getTargetId().toUnqualifiedVersionless().getValue()
+					+ " because at least one resource has a reference to this resource. First reference found was resource " + next.getTargetId().toUnqualifiedVersionless().getValue() + " in path "
 					+ next.getSourcePath();
 			OperationOutcomeUtil.addIssue(getContext(), oo, OO_SEVERITY_ERROR, msg, null, "processing");
 		}
@@ -1585,15 +1437,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow
+	 * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the
-	 * the DAO to ensure that it is valid for persistence. By default, checks for the "subsetted" tag and rejects
+	 * "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.
-	 * resources which have it. Subclasses should call the superclass implementation to preserve this check.
 	 * 
 	 * @param theResource
 	 *           The resource that is about to be persisted
 	 * @param theEntityToSave
 	 *           TODO
-	 * @param theRequestDetails TODO
+	 * @param theRequestDetails
+	 *           TODO
 	 */
 	protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave, RequestDetails theRequestDetails) {
 		Object tag = null;
@@ -1604,7 +1456,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
 			}
 		} else {
-			IAnyResource res = (IAnyResource)theResource;
+			IAnyResource res = (IAnyResource) theResource;
 			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
 		}
 
@@ -1701,12 +1553,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	private static List<BaseCodingDt> toBaseCodingList(List<IBaseCoding> theSecurityLabels) {
-	ArrayList<BaseCodingDt> retVal = new ArrayList<BaseCodingDt>(theSecurityLabels.size());
+		ArrayList<BaseCodingDt> retVal = new ArrayList<BaseCodingDt>(theSecurityLabels.size());
-	for (IBaseCoding next : theSecurityLabels) {
+		for (IBaseCoding next : theSecurityLabels) {
-		retVal.add((BaseCodingDt) next);
+			retVal.add((BaseCodingDt) next);
+		}
+		return retVal;
 	}
-	return retVal;
-}
 
 	static Long translateForcedIdToPid(IIdType theId, EntityManager entityManager) {
 		if (isValidPid(theId)) {
@@ -1820,7 +1672,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 	public static void validateResourceType(BaseHasResource theEntity, String theResourceName) {
 		if (!theResourceName.equals(theEntity.getResourceType())) {
-			throw new ResourceNotFoundException("Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
+			throw new ResourceNotFoundException(
+					"Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
 		}
 	}
 

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

@@ -34,7 +34,6 @@ import java.util.Set;
 
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
-import javax.persistence.TemporalType;
 import javax.persistence.TypedQuery;
 
 import org.hl7.fhir.dstu3.model.IdType;
@@ -55,6 +54,7 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
@@ -73,7 +73,6 @@ import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
@@ -387,113 +386,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		ActionRequestDetails requestDetails = new ActionRequestDetails(theId, getResourceName(), getContext(), theRequestDetails);
 		notifyInterceptors(RestOperationTypeEnum.HISTORY_INSTANCE, requestDetails);
 
-		final InstantDt end = createHistoryToTimestamp();
+		StopWatch w = new StopWatch();
-		final String resourceType = getContext().getResourceDefinition(myResourceType).getName();
 
-		T currentTmp;
+		IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless();
-		try {
+		BaseHasResource entity = readEntity(id);
-			BaseHasResource entity = readEntity(theId.toVersionless(), false);
-			validateResourceType(entity);
-			currentTmp = toResource(myResourceType, entity, true);
-			Date lastUpdated;
-			if (currentTmp instanceof IResource) {
-				lastUpdated = ResourceMetadataKeyEnum.UPDATED.get((IResource) currentTmp).getValue();
-			} else {
-				lastUpdated = ((IAnyResource) currentTmp).getMeta().getLastUpdated();
-			}
-			if (lastUpdated.after(end.getValue())) {
-				currentTmp = null;
-			}
-		} catch (ResourceNotFoundException e) {
-			currentTmp = null;
-		}
 		
-		final T current = currentTmp;
+		IBundleProvider retVal = super.history(myResourceName, entity.getId(), theSince);
-
-		StringBuilder B = new StringBuilder();
-		B.append("SELECT count(h) FROM ResourceHistoryTable h ");
-		B.append("WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE");
-		B.append(" AND h.myUpdated < :END");
-		B.append((theSince != null ? " AND h.myUpdated >= :SINCE" : ""));
-		String querySring = B.toString();
-
-		TypedQuery<Long> countQuery = myEntityManager.createQuery(querySring, Long.class);
-		countQuery.setParameter("PID", translateForcedIdToPid(theId));
-		countQuery.setParameter("RESTYPE", resourceType);
-		countQuery.setParameter("END", end.getValue(), TemporalType.TIMESTAMP);
-		if (theSince != null) {
-			countQuery.setParameter("SINCE", theSince, TemporalType.TIMESTAMP);
-		}
-		int historyCount = countQuery.getSingleResult().intValue();
-
-		final int offset;
-		final int count;
-		if (current != null) {
-			count = historyCount + 1;
-			offset = 1;
-		} else {
-			offset = 0;
-			count = historyCount;
-		}
-
-		if (count == 0) {
-			throw new ResourceNotFoundException(theId);
-		}
-
-		return new IBundleProvider() {
-
-			@Override
-			public InstantDt getPublished() {
-				return end;
-			}
-
-			@Override
-			public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
-				List<IBaseResource> retVal = new ArrayList<IBaseResource>();
-				if (theFromIndex == 0 && current != null) {
-					retVal.add(current);
-				}
-
-				StringBuilder b = new StringBuilder();
-				b.append("SELECT h FROM ResourceHistoryTable h WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE AND h.myUpdated < :END ");
-				b.append((theSince != null ? " AND h.myUpdated >= :SINCE" : ""));
-				b.append(" ORDER BY h.myUpdated DESC");
-				TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(b.toString(), ResourceHistoryTable.class);
-				q.setParameter("PID", translateForcedIdToPid(theId));
-				q.setParameter("RESTYPE", resourceType);
-				q.setParameter("END", end.getValue(), TemporalType.TIMESTAMP);
-				if (theSince != null) {
-					q.setParameter("SINCE", theSince, TemporalType.TIMESTAMP);
-				}
-
-				int firstResult = Math.max(0, theFromIndex - offset);
-				q.setFirstResult(firstResult);
-
-				int maxResults = (theToIndex - theFromIndex) + 1;
-				q.setMaxResults(maxResults);
-
-				List<ResourceHistoryTable> results = q.getResultList();
-				for (ResourceHistoryTable next : results) {
-					if (retVal.size() == maxResults) {
-						break;
-					}
-					retVal.add(toResource(myResourceType, next, true));
-				}
-
-				return retVal;
-			}
-
-			@Override
-			public Integer preferredPageSize() {
-				return null;
-			}
-
-			@Override
-			public int size() {
-				return count;
-			}
-		};
 
+		ourLog.info("Processed history on {} in {}ms", id, w.getMillisAndRestart());
+		return retVal;
 	}
 
 	@Override
@@ -508,6 +409,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
+	@Autowired
+	private IResourceHistoryTableDao myResourceHistoryTableDao;
+	
 	@Override
 	public <MT extends IBaseMetaType> MT metaAddOperation(IIdType theResourceId, MT theMetaAdd, RequestDetails theRequestDetails) {
 		// Notify interceptors
@@ -520,6 +424,25 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw new ResourceNotFoundException(theResourceId);
 		}
 
+		ResourceTable latestVersion = readEntityLatestVersion(theResourceId);
+		if (latestVersion.getVersion() != entity.getVersion()) {
+			doMetaAdd(theMetaAdd, entity);
+		} else {
+			doMetaAdd(theMetaAdd, latestVersion);
+			
+			// Also update history entry
+			ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion());
+			doMetaAdd(theMetaAdd, history);
+		}
+		
+		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
+
+		@SuppressWarnings("unchecked")
+		MT retVal = (MT) metaGetOperation(theMetaAdd.getClass(), theResourceId, theRequestDetails);
+		return retVal;
+	}
+
+	private <MT extends IBaseMetaType> void doMetaAdd(MT theMetaAdd, BaseHasResource entity) {
 		List<TagDefinition> tags = toTagList(theMetaAdd);
 
 		//@formatter:off
@@ -546,11 +469,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		//@formatter:on
 
 		myEntityManager.merge(entity);
-		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
-
-		@SuppressWarnings("unchecked")
-		MT retVal = (MT) metaGetOperation(theMetaAdd.getClass(), theResourceId, theRequestDetails);
-		return retVal;
 	}
 
 	// @Override
@@ -647,6 +565,27 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw new ResourceNotFoundException(theResourceId);
 		}
 
+		ResourceTable latestVersion = readEntityLatestVersion(theResourceId);
+		if (latestVersion.getVersion() != entity.getVersion()) {
+			doMetaDelete(theMetaDel, entity);
+		} else {
+			doMetaDelete(theMetaDel, latestVersion);
+			
+			// Also update history entry
+			ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion());
+			doMetaDelete(theMetaDel, history);
+		}
+		
+		myEntityManager.flush();
+
+		ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
+
+		@SuppressWarnings("unchecked")
+		MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails);
+		return retVal;
+	}
+
+	private <MT extends IBaseMetaType> void doMetaDelete(MT theMetaDel, BaseHasResource entity) {
 		List<TagDefinition> tags = toTagList(theMetaDel);
 
 		//@formatter:off
@@ -667,13 +606,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		myEntityManager.merge(entity);
-		myEntityManager.flush();
-
-		ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
-
-		@SuppressWarnings("unchecked")
-		MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails);
-		return retVal;
 	}
 
 	@Override

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

@@ -3,7 +3,9 @@ package ca.uhn.fhir.jpa.dao;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupportingAnyResource;
 
@@ -33,30 +35,35 @@ public interface IDao {
 
 		private static final long serialVersionUID = 1L;
 
-		@Override
-		public Long get(IResource theResource) {
-			return (Long) theResource.getResourceMetadata().get(RESOURCE_PID);
-		}
-
-		@Override
-		public void put(IResource theResource, Long theObject) {
-			theResource.getResourceMetadata().put(RESOURCE_PID, theObject);
-		}
-
 		@Override
 		public Long get(IAnyResource theResource) {
 			return (Long) theResource.getUserData(RESOURCE_PID.name());
 		}
 
+		@Override
+		public Long get(IResource theResource) {
+			return (Long) theResource.getResourceMetadata().get(RESOURCE_PID);
+		}
+
 		@Override
 		public void put(IAnyResource theResource, Long theObject) {
 			theResource.setUserData(RESOURCE_PID.name(), theObject);
 		}
+
+		@Override
+		public void put(IResource theResource, Long theObject) {
+			theResource.getResourceMetadata().put(RESOURCE_PID, theObject);
+		}
 	};
 
+	FhirContext getContext();
+
+	/**
+	 * Populate all of the runtime dependencies that a bundle provider requires in order to work
+	 */
+	void injectDependenciesIntoBundleProvider(PersistedJpaBundleProvider theProvider);
+
 	IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation);
 	
 	<R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation);
-
-	
 }

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

@@ -42,7 +42,6 @@ import java.util.Set;
 import java.util.UUID;
 
 import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
 import javax.persistence.Tuple;
 import javax.persistence.TypedQuery;
 import javax.persistence.criteria.CriteriaBuilder;
@@ -62,9 +61,6 @@ import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.springframework.data.domain.Page;
-import org.springframework.data.domain.PageRequest;
-import org.springframework.data.domain.Pageable;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -93,8 +89,10 @@ import ca.uhn.fhir.jpa.entity.ResourceTag;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.entity.SearchInclude;
 import ca.uhn.fhir.jpa.entity.SearchResult;
+import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -943,21 +941,6 @@ public class SearchBuilder {
 		return retVal;
 	}
 
-	private static List<Predicate> createLastUpdatedPredicates(final DateRangeParam theLastUpdated, CriteriaBuilder builder, From<?, ResourceTable> from) {
-		List<Predicate> lastUpdatedPredicates = new ArrayList<Predicate>();
-		if (theLastUpdated != null) {
-			if (theLastUpdated.getLowerBoundAsInstant() != null) {
-				Predicate predicateLower = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theLastUpdated.getLowerBoundAsInstant());
-				lastUpdatedPredicates.add(predicateLower);
-			}
-			if (theLastUpdated.getUpperBoundAsInstant() != null) {
-				Predicate predicateUpper = builder.lessThanOrEqualTo(from.<Date> get("myUpdated"), theLastUpdated.getUpperBoundAsInstant());
-				lastUpdatedPredicates.add(predicateUpper);
-			}
-		}
-		return lastUpdatedPredicates;
-	}
-
 	private Predicate createPredicateDate(CriteriaBuilder theBuilder, From<ResourceIndexedSearchParamDate, ResourceIndexedSearchParamDate> theFrom, IQueryParameterType theParam) {
 		Predicate p;
 		if (theParam instanceof DateParam) {
@@ -1307,7 +1290,7 @@ public class SearchBuilder {
 			mySearchEntity.setCreated(new Date());
 			mySearchEntity.setTotalCount(-1);
 			mySearchEntity.setPreferredPageSize(myParams.getCount());
-			mySearchEntity.setEverythingMode(myParams.getEverythingMode());
+			mySearchEntity.setSearchType(myParams.getEverythingMode() != null ? SearchTypeEnum.EVERYTHING : SearchTypeEnum.SEARCH);
 			mySearchEntity.setLastUpdated(myParams.getLastUpdated());
 
 			for (Include next : myParams.getIncludes()) {
@@ -1329,7 +1312,7 @@ public class SearchBuilder {
 
 	private IBundleProvider doReturnProvider() {
 		if (myParams.isPersistResults()) {
-			return new BundleProviderPersisted(mySearchEntity.getUuid(), myPlatformTransactionManager, mySearchResultDao, myEntityManager, myContext, myCallingDao);
+			return new PersistedJpaBundleProvider(mySearchEntity.getUuid(), myCallingDao);
 		} else {
 			if (myPids == null) {
 				return new SimpleBundleProvider();
@@ -1381,22 +1364,6 @@ public class SearchBuilder {
 		doSetPids(resultList);
 	}
 
-	private static List<Long> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<Long> thePids) {
-		CriteriaBuilder builder = theEntityManager.getCriteriaBuilder();
-		CriteriaQuery<Long> cq = builder.createQuery(Long.class);
-		Root<ResourceTable> from = cq.from(ResourceTable.class);
-		cq.select(from.get("myId").as(Long.class));
-
-		List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(theLastUpdated, builder, from);
-		lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(thePids));
-
-		cq.where(SearchBuilder.toArray(lastUpdatedPredicates));
-		TypedQuery<Long> query = theEntityManager.createQuery(cq);
-
-		List<Long> resultList = query.getResultList();
-		return resultList;
-	}
-
 	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation) {
 		EntityManager entityManager = myEntityManager;
 		FhirContext context = myContext;
@@ -1405,179 +1372,6 @@ public class SearchBuilder {
 		loadResourcesByPid(theIncludePids, theResourceListToPopulate, theRevIncludedPids, theForHistoryOperation, entityManager, context, dao);
 	}
 
-	private static void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation,
-			EntityManager entityManager, FhirContext context, IDao theDao) {
-		if (theIncludePids.isEmpty()) {
-			return;
-		}
-
-		Map<Long, Integer> position = new HashMap<Long, Integer>();
-		for (Long next : theIncludePids) {
-			position.put(next, theResourceListToPopulate.size());
-			theResourceListToPopulate.add(null);
-		}
-
-		CriteriaBuilder builder = entityManager.getCriteriaBuilder();
-		CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
-		Root<ResourceTable> from = cq.from(ResourceTable.class);
-		cq.where(from.get("myId").in(theIncludePids));
-		TypedQuery<ResourceTable> q = entityManager.createQuery(cq);
-
-		for (ResourceTable next : q.getResultList()) {
-			Class<? extends IBaseResource> resourceType = context.getResourceDefinition(next.getResourceType()).getImplementingClass();
-			IBaseResource resource = (IBaseResource) theDao.toResource(resourceType, next, theForHistoryOperation);
-			Integer index = position.get(next.getId());
-			if (index == null) {
-				ourLog.warn("Got back unexpected resource PID {}", next.getId());
-				continue;
-			}
-
-			if (resource instanceof IResource) {
-				if (theRevIncludedPids.contains(next.getId())) {
-					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.INCLUDE);
-				} else {
-					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.MATCH);
-				}
-			} else {
-				if (theRevIncludedPids.contains(next.getId())) {
-					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.INCLUDE.getCode());
-				} else {
-					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.MATCH.getCode());
-				}
-			}
-
-			theResourceListToPopulate.set(index, resource);
-		}
-	}
-
-	/**
-	 * THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
-	 * 
-	 * @param theLastUpdated
-	 */
-	private static HashSet<Long> loadReverseIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
-			DateRangeParam theLastUpdated) {
-		if (theMatches.size() == 0) {
-			return new HashSet<Long>();
-		}
-		if (theRevIncludes == null || theRevIncludes.isEmpty()) {
-			return new HashSet<Long>();
-		}
-		String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
-
-		Collection<Long> nextRoundMatches = theMatches;
-		HashSet<Long> allAdded = new HashSet<Long>();
-		HashSet<Long> original = new HashSet<Long>(theMatches);
-		ArrayList<Include> includes = new ArrayList<Include>(theRevIncludes);
-
-		int roundCounts = 0;
-		StopWatch w = new StopWatch();
-
-		boolean addedSomeThisRound;
-		do {
-			roundCounts++;
-
-			HashSet<Long> pidsToInclude = new HashSet<Long>();
-			Set<Long> nextRoundOmit = new HashSet<Long>();
-
-			for (Iterator<Include> iter = includes.iterator(); iter.hasNext();) {
-				Include nextInclude = iter.next();
-				if (nextInclude.isRecurse() == false) {
-					iter.remove();
-				}
-
-				boolean matchAll = "*".equals(nextInclude.getValue());
-				if (matchAll) {
-					String sql;
-					sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids)";
-					TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
-					q.setParameter("target_pids", nextRoundMatches);
-					List<ResourceLink> results = q.getResultList();
-					for (ResourceLink resourceLink : results) {
-						if (theReverseMode) {
-							// if (theEverythingModeEnum.isEncounter()) {
-							// if (resourceLink.getSourcePath().equals("Encounter.subject") ||
-							// resourceLink.getSourcePath().equals("Encounter.patient")) {
-							// nextRoundOmit.add(resourceLink.getSourceResourcePid());
-							// }
-							// }
-							pidsToInclude.add(resourceLink.getSourceResourcePid());
-						} else {
-							pidsToInclude.add(resourceLink.getTargetResourcePid());
-						}
-					}
-				} else {
-
-					List<String> paths;
-					if (theContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
-						paths = Collections.singletonList(nextInclude.getValue());
-					} else {
-						String resType = nextInclude.getParamType();
-						if (isBlank(resType)) {
-							continue;
-						}
-						RuntimeResourceDefinition def = theContext.getResourceDefinition(resType);
-						if (def == null) {
-							ourLog.warn("Unknown resource type in include/revinclude=" + nextInclude.getValue());
-							continue;
-						}
-
-						String paramName = nextInclude.getParamName();
-						RuntimeSearchParam param = isNotBlank(paramName) ? def.getSearchParam(paramName) : null;
-						if (param == null) {
-							ourLog.warn("Unknown param name in include/revinclude=" + nextInclude.getValue());
-							continue;
-						}
-
-						paths = param.getPathsSplit();
-					}
-
-					String targetResourceType = defaultString(nextInclude.getParamTargetType(), null);
-					for (String nextPath : paths) {
-						String sql;
-						if (targetResourceType != null) {
-							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
-						} else {
-							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
-						}
-						TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
-						q.setParameter("src_path", nextPath);
-						q.setParameter("target_pids", nextRoundMatches);
-						if (targetResourceType != null) {
-							q.setParameter("target_resource_type", targetResourceType);
-						}
-						List<ResourceLink> results = q.getResultList();
-						for (ResourceLink resourceLink : results) {
-							if (theReverseMode) {
-								pidsToInclude.add(resourceLink.getSourceResourcePid());
-							} else {
-								pidsToInclude.add(resourceLink.getTargetResourcePid());
-							}
-						}
-					}
-				}
-			}
-
-			if (theLastUpdated != null && (theLastUpdated.getLowerBoundAsInstant() != null || theLastUpdated.getUpperBoundAsInstant() != null)) {
-				pidsToInclude = new HashSet<Long>(filterResourceIdsByLastUpdated(theEntityManager, theLastUpdated, pidsToInclude));
-			}
-			for (Long next : pidsToInclude) {
-				if (original.contains(next) == false && allAdded.contains(next) == false) {
-					theMatches.add(next);
-				}
-			}
-
-			pidsToInclude.removeAll(nextRoundOmit);
-
-			addedSomeThisRound = allAdded.addAll(pidsToInclude);
-			nextRoundMatches = pidsToInclude;
-		} while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound);
-
-		ourLog.info("Loaded {} {} in {} rounds and {} ms", new Object[] { allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart() });
-
-		return allAdded;
-	}
-
 	private void processSort(final SearchParameterMap theParams) {
 
 		// Set<Long> loadPids = theLoadPids;
@@ -1957,10 +1751,214 @@ public class SearchBuilder {
 		}
 	}
 
+	private static List<Predicate> createLastUpdatedPredicates(final DateRangeParam theLastUpdated, CriteriaBuilder builder, From<?, ResourceTable> from) {
+		List<Predicate> lastUpdatedPredicates = new ArrayList<Predicate>();
+		if (theLastUpdated != null) {
+			if (theLastUpdated.getLowerBoundAsInstant() != null) {
+				Predicate predicateLower = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theLastUpdated.getLowerBoundAsInstant());
+				lastUpdatedPredicates.add(predicateLower);
+			}
+			if (theLastUpdated.getUpperBoundAsInstant() != null) {
+				Predicate predicateUpper = builder.lessThanOrEqualTo(from.<Date> get("myUpdated"), theLastUpdated.getUpperBoundAsInstant());
+				lastUpdatedPredicates.add(predicateUpper);
+			}
+		}
+		return lastUpdatedPredicates;
+	}
+
 	private static String createLeftMatchLikeExpression(String likeExpression) {
 		return likeExpression.replace("%", "[%]") + "%";
 	}
 
+	private static List<Long> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<Long> thePids) {
+		CriteriaBuilder builder = theEntityManager.getCriteriaBuilder();
+		CriteriaQuery<Long> cq = builder.createQuery(Long.class);
+		Root<ResourceTable> from = cq.from(ResourceTable.class);
+		cq.select(from.get("myId").as(Long.class));
+
+		List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(theLastUpdated, builder, from);
+		lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(thePids));
+
+		cq.where(SearchBuilder.toArray(lastUpdatedPredicates));
+		TypedQuery<Long> query = theEntityManager.createQuery(cq);
+
+		List<Long> resultList = query.getResultList();
+		return resultList;
+	}
+
+	public static void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation,
+			EntityManager entityManager, FhirContext context, IDao theDao) {
+		if (theIncludePids.isEmpty()) {
+			return;
+		}
+
+		Map<Long, Integer> position = new HashMap<Long, Integer>();
+		for (Long next : theIncludePids) {
+			position.put(next, theResourceListToPopulate.size());
+			theResourceListToPopulate.add(null);
+		}
+
+		CriteriaBuilder builder = entityManager.getCriteriaBuilder();
+		CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
+		Root<ResourceTable> from = cq.from(ResourceTable.class);
+		cq.where(from.get("myId").in(theIncludePids));
+		TypedQuery<ResourceTable> q = entityManager.createQuery(cq);
+
+		for (ResourceTable next : q.getResultList()) {
+			Class<? extends IBaseResource> resourceType = context.getResourceDefinition(next.getResourceType()).getImplementingClass();
+			IBaseResource resource = (IBaseResource) theDao.toResource(resourceType, next, theForHistoryOperation);
+			Integer index = position.get(next.getId());
+			if (index == null) {
+				ourLog.warn("Got back unexpected resource PID {}", next.getId());
+				continue;
+			}
+
+			if (resource instanceof IResource) {
+				if (theRevIncludedPids.contains(next.getId())) {
+					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.INCLUDE);
+				} else {
+					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.MATCH);
+				}
+			} else {
+				if (theRevIncludedPids.contains(next.getId())) {
+					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.INCLUDE.getCode());
+				} else {
+					ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.MATCH.getCode());
+				}
+			}
+
+			theResourceListToPopulate.set(index, resource);
+		}
+	}
+
+	/**
+	 * THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
+	 * 
+	 * @param theLastUpdated
+	 */
+	public static HashSet<Long> loadReverseIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
+			DateRangeParam theLastUpdated) {
+		if (theMatches.size() == 0) {
+			return new HashSet<Long>();
+		}
+		if (theRevIncludes == null || theRevIncludes.isEmpty()) {
+			return new HashSet<Long>();
+		}
+		String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
+
+		Collection<Long> nextRoundMatches = theMatches;
+		HashSet<Long> allAdded = new HashSet<Long>();
+		HashSet<Long> original = new HashSet<Long>(theMatches);
+		ArrayList<Include> includes = new ArrayList<Include>(theRevIncludes);
+
+		int roundCounts = 0;
+		StopWatch w = new StopWatch();
+
+		boolean addedSomeThisRound;
+		do {
+			roundCounts++;
+
+			HashSet<Long> pidsToInclude = new HashSet<Long>();
+			Set<Long> nextRoundOmit = new HashSet<Long>();
+
+			for (Iterator<Include> iter = includes.iterator(); iter.hasNext();) {
+				Include nextInclude = iter.next();
+				if (nextInclude.isRecurse() == false) {
+					iter.remove();
+				}
+
+				boolean matchAll = "*".equals(nextInclude.getValue());
+				if (matchAll) {
+					String sql;
+					sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids)";
+					TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
+					q.setParameter("target_pids", nextRoundMatches);
+					List<ResourceLink> results = q.getResultList();
+					for (ResourceLink resourceLink : results) {
+						if (theReverseMode) {
+							// if (theEverythingModeEnum.isEncounter()) {
+							// if (resourceLink.getSourcePath().equals("Encounter.subject") ||
+							// resourceLink.getSourcePath().equals("Encounter.patient")) {
+							// nextRoundOmit.add(resourceLink.getSourceResourcePid());
+							// }
+							// }
+							pidsToInclude.add(resourceLink.getSourceResourcePid());
+						} else {
+							pidsToInclude.add(resourceLink.getTargetResourcePid());
+						}
+					}
+				} else {
+
+					List<String> paths;
+					if (theContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
+						paths = Collections.singletonList(nextInclude.getValue());
+					} else {
+						String resType = nextInclude.getParamType();
+						if (isBlank(resType)) {
+							continue;
+						}
+						RuntimeResourceDefinition def = theContext.getResourceDefinition(resType);
+						if (def == null) {
+							ourLog.warn("Unknown resource type in include/revinclude=" + nextInclude.getValue());
+							continue;
+						}
+
+						String paramName = nextInclude.getParamName();
+						RuntimeSearchParam param = isNotBlank(paramName) ? def.getSearchParam(paramName) : null;
+						if (param == null) {
+							ourLog.warn("Unknown param name in include/revinclude=" + nextInclude.getValue());
+							continue;
+						}
+
+						paths = param.getPathsSplit();
+					}
+
+					String targetResourceType = defaultString(nextInclude.getParamTargetType(), null);
+					for (String nextPath : paths) {
+						String sql;
+						if (targetResourceType != null) {
+							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
+						} else {
+							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
+						}
+						TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
+						q.setParameter("src_path", nextPath);
+						q.setParameter("target_pids", nextRoundMatches);
+						if (targetResourceType != null) {
+							q.setParameter("target_resource_type", targetResourceType);
+						}
+						List<ResourceLink> results = q.getResultList();
+						for (ResourceLink resourceLink : results) {
+							if (theReverseMode) {
+								pidsToInclude.add(resourceLink.getSourceResourcePid());
+							} else {
+								pidsToInclude.add(resourceLink.getTargetResourcePid());
+							}
+						}
+					}
+				}
+			}
+
+			if (theLastUpdated != null && (theLastUpdated.getLowerBoundAsInstant() != null || theLastUpdated.getUpperBoundAsInstant() != null)) {
+				pidsToInclude = new HashSet<Long>(filterResourceIdsByLastUpdated(theEntityManager, theLastUpdated, pidsToInclude));
+			}
+			for (Long next : pidsToInclude) {
+				if (original.contains(next) == false && allAdded.contains(next) == false) {
+					theMatches.add(next);
+				}
+			}
+
+			pidsToInclude.removeAll(nextRoundOmit);
+
+			addedSomeThisRound = allAdded.addAll(pidsToInclude);
+			nextRoundMatches = pidsToInclude;
+		} while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound);
+
+		ourLog.info("Loaded {} {} in {} rounds and {} ms", new Object[] { allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart() });
+
+		return allAdded;
+	}
+
 	static Predicate[] toArray(List<Predicate> thePredicates) {
 		return thePredicates.toArray(new Predicate[thePredicates.size()]);
 	}
@@ -2021,117 +2019,4 @@ public class SearchBuilder {
 		}
 	}
 
-	public final static class BundleProviderPersisted implements IBundleProvider {
-
-		private String myUuid;
-		private PlatformTransactionManager myPlatformTransactionManager;
-		private ISearchResultDao mySearchResultDao;
-		private Search mySearchEntity;
-		private EntityManager myEntityManager;
-		private FhirContext myContext;
-		private IDao myDao;
-
-		public BundleProviderPersisted(String theSearchUuid, PlatformTransactionManager thePlatformTransactionManager, ISearchResultDao theSearchResultDao, EntityManager theEntityManager,
-				FhirContext theContext, IDao theDao) {
-			myUuid = theSearchUuid;
-			myPlatformTransactionManager = thePlatformTransactionManager;
-			mySearchResultDao = theSearchResultDao;
-			myEntityManager = theEntityManager;
-			myContext = theContext;
-			myDao = theDao;
-		}
-
-		@Override
-		public InstantDt getPublished() {
-			ensureSearchEntityLoaded();
-			return new InstantDt(mySearchEntity.getCreated());
-		}
-
-		@Override
-		public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
-			TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-
-			return template.execute(new TransactionCallback<List<IBaseResource>>() {
-				@Override
-				public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
-					ensureSearchEntityLoaded();
-
-					int pageSize = theToIndex - theFromIndex;
-					if (pageSize < 1) {
-						return Collections.emptyList();
-					}
-
-					int pageIndex = theFromIndex / pageSize;
-
-					Pageable page = new PageRequest(pageIndex, pageSize);
-					Page<SearchResult> search = mySearchResultDao.findWithSearchUuid(mySearchEntity, page);
-
-					List<Long> pidsSubList = new ArrayList<Long>();
-					for (SearchResult next : search) {
-						pidsSubList.add(next.getResourcePid());
-					}
-
-					// Load includes
-					pidsSubList = new ArrayList<Long>(pidsSubList);
-
-					Set<Long> revIncludedPids = new HashSet<Long>();
-					if (mySearchEntity.getEverythingMode() == null) {
-						revIncludedPids.addAll(loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
-					}
-					revIncludedPids.addAll(loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
-
-					// Execute the query and make sure we return distinct results
-					List<IBaseResource> resources = new ArrayList<IBaseResource>();
-					loadResourcesByPid(pidsSubList, resources, revIncludedPids, false, myEntityManager, myContext, myDao);
-
-					return resources;
-				}
-
-			});
-		}
-
-		@Override
-		public Integer preferredPageSize() {
-			ensureSearchEntityLoaded();
-			return mySearchEntity.getPreferredPageSize();
-		}
-
-		@Override
-		public int size() {
-			ensureSearchEntityLoaded();
-			return mySearchEntity.getTotalCount();
-		}
-
-		public String getSearchUuid() {
-			return myUuid;
-		}
-
-		/**
-		 * Returns false if the entity can't be found
-		 */
-		public boolean ensureSearchEntityLoaded() {
-			if (mySearchEntity == null) {
-				TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-				template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
-				return template.execute(new TransactionCallback<Boolean>() {
-					@Override
-					public Boolean doInTransaction(TransactionStatus theStatus) {
-						TypedQuery<Search> q = myEntityManager.createQuery("SELECT s FROM Search s WHERE s.myUuid = :uuid", Search.class);
-						q.setParameter("uuid", myUuid);
-						try {
-							mySearchEntity = q.getSingleResult();
-							
-							// Ensure includes are loaded
-							mySearchEntity.getIncludes().size();
-							return true;
-						} catch (NoResultException e) {
-							return false;
-						}
-					}
-				});
-			}
-			return true;
-		}
-	}
-
 }

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

@@ -0,0 +1,106 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import java.util.Date;
+import java.util.List;
+
+import javax.persistence.TemporalType;
+
+import org.springframework.data.domain.Pageable;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.jpa.repository.Temporal;
+import org.springframework.data.repository.query.Param;
+
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+
+public interface IResourceHistoryTableDao extends JpaRepository<ResourceHistoryTable, Long> {
+	//@formatter:off
+	
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t WHERE t.myUpdated >= :cutoff")
+	int countForAllResourceTypes(
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff
+		);
+	
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t WHERE t.myResourceId = :id AND t.myUpdated >= :cutoff")
+	int countForResourceInstance(
+		@Param("id") Long theId,
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff
+		);
+
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t WHERE t.myResourceType = :type AND t.myUpdated >= :cutoff")
+	int countForResourceType(
+		@Param("type") String theType,
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff
+		);
+
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t")
+	int countForAllResourceTypes(
+		);
+	
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t WHERE t.myResourceId = :id")
+	int countForResourceInstance(
+		@Param("id") Long theId
+		);
+
+	@Query("SELECT COUNT(*) FROM ResourceHistoryTable t WHERE t.myResourceType = :type")
+	int countForResourceType(
+		@Param("type") String theType
+		);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myUpdated >= :cutoff ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForAllResourceTypes(
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff, 
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myResourceId = :id AND t.myUpdated >= :cutoff ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForResourceInstance(
+		@Param("id") Long theId,
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff, 
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myResourceType = :type AND t.myUpdated >= :cutoff ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForResourceType(
+		@Param("type") String theType,
+		@Temporal(value=TemporalType.TIMESTAMP) @Param("cutoff") Date theCutoff, 
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForAllResourceTypes(
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myResourceId = :id ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForResourceInstance(
+		@Param("id") Long theId,
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myResourceType = :type ORDER BY t.myUpdated DESC")
+	List<ResourceHistoryTable> findForResourceType(
+		@Param("type") String theType,
+		Pageable thePageable);
+
+	@Query("SELECT t FROM ResourceHistoryTable t WHERE t.myResourceId = :id AND t.myResourceVersion = :version")
+	ResourceHistoryTable findForIdAndVersion(@Param("id") long theId, @Param("version") long theVersion);
+	
+	//@formatter:on
+}

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

@@ -25,5 +25,5 @@ import org.springframework.data.jpa.repository.JpaRepository;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 
 public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
-	
+	// nothing yet
 }

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

@@ -29,7 +29,10 @@ import org.springframework.data.repository.query.Param;
 
 import ca.uhn.fhir.jpa.entity.Search;
 
-public interface ISearchDao  extends JpaRepository<Search, Long> {
+public interface ISearchDao extends JpaRepository<Search, Long> {
+
+	@Query("SELECT s FROM Search s WHERE s.myUuid = :uuid")
+	public Search findByUuid(@Param("uuid") String theUuid);
 
 	@Query("SELECT s FROM Search s WHERE s.myCreated < :cutoff")
 	public Collection<Search> findWhereCreatedBefore(@Param("cutoff") Date theCutoff);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java

@@ -31,21 +31,25 @@ import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
-import javax.persistence.JoinColumn;
+import javax.persistence.Index;
 import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
-import org.hibernate.annotations.Index;
-
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.server.Constants;
 
+//@formatter:off
 @Entity
-@Table(name = "HFJ_RES_VER", uniqueConstraints = { @UniqueConstraint(name = "IDX_RES_VER_ALL", columnNames = { "RES_ID", "RES_TYPE", "RES_VER" }) })
+@Table(name = "HFJ_RES_VER", uniqueConstraints = {
-@org.hibernate.annotations.Table(appliesTo = "HFJ_RES_VER", indexes = { @Index(name = "IDX_RES_VER_DATE", columnNames = { "RES_UPDATED" }) })
+	@UniqueConstraint(name="IDX_RESVER_ID_VER", columnNames = { "RES_ID", "RES_VER" }) 
+}, indexes= {
+	@Index(name="IDX_RESVER_TYPE_DATE", columnList="RES_TYPE,RES_UPDATED"), 
+	@Index(name="IDX_RESVER_ID_DATE", columnList="RES_ID,RES_UPDATED"), 
+	@Index(name="IDX_RESVER_DATE", columnList="RES_UPDATED") 
+})
+//@formatter:on
 public class ResourceHistoryTable extends BaseHasResource implements Serializable {
 
 	private static final long serialVersionUID = 1L;
@@ -68,13 +72,6 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	@OneToMany(mappedBy = "myResourceHistory", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
 	private Collection<ResourceHistoryTag> myTags;
 
-	/**
-	 * This field is only populated if this specific histor entry corresponds to 
-	 * the most recent version of a resource
-	 */
-	@OneToOne(fetch=FetchType.LAZY, optional=true, mappedBy="myHistory")
-	private ResourceTable myCorrespondsToVersion;
-	
 	public void addTag(ResourceHistoryTag theTag) {
 		for (ResourceHistoryTag next : getTags()) {
 			if (next.getTag().equals(theTag)) {
@@ -139,6 +136,10 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return false;
 	}
 
+	public void setId(Long theId) {
+		myId = theId;
+	}
+
 	public void setResourceId(Long theResourceId) {
 		myResourceId = theResourceId;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -35,9 +35,7 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.Index;
-import javax.persistence.JoinColumn;
 import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
@@ -152,10 +150,6 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@Column(name = "SP_HAS_LINKS")
 	private boolean myHasLinks;
 
-	@OneToOne(fetch=FetchType.LAZY, optional=true)
-	@JoinColumn(name="HISTORY_VERSION_PID", referencedColumnName="PID", nullable=true)
-	private ResourceHistoryTable myHistory;
-	
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO)
 	@Column(name = "RES_ID")
@@ -534,8 +528,8 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myVersion = theVersion;
 	}
 
-	public ResourceHistoryTable toHistory() {
+	public ResourceHistoryTable toHistory(ResourceHistoryTable theResourceHistoryTable) {
-		ResourceHistoryTable retVal = new ResourceHistoryTable();
+		ResourceHistoryTable retVal = theResourceHistoryTable != null ? theResourceHistoryTable : new ResourceHistoryTable();
 
 		retVal.setResourceId(myId);
 		retVal.setResourceType(myResourceType);
@@ -550,6 +544,9 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		retVal.setDeleted(getDeleted());
 		retVal.setForcedId(getForcedId());
 
+		retVal.getTags().clear();
+		
+		retVal.setHasTags(isHasTags());
 		if (isHasTags()) {
 			for (ResourceTag next : getTags()) {
 				retVal.addTag(next);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Search.java

@@ -43,7 +43,6 @@ import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import javax.persistence.UniqueConstraint;
 
-import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 
@@ -63,10 +62,6 @@ public class Search implements Serializable {
 	@Column(name="CREATED", nullable=false, updatable=false)
 	private Date myCreated;
 
-	@Enumerated(EnumType.ORDINAL)
-	@Column(name="EVERYTHING_MODE", nullable=true)
-	private EverythingModeEnum myEverythingMode;
-
 	@Id
 	@GeneratedValue(strategy = GenerationType.AUTO, generator="SEQ_SEARCH")
 	@SequenceGenerator(name="SEQ_SEARCH", sequenceName="SEQ_SEARCH")
@@ -87,9 +82,19 @@ public class Search implements Serializable {
 	@Column(name="PREFERRED_PAGE_SIZE", nullable=true)
 	private Integer myPreferredPageSize;
 	
+	@Column(name="RESOURCE_ID", nullable=true)
+	private Long myResourceId;
+	
+	@Column(name="RESOURCE_TYPE", length=200, nullable=true)
+	private String myResourceType;
+
 	@OneToMany(mappedBy="mySearch")
 	private Collection<SearchResult> myResults;
 
+	@Enumerated(EnumType.ORDINAL)
+	@Column(name="SEARCH_TYPE", nullable=false)
+	private SearchTypeEnum mySearchType;
+
 	@Column(name="TOTAL_COUNT")
 	private int myTotalCount;
 
@@ -100,10 +105,6 @@ public class Search implements Serializable {
 		return myCreated;
 	}
 
-	public EverythingModeEnum getEverythingMode() {
-		return myEverythingMode;
-	}
-
 	public Long getId() {
 		return myId;
 	}
@@ -115,6 +116,10 @@ public class Search implements Serializable {
 		return myIncludes;
 	}
 	
+	public Date getLastUpdatedHigh() {
+		return myLastUpdatedHigh;
+	}
+
 	public DateRangeParam getLastUpdated() {
 		if (myLastUpdatedLow == null && myLastUpdatedHigh == null) {
 			return null;
@@ -127,6 +132,19 @@ public class Search implements Serializable {
 		return myPreferredPageSize;
 	}
 
+	public Long getResourceId() {
+		return myResourceId;
+	}
+	
+	public String getResourceType() {
+		return myResourceType;
+	}
+
+	public SearchTypeEnum getSearchType() {
+		return mySearchType;
+	}
+
+
 	public int getTotalCount() {
 		return myTotalCount;
 	}
@@ -138,9 +156,9 @@ public class Search implements Serializable {
 	public void setCreated(Date theCreated) {
 		myCreated = theCreated;
 	}
-
+	public void setLastUpdated(Date theLowerBound, Date theUpperBound) {
-	public void setEverythingMode(EverythingModeEnum theEverythingMode) {
+		myLastUpdatedLow = theLowerBound;
-		myEverythingMode = theEverythingMode;
+		myLastUpdatedHigh = theUpperBound;
 	}
 	
 	public void setLastUpdated(DateRangeParam theLastUpdated) {
@@ -157,6 +175,19 @@ public class Search implements Serializable {
 		myPreferredPageSize = thePreferredPageSize;
 	}
 	
+	public void setResourceId(Long theResourceId) {
+		myResourceId = theResourceId;
+	}
+
+
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
+	public void setSearchType(SearchTypeEnum theSearchType) {
+		mySearchType = theSearchType;
+	}
+
 	public void setTotalCount(int theTotalCount) {
 		myTotalCount = theTotalCount;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SearchTypeEnum.java

@@ -0,0 +1,9 @@
+package ca.uhn.fhir.jpa.entity;
+
+public enum SearchTypeEnum {
+
+	EVERYTHING,
+	SEARCH,
+	HISTORY, 
+	
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TagDefinition.java

@@ -37,6 +37,8 @@ import javax.persistence.UniqueConstraint;
 
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 
 import ca.uhn.fhir.model.api.Tag;
 
@@ -146,4 +148,16 @@ public class TagDefinition implements Serializable {
 		return b.toHashCode();
 	}
 
+	@Override
+	public String toString() {
+		ToStringBuilder retVal = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		retVal.append("id", myId);
+		retVal.append("system", mySystem);
+		retVal.append("code", myCode);
+		retVal.append("display", myDisplay);
+		return retVal.build();
+	}
+	
+	
+	
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DatabaseBackedPagingProvider.java

@@ -9,8 +9,6 @@ import org.springframework.transaction.PlatformTransactionManager;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IDao;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.dao.SearchBuilder;
-import ca.uhn.fhir.jpa.dao.SearchBuilder.BundleProviderPersisted;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.IBundleProvider;
@@ -36,8 +34,7 @@ public class DatabaseBackedPagingProvider extends FifoMemoryPagingProvider {
 	public synchronized IBundleProvider retrieveResultList(String theId) {
 		IBundleProvider retVal = super.retrieveResultList(theId);
 		if (retVal == null) {
-			BundleProviderPersisted provider = new SearchBuilder.BundleProviderPersisted(theId, thePlatformTransactionManager, theSearchResultDao, theEntityManager,
+			PersistedJpaBundleProvider provider = new PersistedJpaBundleProvider(theId, theDao);
-					theContext, theDao);
 			if (!provider.ensureSearchEntityLoaded()) {
 				return null;
 			}
@@ -48,8 +45,8 @@ public class DatabaseBackedPagingProvider extends FifoMemoryPagingProvider {
 
 	@Override
 	public synchronized String storeResultList(IBundleProvider theList) {
-		if (theList instanceof SearchBuilder.BundleProviderPersisted) {
+		if (theList instanceof PersistedJpaBundleProvider) {
-			return ((BundleProviderPersisted)theList).getSearchUuid();
+			return ((PersistedJpaBundleProvider)theList).getSearchUuid();
 		}
 		return super.storeResultList(theList);
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java

@@ -0,0 +1,246 @@
+package ca.uhn.fhir.jpa.search;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.EntityManager;
+import javax.persistence.NoResultException;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.IDao;
+import ca.uhn.fhir.jpa.dao.SearchBuilder;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchDao;
+import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.entity.Search;
+import ca.uhn.fhir.jpa.entity.SearchResult;
+import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
+import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+
+public final class PersistedJpaBundleProvider implements IBundleProvider {
+
+	private FhirContext myContext;
+	private IDao myDao;
+	private EntityManager myEntityManager;
+	private PlatformTransactionManager myPlatformTransactionManager;
+	private IResourceHistoryTableDao myResourceHistoryTableDao;
+	private ISearchDao mySearchDao;
+	private Search mySearchEntity;
+	private ISearchResultDao mySearchResultDao;
+	private String myUuid;
+
+	public PersistedJpaBundleProvider(String theSearchUuid, IDao theDao) {
+		myUuid = theSearchUuid;
+		myDao = theDao;
+	}
+
+	@Autowired
+	private IResourceTableDao myResourceTableDao;
+	
+	protected List<IBaseResource> doHistoryInTransaction(int theFromIndex, int theToIndex) {
+		
+		Date cutoff = mySearchEntity.getLastUpdatedHigh();
+		
+		Pageable pageable = toPage(theFromIndex, theToIndex);
+		
+		List<ResourceHistoryTable> results;
+		
+		if (cutoff != null) {
+			if (mySearchEntity.getResourceType() == null) {
+				results = myResourceHistoryTableDao.findForAllResourceTypes(cutoff, pageable);
+			} else if (mySearchEntity.getResourceId() == null) {
+				results = myResourceHistoryTableDao.findForResourceType(mySearchEntity.getResourceType(), cutoff, pageable);
+			} else {
+				results = myResourceHistoryTableDao.findForResourceInstance(mySearchEntity.getResourceId(), cutoff, pageable);
+			}
+		} else {
+			if (mySearchEntity.getResourceType() == null) {
+				results = myResourceHistoryTableDao.findForAllResourceTypes(pageable);
+			} else if (mySearchEntity.getResourceId() == null) {
+				results = myResourceHistoryTableDao.findForResourceType(mySearchEntity.getResourceType(), pageable);
+			} else {
+				results = myResourceHistoryTableDao.findForResourceInstance(mySearchEntity.getResourceId(), pageable);
+			}
+		}
+		
+		ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
+		for (ResourceHistoryTable next : results) {
+			BaseHasResource resource;
+			resource = next;
+			
+			retVal.add(myDao.toResource(resource, true));
+		}
+		
+		return retVal;
+	}
+
+	protected List<IBaseResource> doSearchOrEverythingInTransaction(final int theFromIndex, final int theToIndex) {
+
+		Pageable page = toPage(theFromIndex, theToIndex);
+		if (page == null) {
+			return Collections.emptyList();
+		}
+		
+		Page<SearchResult> search = mySearchResultDao.findWithSearchUuid(mySearchEntity, page);
+
+		List<Long> pidsSubList = new ArrayList<Long>();
+		for (SearchResult next : search) {
+			pidsSubList.add(next.getResourcePid());
+		}
+
+		// Load includes
+		pidsSubList = new ArrayList<Long>(pidsSubList);
+
+		Set<Long> revIncludedPids = new HashSet<Long>();
+		if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
+			revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
+		}
+		revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
+
+		// Execute the query and make sure we return distinct results
+		List<IBaseResource> resources = new ArrayList<IBaseResource>();
+		SearchBuilder.loadResourcesByPid(pidsSubList, resources, revIncludedPids, false, myEntityManager, myContext, myDao);
+
+		return resources;
+	}
+
+	/**
+	 * Returns false if the entity can't be found
+	 */
+	public boolean ensureSearchEntityLoaded() {
+		if (mySearchEntity == null) {
+			ensureDependenciesInjected();
+			
+			TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+			template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
+			return template.execute(new TransactionCallback<Boolean>() {
+				@Override
+				public Boolean doInTransaction(TransactionStatus theStatus) {
+					try {
+						mySearchEntity = mySearchDao.findByUuid(myUuid);
+						
+						if (mySearchEntity == null) {
+							return false;
+						}
+
+						// Load the includes now so that they are available outside of this transaction
+						mySearchEntity.getIncludes().size();
+						
+						return true;
+					} catch (NoResultException e) {
+						return false;
+					}
+				}
+			});
+		}
+		return true;
+	}
+
+	private void ensureDependenciesInjected() {
+		if (myPlatformTransactionManager == null) {
+		myDao.injectDependenciesIntoBundleProvider(this);
+		}
+	}
+
+	@Override
+	public InstantDt getPublished() {
+		ensureSearchEntityLoaded();
+		return new InstantDt(mySearchEntity.getCreated());
+	}
+
+	@Override
+	public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
+		ensureDependenciesInjected();
+
+		TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
+
+		return template.execute(new TransactionCallback<List<IBaseResource>>() {
+			@Override
+			public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
+				ensureSearchEntityLoaded();
+
+				switch (mySearchEntity.getSearchType()) {
+				case HISTORY:
+					return doHistoryInTransaction(theFromIndex, theToIndex);
+				case SEARCH:
+				case EVERYTHING:
+				default:
+					return doSearchOrEverythingInTransaction(theFromIndex, theToIndex);
+				}
+			}
+
+
+		});
+	}
+
+	public String getSearchUuid() {
+		return myUuid;
+	}
+
+	@Override
+	public Integer preferredPageSize() {
+		ensureSearchEntityLoaded();
+		return mySearchEntity.getPreferredPageSize();
+	}
+
+	public void setContext(FhirContext theContext) {
+		myContext = theContext;
+	}
+
+	public void setEntityManager(EntityManager theEntityManager) {
+		myEntityManager = theEntityManager;
+	}
+
+	
+	public void setPlatformTransactionManager(PlatformTransactionManager thePlatformTransactionManager) {
+		myPlatformTransactionManager = thePlatformTransactionManager;
+	}
+
+	public void setResourceHistoryTableDao(IResourceHistoryTableDao theResourceHistoryTableDao) {
+		myResourceHistoryTableDao = theResourceHistoryTableDao;
+	}
+
+	public void setSearchDao(ISearchDao theSearchDao) {
+		mySearchDao = theSearchDao;
+	}
+
+	public void setSearchResultDao(ISearchResultDao theSearchResultDao) {
+		mySearchResultDao = theSearchResultDao;
+	}
+
+	@Override
+	public int size() {
+		ensureSearchEntityLoaded();
+		return mySearchEntity.getTotalCount();
+	}
+
+	private Pageable toPage(int theFromIndex, int theToIndex) {
+		int pageSize = theToIndex - theFromIndex;
+		if (pageSize < 1) {
+			return null;
+		}
+
+		int pageIndex = theFromIndex / pageSize;
+
+		Pageable page = new PageRequest(pageIndex, pageSize);
+		return page;
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu1Config.java

@@ -55,7 +55,7 @@ public class TestDstu1Config extends BaseJavaConfigDstu1 {
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.format_sql", "true");
+		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
 		return extraProperties;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java

@@ -19,6 +19,8 @@ import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
+import javax.persistence.EntityManager;
+
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
@@ -26,6 +28,7 @@ import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.springframework.context.annotation.AnnotationConfigApplicationContext;
+import org.springframework.transaction.PlatformTransactionManager;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu1Config;
@@ -59,6 +62,14 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 	private static IFhirResourceDao<Patient> ourPatientDao;
 	private static IFhirSystemDao<List<IResource>, MetaDt> ourSystemDao;
 	private RequestDetails myRequestDetails;
+	private static EntityManager ourEntityManager;
+	private static PlatformTransactionManager ourTxManager;
+
+	@Before
+	public void before() {
+		myRequestDetails = mock(RequestDetails.class);
+		super.purgeDatabase(ourEntityManager, ourTxManager);
+	}
 
 	@Test
 	public void testGetResourceCounts() {
@@ -188,11 +199,6 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 
 	}
 
-	@Before
-	public void before() {
-		myRequestDetails = mock(RequestDetails.class);
-	}
-
 	@Test
 	public void testPersistWithUnknownId() {
 		Observation obs = new Observation();
@@ -484,6 +490,8 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 		ourObservationDao = ourCtx.getBean("myObservationDaoDstu1", IFhirResourceDao.class);
 		ourLocationDao = ourCtx.getBean("myLocationDaoDstu1", IFhirResourceDao.class);
 		ourSystemDao = ourCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
+		ourEntityManager = ourCtx.getBean(EntityManager.class);
+		ourTxManager = ourCtx.getBean(PlatformTransactionManager.class);
 	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -112,6 +112,28 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2Test.class);
 
+	private void assertGone(IIdType theId) {
+		try {
+			assertNotGone(theId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+	}
+
+	/**
+	 * This gets called from assertGone too! Careful about exceptions...
+	 */
+	private void assertNotGone(IIdType theId) {
+		if ("Patient".equals(theId.getResourceType())) {
+			myPatientDao.read(theId, new ServletRequestDetails());
+		} else if ("Organization".equals(theId.getResourceType())){
+			myOrganizationDao.read(theId, new ServletRequestDetails());
+		} else {
+			fail("No type");
+		}
+	}
+
 	private List<String> extractNames(IBundleProvider theSearch) {
 		ArrayList<String> retVal = new ArrayList<String>();
 		for (IBaseResource next : theSearch.getResources(0, theSearch.size())) {
@@ -121,6 +143,14 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		return retVal;
 	}
 
+	private String log(IBundleProvider theHistory) {
+		StringBuilder b =new StringBuilder(theHistory.size() + " results: ");
+		for (IBaseResource next : theHistory.getResources(0, theHistory.size())) {
+			b.append("\n ").append(next.getIdElement().toUnqualified().getValue());
+		}
+		return b.toString();
+	}
+
 	private void sort(TagList thePublished) {
 		ArrayList<Tag> tags = new ArrayList<Tag>(thePublished);
 		Collections.sort(tags, new Comparator<Tag>() {
@@ -744,6 +774,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 	
+	
 	@Test
 	public void testDeleteResource() {
 		int initialHistory = myPatientDao.history(null, new ServletRequestDetails()).size();
@@ -807,6 +838,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 	
+
 	@Test
 	public void testDeleteThenUndelete() {
 		Patient patient = new Patient();
@@ -840,27 +872,44 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals(id2, gotId);
 	}
 
-	@Test
-	public void testDeleteWithMatchUrlChainedString() {
-		String methodName = "testDeleteWithMatchUrlChainedString";
 	
-		Organization org = new Organization();
+	@Test
-		org.setName(methodName);
+	public void testDeleteWithMatchUrl() {
-		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		String methodName = "testDeleteWithMatchUrl";
 
 		Patient p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId();
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
 		ourLog.info("Created patient, got it: {}", id);
 
-		myPatientDao.deleteByUrl("Patient?organization.name=" + methodName, new ServletRequestDetails());
+		Bundle request = new Bundle();
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		myPatientDao.deleteByUrl("Patient?identifier=urn%3Asystem%7C" + methodName, new ServletRequestDetails());
+
+		try {
+			myPatientDao.read(id.toVersionless(), new ServletRequestDetails());
+			fail();
+		} catch (ResourceGoneException e) {
+			// ok
+		}
+
+		try {
+			myPatientDao.read(new IdDt("Patient/" + methodName), new ServletRequestDetails());
+			fail();
+		} catch (ResourceNotFoundException e) {
+			// ok
+		}
+
+		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
+		assertEquals(2, history.size());
+
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)).getValue());
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 2).get(0)));
 
-		assertGone(id);
 	}
 
-	
 	@Test
 	public void testDeleteWithMatchUrlChainedIdentifier() {
 		String methodName = "testDeleteWithMatchUrlChainedIdentifer";
@@ -886,7 +935,74 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertGone(orgId);
 
 	}
+	@Test
+	public void testDeleteWithMatchUrlChainedProfile() {
+		String methodName = "testDeleteWithMatchUrlChainedProfile";
 
+		List<IdDt> profileList = new ArrayList<IdDt>();
+		profileList.add(new IdDt("http://foo"));
+		
+		Organization org = new Organization();
+		ResourceMetadataKeyEnum.PROFILES.put(org, profileList);
+		org.setName(methodName);
+		
+		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo", new ServletRequestDetails());
+		assertGone(id);
+		
+		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo", new ServletRequestDetails());
+		try {
+			myOrganizationDao.read(orgId, new ServletRequestDetails());
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myPatientDao.deleteByUrl("Patient?organization._profile.identifier=http://foo", new ServletRequestDetails());
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: organization._profile.identifier", e.getMessage());
+		}
+
+		try {
+			myOrganizationDao.deleteByUrl("Organization?_profile.identifier=http://foo", new ServletRequestDetails());
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: _profile.identifier", e.getMessage());
+		}
+
+	}
+
+	
+	
+	@Test
+	public void testDeleteWithMatchUrlChainedString() {
+		String methodName = "testDeleteWithMatchUrlChainedString";
+
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization.name=" + methodName, new ServletRequestDetails());
+
+		assertGone(id);
+	}
 
 	@Test
 	public void testDeleteWithMatchUrlChainedTag() {
@@ -935,7 +1051,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
-	
 	@Test
 	public void testDeleteWithMatchUrlQualifierMissing() {
 		String methodName = "testDeleteWithMatchUrlChainedProfile";
@@ -997,113 +1112,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertGone(org2Id);
 	}
 
-	/**
-	 * This gets called from assertGone too! Careful about exceptions...
-	 */
-	private void assertNotGone(IIdType theId) {
-		if ("Patient".equals(theId.getResourceType())) {
-			myPatientDao.read(theId, new ServletRequestDetails());
-		} else if ("Organization".equals(theId.getResourceType())){
-			myOrganizationDao.read(theId, new ServletRequestDetails());
-		} else {
-			fail("No type");
-		}
-	}
-	private void assertGone(IIdType theId) {
-		try {
-			assertNotGone(theId);
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
-	}
-
-	
-	
-	@Test
-	public void testDeleteWithMatchUrlChainedProfile() {
-		String methodName = "testDeleteWithMatchUrlChainedProfile";
-
-		List<IdDt> profileList = new ArrayList<IdDt>();
-		profileList.add(new IdDt("http://foo"));
-		
-		Organization org = new Organization();
-		ResourceMetadataKeyEnum.PROFILES.put(org, profileList);
-		org.setName(methodName);
-		
-		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.getManagingOrganization().setReference(orgId);
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		ourLog.info("Created patient, got it: {}", id);
-
-		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo", new ServletRequestDetails());
-		assertGone(id);
-		
-		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo", new ServletRequestDetails());
-		try {
-			myOrganizationDao.read(orgId, new ServletRequestDetails());
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
-
-		try {
-			myPatientDao.deleteByUrl("Patient?organization._profile.identifier=http://foo", new ServletRequestDetails());
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Invalid parameter chain: organization._profile.identifier", e.getMessage());
-		}
-
-		try {
-			myOrganizationDao.deleteByUrl("Organization?_profile.identifier=http://foo", new ServletRequestDetails());
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Invalid parameter chain: _profile.identifier", e.getMessage());
-		}
-
-	}
-
-	@Test
-	public void testDeleteWithMatchUrl() {
-		String methodName = "testDeleteWithMatchUrl";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		Bundle request = new Bundle();
-		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		myPatientDao.deleteByUrl("Patient?identifier=urn%3Asystem%7C" + methodName, new ServletRequestDetails());
-
-		try {
-			myPatientDao.read(id.toVersionless(), new ServletRequestDetails());
-			fail();
-		} catch (ResourceGoneException e) {
-			// ok
-		}
-
-		try {
-			myPatientDao.read(new IdDt("Patient/" + methodName), new ServletRequestDetails());
-			fail();
-		} catch (ResourceNotFoundException e) {
-			// ok
-		}
-
-		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
-		assertEquals(2, history.size());
-
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 1).get(0)));
-
-	}
-
 	@Test
 	public void testHistoryByForcedId() {
 		IIdType idv1;
@@ -1287,14 +1295,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
-	private String log(IBundleProvider theHistory) {
-		StringBuilder b =new StringBuilder(theHistory.size() + " results: ");
-		for (IBaseResource next : theHistory.getResources(0, theHistory.size())) {
-			b.append("\n ").append(next.getIdElement().toUnqualified().getValue());
-		}
-		return b.toString();
-	}
-
 	@Test
 	public void testHistoryWithDeletedResource() throws Exception {
 		String methodName = "testHistoryWithDeletedResource";
@@ -2263,79 +2263,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
-	@Test
-	public void testSortByLastUpdated() {
-		String methodName = "testSortByLastUpdated";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system1").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system2").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id2 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system3").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id3 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system4").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id4 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap pm;
-		List<IIdType> actual;
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id1, id2, id3, id4));
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id1, id2, id3, id4));
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id4, id3, id2, id1));
-
-		pm = new SearchParameterMap();
-		pm.add(Patient.SP_IDENTIFIER, new TokenParam(null, methodName));
-		pm.setSort(new SortSpec(Patient.SP_NAME).setChain(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC)));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id4, id3, id2, id1));
-	}
-
-	@Test
-	public void testSortNoMatches() {
-		String methodName = "testSortNoMatches";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap map;
-
-		map = new SearchParameterMap();
-		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
-		map.setLastUpdated(new DateRangeParam("2001", "2003"));
-		map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
-
-		map = new SearchParameterMap();
-		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
-		map.setLastUpdated(new DateRangeParam("2001", "2003"));
-		map.setSort(new SortSpec(Patient.SP_NAME));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
-
-	}
-
 	@Test
 	public void testSortById() {
 		String methodName = "testSortBTyId";
@@ -2387,6 +2314,55 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertThat(actual, contains(id4, id3, id2, id1, idMethodName));
 	}
 
+	@Test
+	public void testSortByLastUpdated() {
+		String methodName = "testSortByLastUpdated";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system1").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system2").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id2 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system3").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id3 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system4").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id4 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap pm;
+		List<IIdType> actual;
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id1, id2, id3, id4));
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id1, id2, id3, id4));
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id4, id3, id2, id1));
+
+		pm = new SearchParameterMap();
+		pm.add(Patient.SP_IDENTIFIER, new TokenParam(null, methodName));
+		pm.setSort(new SortSpec(Patient.SP_NAME).setChain(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC)));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id4, id3, id2, id1));
+	}
+
 	@Test
 	public void testSortByNumber() {
 		String methodName = "testSortByNumber";
@@ -2714,6 +2690,30 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	@Test
+	public void testSortNoMatches() {
+		String methodName = "testSortNoMatches";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
+		map.setLastUpdated(new DateRangeParam("2001", "2003"));
+		map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
+
+		map = new SearchParameterMap();
+		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
+		map.setLastUpdated(new DateRangeParam("2001", "2003"));
+		map.setSort(new SortSpec(Patient.SP_NAME));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
+
+	}
+
 	@Test
 	public void testStoreUnversionedResources() {
 		Organization o1 = new Organization();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -745,9 +745,9 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
 		assertEquals(2, history.size());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)).getValue());
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 1).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 1).get(0)));
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 2).get(0)));
 
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -80,6 +80,7 @@ import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -109,6 +110,28 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3Test.class);
 
+	private void assertGone(IIdType theId) {
+		try {
+			assertNotGone(theId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+	}
+
+	/**
+	 * This gets called from assertGone too! Careful about exceptions...
+	 */
+	private void assertNotGone(IIdType theId) {
+		if ("Patient".equals(theId.getResourceType())) {
+			myPatientDao.read(theId, new ServletRequestDetails());
+		} else if ("Organization".equals(theId.getResourceType())) {
+			myOrganizationDao.read(theId, new ServletRequestDetails());
+		} else {
+			fail("No type");
+		}
+	}
+
 	private List<String> extractNames(IBundleProvider theSearch) {
 		ArrayList<String> retVal = new ArrayList<String>();
 		for (IBaseResource next : theSearch.getResources(0, theSearch.size())) {
@@ -118,6 +141,12 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		return retVal;
 	}
 
+	private CodeableConcept newCodeableConcept(String theSystem, String theCode) {
+		CodeableConcept retVal = new CodeableConcept();
+		retVal.addCoding().setSystem(theSystem).setCode(theCode);
+		return retVal;
+	}
+
 	private void sort(ArrayList<Coding> thePublished) {
 		ArrayList<Coding> tags = new ArrayList<Coding>(thePublished);
 		Collections.sort(tags, new Comparator<Coding>() {
@@ -202,6 +231,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	
 	@Test
 	public void testChoiceParamDate() {
 		Observation o2 = new Observation();
@@ -216,6 +246,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 	
+	
 	@Test
 	public void testChoiceParamDateAlt() {
 		Observation o2 = new Observation();
@@ -272,47 +303,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
-	
-	@Test
-	public void testChoiceParamQuantityPrecision() {
-		Observation o3 = new Observation();
-		o3.getCode().addCoding().setSystem("foo").setCode("testChoiceParam03");
-		o3.setValue(new Quantity(null, 123.01, "foo", "bar", "bar"));
-		IIdType id3 = myObservationDao.create(o3, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder(id3));
-		}
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.0", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder(id3));
-		}
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.01", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder(id3));
-		}
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.010", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder(id3));
-		}
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.02", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder());
-		}
-		{
-			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.001", "foo", "bar"));
-			List<IIdType> list = toUnqualifiedVersionlessIds(found);
-			assertThat(list, containsInAnyOrder());
-		}
-	}
-	
-	
 	@Test
 	public void testChoiceParamQuantity() {
 		Observation o3 = new Observation();
@@ -372,6 +362,45 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testChoiceParamQuantityPrecision() {
+		Observation o3 = new Observation();
+		o3.getCode().addCoding().setSystem("foo").setCode("testChoiceParam03");
+		o3.setValue(new Quantity(null, 123.01, "foo", "bar", "bar"));
+		IIdType id3 = myObservationDao.create(o3, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder(id3));
+		}
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.0", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder(id3));
+		}
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.01", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder(id3));
+		}
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.010", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder(id3));
+		}
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.02", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder());
+		}
+		{
+			IBundleProvider found = myObservationDao.search(Observation.SP_VALUE_QUANTITY, new QuantityParam("123.001", "foo", "bar"));
+			List<IIdType> list = toUnqualifiedVersionlessIds(found);
+			assertThat(list, containsInAnyOrder());
+		}
+	}
+
 	@Test
 	public void testChoiceParamString() {
 
@@ -387,6 +416,34 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testCreateLongString() {
+		//@formatter:off
+		String input = "<NamingSystem>\n" + 
+				"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + 
+				"        <status value=\"draft\"/>\n" + 
+				"        <kind value=\"codesystem\"/>\n" + 
+				"        <publisher value=\"HL7, Inc\"/>\n" + 
+				"        <date value=\"2015-08-21\"/>\n" + 
+				"        <uniqueId>\n" + 
+				"          <type value=\"uri\"/>\n" + 
+				"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + 
+				"          <preferred value=\"true\"/>\n" + 
+				"        </uniqueId>\n" + 
+				"        <uniqueId>\n" + 
+				"          <type value=\"oid\"/>\n" + 
+				"          <value value=\"2.16.840.1.113883.6.209\"/>\n" + 
+				"          <preferred value=\"false\"/>\n" + 
+				"        </uniqueId>\n" + 
+				"      </NamingSystem>";
+		//@formatter:on
+
+		NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
+		IIdType id = myNamingSystemDao.create(res, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		
+		assertThat(toUnqualifiedVersionlessIdValues(myNamingSystemDao.search(NamingSystem.SP_NAME, new StringParam("NDF"))), contains(id.getValue()));
+	}
+
 	@Test
 	public void testCreateOperationOutcome() {
 		/*
@@ -439,51 +496,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
-	@Test
-	public void testCreateLongString() {
-		//@formatter:off
-		String input = "<NamingSystem>\n" + 
-				"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + 
-				"        <status value=\"draft\"/>\n" + 
-				"        <kind value=\"codesystem\"/>\n" + 
-				"        <publisher value=\"HL7, Inc\"/>\n" + 
-				"        <date value=\"2015-08-21\"/>\n" + 
-				"        <uniqueId>\n" + 
-				"          <type value=\"uri\"/>\n" + 
-				"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + 
-				"          <preferred value=\"true\"/>\n" + 
-				"        </uniqueId>\n" + 
-				"        <uniqueId>\n" + 
-				"          <type value=\"oid\"/>\n" + 
-				"          <value value=\"2.16.840.1.113883.6.209\"/>\n" + 
-				"          <preferred value=\"false\"/>\n" + 
-				"        </uniqueId>\n" + 
-				"      </NamingSystem>";
-		//@formatter:on
-
-		NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
-		IIdType id = myNamingSystemDao.create(res, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-		
-		assertThat(toUnqualifiedVersionlessIdValues(myNamingSystemDao.search(NamingSystem.SP_NAME, new StringParam("NDF"))), contains(id.getValue()));
-	}
-
-	@Test
-	public void testCreateWrongType() {
-
-		// Lose typing so we can put the wrong type in
-		@SuppressWarnings("rawtypes")
-		IFhirResourceDao dao = myNamingSystemDao;
-		
-		Patient resource = new Patient();
-		resource.addName().addFamily("My Name");
-		try {
-			dao.create(resource, new ServletRequestDetails());
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Incorrect resource type detected for endpoint, found Patient but expected NamingSystem", e.getMessage());
-		}
-	}
-	
 	@Test
 	public void testCreateTextIdFails() {
 		Patient p = new Patient();
@@ -629,12 +641,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
-	private CodeableConcept newCodeableConcept(String theSystem, String theCode) {
-		CodeableConcept retVal = new CodeableConcept();
-		retVal.addCoding().setSystem(theSystem).setCode(theCode);
-		return retVal;
-	}
-
 	@Test
 	public void testCreateWithInvalidReferenceFailsGracefully() {
 		Patient patient = new Patient();
@@ -691,6 +697,23 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testCreateWrongType() {
+
+		// Lose typing so we can put the wrong type in
+		@SuppressWarnings("rawtypes")
+		IFhirResourceDao dao = myNamingSystemDao;
+		
+		Patient resource = new Patient();
+		resource.addName().addFamily("My Name");
+		try {
+			dao.create(resource, new ServletRequestDetails());
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Incorrect resource type detected for endpoint, found Patient but expected NamingSystem", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testDatePeriodParamEndOnly() {
 		{
@@ -969,23 +992,40 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	@Test
-	public void testDeleteWithMatchUrlChainedString() {
+	public void testDeleteWithMatchUrl() {
-		String methodName = "testDeleteWithMatchUrlChainedString";
+		String methodName = "testDeleteWithMatchUrl";
-
-		Organization org = new Organization();
-		org.setName(methodName);
-		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
 
 		Patient p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.getManagingOrganization().setReferenceElement(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId();
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
 		ourLog.info("Created patient, got it: {}", id);
 
-		myPatientDao.deleteByUrl("Patient?organization.name=" + methodName, new ServletRequestDetails());
+		Bundle request = new Bundle();
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
+
+		myPatientDao.deleteByUrl("Patient?identifier=urn%3Asystem%7C" + methodName, new ServletRequestDetails());
+
+		try {
+			myPatientDao.read(id.toVersionless(), new ServletRequestDetails());
+			fail();
+		} catch (ResourceGoneException e) {
+			// ok
+		}
+
+		try {
+			myPatientDao.read(new IdType("Patient/" + methodName), new ServletRequestDetails());
+			fail();
+		} catch (ResourceNotFoundException e) {
+			// ok
+		}
+
+		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
+		assertEquals(2, history.size());
+
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 1).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 1).get(0)).getValue());
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(1, 2).get(0)));
 
-		assertGone(id);
 	}
 
 	@Test
@@ -1014,6 +1054,73 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testDeleteWithMatchUrlChainedProfile() {
+		String methodName = "testDeleteWithMatchUrlChainedProfile";
+
+		List<IdType> profileList = new ArrayList<IdType>();
+
+		Organization org = new Organization();
+
+		org.getMeta().getProfile().add(new IdType("http://foo"));
+		org.setName(methodName);
+
+		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReferenceElement(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo", new ServletRequestDetails());
+		assertGone(id);
+
+		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo", new ServletRequestDetails());
+		try {
+			myOrganizationDao.read(orgId, new ServletRequestDetails());
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myPatientDao.deleteByUrl("Patient?organization._profile.identifier=http://foo", new ServletRequestDetails());
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: organization._profile.identifier", e.getMessage());
+		}
+
+		try {
+			myOrganizationDao.deleteByUrl("Organization?_profile.identifier=http://foo", new ServletRequestDetails());
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: _profile.identifier", e.getMessage());
+		}
+
+	}
+
+	@Test
+	public void testDeleteWithMatchUrlChainedString() {
+		String methodName = "testDeleteWithMatchUrlChainedString";
+
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReferenceElement(orgId);
+		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization.name=" + methodName, new ServletRequestDetails());
+
+		assertGone(id);
+	}
+
 	@Test
 	public void testDeleteWithMatchUrlChainedTag() {
 		String methodName = "testDeleteWithMatchUrlChainedString";
@@ -1120,112 +1227,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertGone(org2Id);
 	}
 
-	/**
-	 * This gets called from assertGone too! Careful about exceptions...
-	 */
-	private void assertNotGone(IIdType theId) {
-		if ("Patient".equals(theId.getResourceType())) {
-			myPatientDao.read(theId, new ServletRequestDetails());
-		} else if ("Organization".equals(theId.getResourceType())) {
-			myOrganizationDao.read(theId, new ServletRequestDetails());
-		} else {
-			fail("No type");
-		}
-	}
-
-	private void assertGone(IIdType theId) {
-		try {
-			assertNotGone(theId);
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
-	}
-
-	@Test
-	public void testDeleteWithMatchUrlChainedProfile() {
-		String methodName = "testDeleteWithMatchUrlChainedProfile";
-
-		List<IdType> profileList = new ArrayList<IdType>();
-
-		Organization org = new Organization();
-
-		org.getMeta().getProfile().add(new IdType("http://foo"));
-		org.setName(methodName);
-
-		IIdType orgId = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		p.getManagingOrganization().setReferenceElement(orgId);
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		ourLog.info("Created patient, got it: {}", id);
-
-		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo", new ServletRequestDetails());
-		assertGone(id);
-
-		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo", new ServletRequestDetails());
-		try {
-			myOrganizationDao.read(orgId, new ServletRequestDetails());
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
-
-		try {
-			myPatientDao.deleteByUrl("Patient?organization._profile.identifier=http://foo", new ServletRequestDetails());
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Invalid parameter chain: organization._profile.identifier", e.getMessage());
-		}
-
-		try {
-			myOrganizationDao.deleteByUrl("Organization?_profile.identifier=http://foo", new ServletRequestDetails());
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Invalid parameter chain: _profile.identifier", e.getMessage());
-		}
-
-	}
-
-	@Test
-	public void testDeleteWithMatchUrl() {
-		String methodName = "testDeleteWithMatchUrl";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType id = myPatientDao.create(p, new ServletRequestDetails()).getId();
-		ourLog.info("Created patient, got it: {}", id);
-
-		Bundle request = new Bundle();
-		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
-
-		myPatientDao.deleteByUrl("Patient?identifier=urn%3Asystem%7C" + methodName, new ServletRequestDetails());
-
-		try {
-			myPatientDao.read(id.toVersionless(), new ServletRequestDetails());
-			fail();
-		} catch (ResourceGoneException e) {
-			// ok
-		}
-
-		try {
-			myPatientDao.read(new IdType("Patient/" + methodName), new ServletRequestDetails());
-			fail();
-		} catch (ResourceNotFoundException e) {
-			// ok
-		}
-
-		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
-		assertEquals(2, history.size());
-
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 0).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 0).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(1, 1).get(0)));
-
-	}
-
 	@Test
 	public void testHistoryByForcedId() {
 		IIdType idv1;
@@ -1262,6 +1263,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		int halfSize = 50;
 		int fullSize = 100;
 		for (int i = 0; i < fullSize; i++) {
+			ourLog.info("Pass {}", i);
 			if (i == halfSize) {
 				Thread.sleep(fullSize);
 				middleDate = new Date();
@@ -1399,6 +1401,57 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 	
+	@Test
+	public void testHistoryReflectsMetaOperations() throws Exception {
+		Patient inPatient = new Patient();
+		inPatient.addName().addFamily("version1");
+		inPatient.getMeta().addProfile("http://example.com/1");
+		IIdType id = myPatientDao.create(inPatient, mySrd).getId().toUnqualifiedVersionless();
+
+		IBundleProvider history = myPatientDao.history(null, mySrd);
+		assertEquals(1, history.size());
+		Patient outPatient = (Patient) history.getResources(0, 1).get(0);
+		assertEquals("version1", inPatient.getName().get(0).getFamilyAsSingleString());
+		List<String> profiles = toStringList(outPatient.getMeta().getProfile());
+		assertThat(profiles, contains("http://example.com/1"));
+		
+		/*
+		 * Change metadata
+		 */
+		
+		inPatient.getMeta().addProfile("http://example.com/2");
+		myPatientDao.metaAddOperation(id, inPatient.getMeta(), mySrd);
+		
+		history = myPatientDao.history(null, mySrd);
+		assertEquals(1, history.size());
+		outPatient = (Patient) history.getResources(0, 1).get(0);
+		assertEquals("version1", inPatient.getName().get(0).getFamilyAsSingleString());
+		profiles = toStringList(outPatient.getMeta().getProfile());
+		assertThat(profiles, containsInAnyOrder("http://example.com/1", "http://example.com/2"));
+		
+		/*
+		 * Do an update
+		 */
+		
+		inPatient.setId(id);
+		inPatient.getMeta().addProfile("http://example.com/3");
+		inPatient.getName().get(0).addFamily("version2");
+		myPatientDao.update(inPatient, mySrd);
+
+		history = myPatientDao.history(null, mySrd);
+		assertEquals(2, history.size());
+		outPatient = (Patient) history.getResources(0, 2).get(0);
+		assertEquals("version1 version2", outPatient.getName().get(0).getFamilyAsSingleString());
+		profiles = toStringList(outPatient.getMeta().getProfile());
+		ourLog.info(profiles.toString());
+		assertThat(profiles, containsInAnyOrder("http://example.com/1", "http://example.com/2", "http://example.com/3"));
+
+		outPatient = (Patient) history.getResources(0, 2).get(1);
+		assertEquals("version1", outPatient.getName().get(0).getFamilyAsSingleString());
+		profiles = toStringList(outPatient.getMeta().getProfile());
+		assertThat(profiles, containsInAnyOrder("http://example.com/1", "http://example.com/2"));
+}
+
 	@Test
 	public void testHistoryWithDeletedResource() throws Exception {
 		String methodName = "testHistoryWithDeletedResource";
@@ -1412,11 +1465,11 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		myPatientDao.update(patient, new ServletRequestDetails());
 
 		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
-		assertEquals(3, history.size());
 		List<IBaseResource> entries = history.getResources(0, 3);
-		ourLog.info("" + ((IAnyResource) entries.get(0)).getMeta().getLastUpdated());
+		ourLog.info(((IAnyResource) entries.get(0)).getIdElement() + " - " + ((IAnyResource) entries.get(0)).getMeta().getLastUpdated());
-		ourLog.info("" + ((IAnyResource) entries.get(1)).getMeta().getLastUpdated());
+		ourLog.info(((IAnyResource) entries.get(1)).getIdElement() + " - " + ((IAnyResource) entries.get(1)).getMeta().getLastUpdated());
-		ourLog.info("" + ((IAnyResource) entries.get(2)).getMeta().getLastUpdated());
+		ourLog.info(((IAnyResource) entries.get(2)).getIdElement() + " - " + ((IAnyResource) entries.get(2)).getMeta().getLastUpdated());
+		assertEquals(3, history.size());
 
 		assertEquals(id.withVersion("3"), entries.get(0).getIdElement());
 		assertEquals(id.withVersion("2"), entries.get(1).getIdElement());
@@ -1432,6 +1485,16 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertEquals(BundleEntryTransactionMethodEnum.POST.getCode(), ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get((IAnyResource) entries.get(2)));
 	}
 
+	@Test
+	public void testHistoryWithInvalidId() throws Exception {
+		try {
+			myPatientDao.history(new IdDt("Patient/FOOFOOFOO"), null, new ServletRequestDetails());
+			fail();
+		} catch (ResourceNotFoundException e) {
+			assertEquals("Resource Patient/FOOFOOFOO is not known", e.getMessage());
+		}
+	}
+	
 	@Test
 	public void testIdParam() {
 		Patient patient = new Patient();
@@ -2327,79 +2390,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
-	@Test
-	public void testSortByLastUpdated() {
-		String methodName = "testSortByLastUpdated";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system1").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system2").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id2 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system3").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id3 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		p = new Patient();
-		p.addIdentifier().setSystem("urn:system4").setValue(methodName);
-		p.addName().addFamily(methodName);
-		IIdType id4 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap pm;
-		List<IIdType> actual;
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id1, id2, id3, id4));
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id1, id2, id3, id4));
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id4, id3, id2, id1));
-
-		pm = new SearchParameterMap();
-		pm.add(Patient.SP_IDENTIFIER, new TokenParam(null, methodName));
-		pm.setSort(new SortSpec(Patient.SP_NAME).setChain(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC)));
-		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
-		assertThat(actual, contains(id4, id3, id2, id1));
-	}
-
-	@Test
-	public void testSortNoMatches() {
-		String methodName = "testSortNoMatches";
-
-		Patient p = new Patient();
-		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap map;
-
-		map = new SearchParameterMap();
-		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
-		map.setLastUpdated(new DateRangeParam("2001", "2003"));
-		map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
-
-		map = new SearchParameterMap();
-		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
-		map.setLastUpdated(new DateRangeParam("2001", "2003"));
-		map.setSort(new SortSpec(Patient.SP_NAME));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
-
-	}
-
 	@Test
 	public void testSortById() {
 		String methodName = "testSortBTyId";
@@ -2451,6 +2441,55 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertThat(actual, contains(id4, id3, id2, id1, idMethodName));
 	}
 
+	@Test
+	public void testSortByLastUpdated() {
+		String methodName = "testSortByLastUpdated";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system1").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system2").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id2 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system3").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id3 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system4").setValue(methodName);
+		p.addName().addFamily(methodName);
+		IIdType id4 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap pm;
+		List<IIdType> actual;
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id1, id2, id3, id4));
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id1, id2, id3, id4));
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id4, id3, id2, id1));
+
+		pm = new SearchParameterMap();
+		pm.add(Patient.SP_IDENTIFIER, new TokenParam(null, methodName));
+		pm.setSort(new SortSpec(Patient.SP_NAME).setChain(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC)));
+		actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
+		assertThat(actual, contains(id4, id3, id2, id1));
+	}
+
 	@Test
 	public void testSortByNumber() {
 		String methodName = "testSortByNumber";
@@ -2778,6 +2817,30 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testSortNoMatches() {
+		String methodName = "testSortNoMatches";
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IIdType id1 = myPatientDao.create(p, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+
+		map = new SearchParameterMap();
+		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
+		map.setLastUpdated(new DateRangeParam("2001", "2003"));
+		map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
+
+		map = new SearchParameterMap();
+		map.add(BaseResource.SP_RES_ID, new StringParam(id1.getIdPart()));
+		map.setLastUpdated(new DateRangeParam("2001", "2003"));
+		map.setSort(new SortSpec(Patient.SP_NAME));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
+
+	}
+
 	@Test
 	public void testStoreUnversionedResources() {
 		Organization o1 = new Organization();
@@ -2994,4 +3057,12 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	private static List<String> toStringList(List<UriType> theUriType) {
+		ArrayList<String> retVal = new ArrayList<String>();
+		for (UriType next : theUriType) {
+			retVal.add(next.getValue());
+		}
+		return retVal;
+	}
+
 }

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

@@ -852,9 +852,9 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		IBundleProvider history = myPatientDao.history(id, null, new ServletRequestDetails());
 		assertEquals(2, history.size());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 1).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 0).get(0)).getValue());
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(0, 1).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(1, 1).get(0)));
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) history.getResources(1, 2).get(0)));
 
 	}
 

hapi-fhir-validation-resources-dstu3/.classpath

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" path="src/main/java"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
 			<attribute name="owner.project.facets" value="java"/>

src/changes/changes.xml

@@ -191,6 +191,17 @@
 				Old searches are deleted after an hour by default, but this can be changed
 				via a setting in the DaoConfig.
 			</action>
+			<action type="add">
+				JPA servers' resource version history mechanism 
+				has been adjusted so that the history table
+				keeps a record of all versions including the
+				current version. This has the very helpful
+				side effect that history no longer needs to be
+				paged into memory as a complete set. Previously
+				history had a hard limit of only being able to 
+				page the most recent 20000 entries. Now it has
+				no limit.
+			</action>
 		</release>
 		<release version="1.4" date="2016-02-04">
 			<action type="add">