It should not be possible to search for deleted resources using the _tag, _id, _profile, or _security search parameters

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -533,6 +533,7 @@ public class JsonParser extends BaseParser implements IParser {
 				INarrativeGenerator gen = myContext.getNarrativeGenerator();
 				if (gen != null) {
 					BaseNarrativeDt<?> narr = ((IResource) theResource).getText();
+					if (narr.getDiv().isEmpty()) {
 						gen.generateNarrative(theResDef.getResourceProfile(), theResource, narr);
 						if (narr != null && !narr.isEmpty()) {
 							RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
@@ -542,6 +543,7 @@ public class JsonParser extends BaseParser implements IParser {
 							continue;
 						}
 					}
+				}
 			} else if (nextChild instanceof RuntimeChildContainedResources) {
 				String childName = nextChild.getValidChildNames().iterator().next();
 				BaseRuntimeElementDefinition<?> child = nextChild.getChildByName(childName);
@@ -1237,7 +1239,6 @@ public class JsonParser extends BaseParser implements IParser {
 	// theState.endingElement();
 	// }
 
-
 	@Override
 	public TagList parseTagList(Reader theReader) {
 		JsonReader reader = Json.createReader(theReader);

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/App.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.cli;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import org.apache.commons.cli.CommandLine;
@@ -16,6 +17,8 @@ public class App {
 	static {
 		ourCommands = new ArrayList<BaseCommand>();
 		ourCommands.add(new RunServerCommand());
+		
+		Collections.sort(ourCommands);
 	}
 
 	public static void main(String[] theArgs) {

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -7,7 +7,7 @@ import org.apache.commons.cli.ParseException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.client.IGenericClient;
 
-public class BaseCommand {
+public abstract class BaseCommand implements Comparable<BaseCommand> {
 
 	public BaseCommand() {
 		super();
@@ -18,18 +18,15 @@ public class BaseCommand {
 		return fhirClient;
 	}
 
-	public Options getOptions() {
+	public abstract Options getOptions();
-		return null;
-	}
 
-	public String getCommandName() {
+	public abstract String getCommandName();
-		// TODO Auto-generated method stub
-		return null;
-	}
 
-	public void run(CommandLine theCommandLine) throws ParseException {
+	public abstract void run(CommandLine theCommandLine) throws ParseException;
-		// TODO Auto-generated method stub
 
+	@Override
+	public int compareTo(BaseCommand theO) {
+		return getCommandName().compareTo(theO.getCommandName());
 	}
 
 }

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

@@ -1068,46 +1068,46 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	@SuppressWarnings("unchecked")
-	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion) {
+	protected ResourceTable updateEntity(final IResource theResource, ResourceTable theEntity, boolean theUpdateHistory, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion) {
 
-		if (entity.getPublished() == null) {
+		if (theEntity.getPublished() == null) {
-			entity.setPublished(new Date());
+			theEntity.setPublished(new Date());
 		}
 
 		if (theResource != null) {
 			validateResourceForStorage((T) theResource);
 			String resourceType = myContext.getResourceDefinition(theResource).getName();
-			if (isNotBlank(entity.getResourceType()) && !entity.getResourceType().equals(resourceType)) {
+			if (isNotBlank(theEntity.getResourceType()) && !theEntity.getResourceType().equals(resourceType)) {
-				throw new UnprocessableEntityException("Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
+				throw new UnprocessableEntityException("Existing resource ID[" + theEntity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + theEntity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
 			}
 		}
 
 		if (theUpdateHistory) {
-			final ResourceHistoryTable historyEntry = entity.toHistory();
+			final ResourceHistoryTable historyEntry = theEntity.toHistory();
 			myEntityManager.persist(historyEntry);
 		}
 
 		if (theUpdateVersion) {
-			entity.setVersion(entity.getVersion() + 1);
+			theEntity.setVersion(theEntity.getVersion() + 1);
 		}
 
-		boolean paramsStringPopulated = entity.isParamsStringPopulated();
+		boolean paramsStringPopulated = theEntity.isParamsStringPopulated();
-		boolean paramsTokenPopulated = entity.isParamsTokenPopulated();
+		boolean paramsTokenPopulated = theEntity.isParamsTokenPopulated();
-		boolean paramsNumberPopulated = entity.isParamsNumberPopulated();
+		boolean paramsNumberPopulated = theEntity.isParamsNumberPopulated();
-		boolean paramsQuantityPopulated = entity.isParamsQuantityPopulated();
+		boolean paramsQuantityPopulated = theEntity.isParamsQuantityPopulated();
-		boolean paramsDatePopulated = entity.isParamsDatePopulated();
+		boolean paramsDatePopulated = theEntity.isParamsDatePopulated();
-		boolean paramsCoordsPopulated = entity.isParamsCoordsPopulated();
+		boolean paramsCoordsPopulated = theEntity.isParamsCoordsPopulated();
-		boolean paramsUriPopulated = entity.isParamsUriPopulated();
+		boolean paramsUriPopulated = theEntity.isParamsUriPopulated();
-		boolean hasLinks = entity.isHasLinks();
+		boolean hasLinks = theEntity.isHasLinks();
 
-		Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>(entity.getParamsString());
+		Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>(theEntity.getParamsString());
-		Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>(entity.getParamsToken());
+		Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>(theEntity.getParamsToken());
-		Collection<ResourceIndexedSearchParamNumber> paramsNumber = new ArrayList<ResourceIndexedSearchParamNumber>(entity.getParamsNumber());
+		Collection<ResourceIndexedSearchParamNumber> paramsNumber = new ArrayList<ResourceIndexedSearchParamNumber>(theEntity.getParamsNumber());
-		Collection<ResourceIndexedSearchParamQuantity> paramsQuantity = new ArrayList<ResourceIndexedSearchParamQuantity>(entity.getParamsQuantity());
+		Collection<ResourceIndexedSearchParamQuantity> paramsQuantity = new ArrayList<ResourceIndexedSearchParamQuantity>(theEntity.getParamsQuantity());
-		Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>(entity.getParamsDate());
+		Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>(theEntity.getParamsDate());
-		Collection<ResourceIndexedSearchParamUri> paramsUri = new ArrayList<ResourceIndexedSearchParamUri>(entity.getParamsUri());
+		Collection<ResourceIndexedSearchParamUri> paramsUri = new ArrayList<ResourceIndexedSearchParamUri>(theEntity.getParamsUri());
-		Collection<ResourceIndexedSearchParamCoords> paramsCoords = new ArrayList<ResourceIndexedSearchParamCoords>(entity.getParamsCoords());
+		Collection<ResourceIndexedSearchParamCoords> paramsCoords = new ArrayList<ResourceIndexedSearchParamCoords>(theEntity.getParamsCoords());
-		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>(entity.getResourceLinks());
+		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>(theEntity.getResourceLinks());
 
 		List<ResourceIndexedSearchParamString> stringParams = null;
 		List<ResourceIndexedSearchParamToken> tokenParams = null;
@@ -1128,27 +1128,27 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			uriParams = Collections.emptyList();
 			coordsParams = Collections.emptyList();
 			links = Collections.emptyList();
-			entity.setDeleted(theDeletedTimestampOrNull);
+			theEntity.setDeleted(theDeletedTimestampOrNull);
-			entity.setUpdated(theDeletedTimestampOrNull);
+			theEntity.setUpdated(theDeletedTimestampOrNull);
 
 		} else {
 
-			entity.setDeleted(null);
+			theEntity.setDeleted(null);
 
 			if (thePerformIndexing) {
 
-				stringParams = extractSearchParamStrings(entity, theResource);
+				stringParams = extractSearchParamStrings(theEntity, theResource);
-				numberParams = extractSearchParamNumber(entity, theResource);
+				numberParams = extractSearchParamNumber(theEntity, theResource);
-				quantityParams = extractSearchParamQuantity(entity, theResource);
+				quantityParams = extractSearchParamQuantity(theEntity, theResource);
-				dateParams = extractSearchParamDates(entity, theResource);
+				dateParams = extractSearchParamDates(theEntity, theResource);
-				uriParams = extractSearchParamUri(entity, theResource);
+				uriParams = extractSearchParamUri(theEntity, theResource);
-				coordsParams = extractSearchParamCoords(entity, theResource);
+				coordsParams = extractSearchParamCoords(theEntity, theResource);
 
 				// ourLog.info("Indexing resource: {}", entity.getId());
 				ourLog.trace("Storing string indexes: {}", stringParams);
 
 				tokenParams = new ArrayList<ResourceIndexedSearchParamToken>();
-				for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(entity, theResource)) {
+				for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theEntity, theResource)) {
 					if (next instanceof ResourceIndexedSearchParamToken) {
 						tokenParams.add((ResourceIndexedSearchParamToken) next);
 					} else {
@@ -1156,49 +1156,49 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					}
 				}
 
-				links = extractResourceLinks(entity, theResource);
+				links = extractResourceLinks(theEntity, theResource);
-				populateResourceIntoEntity(theResource, entity);
+				populateResourceIntoEntity(theResource, theEntity);
 
-				entity.setUpdated(new Date());
+				theEntity.setUpdated(new Date());
-				entity.setLanguage(theResource.getLanguage().getValue());
+				theEntity.setLanguage(theResource.getLanguage().getValue());
-				entity.setParamsString(stringParams);
+				theEntity.setParamsString(stringParams);
-				entity.setParamsStringPopulated(stringParams.isEmpty() == false);
+				theEntity.setParamsStringPopulated(stringParams.isEmpty() == false);
-				entity.setParamsToken(tokenParams);
+				theEntity.setParamsToken(tokenParams);
-				entity.setParamsTokenPopulated(tokenParams.isEmpty() == false);
+				theEntity.setParamsTokenPopulated(tokenParams.isEmpty() == false);
-				entity.setParamsNumber(numberParams);
+				theEntity.setParamsNumber(numberParams);
-				entity.setParamsNumberPopulated(numberParams.isEmpty() == false);
+				theEntity.setParamsNumberPopulated(numberParams.isEmpty() == false);
-				entity.setParamsQuantity(quantityParams);
+				theEntity.setParamsQuantity(quantityParams);
-				entity.setParamsQuantityPopulated(quantityParams.isEmpty() == false);
+				theEntity.setParamsQuantityPopulated(quantityParams.isEmpty() == false);
-				entity.setParamsDate(dateParams);
+				theEntity.setParamsDate(dateParams);
-				entity.setParamsDatePopulated(dateParams.isEmpty() == false);
+				theEntity.setParamsDatePopulated(dateParams.isEmpty() == false);
-				entity.setParamsUri(uriParams);
+				theEntity.setParamsUri(uriParams);
-				entity.setParamsUriPopulated(uriParams.isEmpty() == false);
+				theEntity.setParamsUriPopulated(uriParams.isEmpty() == false);
-				entity.setParamsCoords(coordsParams);
+				theEntity.setParamsCoords(coordsParams);
-				entity.setParamsCoordsPopulated(coordsParams.isEmpty() == false);
+				theEntity.setParamsCoordsPopulated(coordsParams.isEmpty() == false);
-				entity.setResourceLinks(links);
+				theEntity.setResourceLinks(links);
-				entity.setHasLinks(links.isEmpty() == false);
+				theEntity.setHasLinks(links.isEmpty() == false);
-				entity.setIndexStatus(INDEX_STATUS_INDEXED);
+				theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
 
 			} else {
 
-				populateResourceIntoEntity(theResource, entity);
+				populateResourceIntoEntity(theResource, theEntity);
-				entity.setUpdated(new Date());
+				theEntity.setUpdated(new Date());
-				entity.setLanguage(theResource.getLanguage().getValue());
+				theEntity.setLanguage(theResource.getLanguage().getValue());
-				entity.setIndexStatus(null);
+				theEntity.setIndexStatus(null);
 
 			}
 
 		}
 
-		if (entity.getId() == null) {
+		if (theEntity.getId() == null) {
-			myEntityManager.persist(entity);
+			myEntityManager.persist(theEntity);
 
-			if (entity.getForcedId() != null) {
+			if (theEntity.getForcedId() != null) {
-				myEntityManager.persist(entity.getForcedId());
+				myEntityManager.persist(theEntity.getForcedId());
 			}
 
 		} else {
-			entity = myEntityManager.merge(entity);
+			theEntity = myEntityManager.merge(theEntity);
 		}
 
 		if (thePerformIndexing) {
@@ -1283,10 +1283,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		myEntityManager.flush();
 
 		if (theResource != null) {
-			theResource.setId(entity.getIdDt());
+			theResource.setId(theEntity.getIdDt());
 		}
 
-		return entity;
+		return theEntity;
 	}
 
 	/**

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao;
 
+import static org.apache.commons.lang3.StringUtils.INDEX_NOT_FOUND;
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -287,12 +288,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		Predicate typePredicate = builder.equal(from.get("myResourceType"), myResourceName);
 		Predicate langPredicate = from.get("myLanguage").as(String.class).in(values);
 		Predicate masterCodePredicate = builder.and(typePredicate, langPredicate);
+		Predicate notDeletedPredicate = builder.isNull(from.get("myDeleted"));
 		
 		if (thePids.size() > 0) {
 			Predicate inPids = (from.get("myId").in(thePids));
-			cq.where(builder.and(masterCodePredicate, inPids));
+			cq.where(builder.and(masterCodePredicate, inPids, notDeletedPredicate));
 		} else {
-			cq.where(masterCodePredicate);
+			cq.where(builder.and(masterCodePredicate, notDeletedPredicate));
 		}
 
 		TypedQuery<Long> q = myEntityManager.createQuery(cq);
@@ -376,6 +378,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 				andPredicates.add(builder.or(orPredicates.toArray(new Predicate[0])));
 			}
 
+			From<ResourceTag, ResourceTable> defJoin = from.join("myResource");
+			Predicate notDeletedPredicatePrediate = builder.isNull(defJoin.get("myDeleted"));
+			andPredicates.add(notDeletedPredicatePrediate);
+			
 			Predicate masterCodePredicate = builder.and(andPredicates.toArray(new Predicate[0]));
 
 			if (pids.size() > 0) {
@@ -1262,6 +1268,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 			throw new InvalidRequestException("Trying to update " + theId + " but this is not the current version");
 		}
 		
+		verifyOkToDelete(entity);
+
 		// Notify interceptors
 		ActionRequestDetails requestDetails = new ActionRequestDetails(theId, theId.getResourceType());
 		notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
@@ -1274,6 +1282,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return toMethodOutcome(savedEntity, null);
 	}
 
+	private void verifyOkToDelete(ResourceTable theEntity) {
+		TypedQuery<ResourceLink> query = myEntityManager.createQuery("SELECT l FROM ResourceLink l WHERE l.myTargetResourcePid = :target_pid", ResourceLink.class);
+		query.setParameter("target_pid", theEntity.getId());
+		query.setMaxResults(1);
+		List<ResourceLink> resultList = query.getResultList();
+		if (resultList.isEmpty()) {
+			return;
+		}
+		
+		ResourceLink link = resultList.get(0);
+		String targetId = theEntity.getIdDt().toUnqualifiedVersionless().getValue();
+		String sourceId = link.getSourceResource().getIdDt().toUnqualifiedVersionless().getValue();
+		String sourcePath = link.getSourcePath();
+		
+		throw new PreconditionFailedException("Unable to delete " + targetId + " because at least one resource has a reference to this resource. First reference found was resource " + sourceId + " in path " + sourcePath );
+	}
+
 	@Override
 	public DaoMethodOutcome deleteByUrl(String theUrl) {
 		StopWatch w = new StopWatch();
@@ -1288,6 +1313,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		Long pid = resource.iterator().next();
 		ResourceTable entity = myEntityManager.find(ResourceTable.class, pid);
 
+		verifyOkToDelete(entity);
+
 		// Notify interceptors
 		IdDt idToDelete = entity.getIdDt();
 		ActionRequestDetails requestDetails = new ActionRequestDetails(idToDelete, idToDelete.getResourceType());
@@ -1369,6 +1396,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 	protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IBaseResource theResource, RuntimeResourceDefinition theResourceDef);
 
+	@Override
 	public Class<T> getResourceType() {
 		return myResourceType;
 	}
@@ -2126,18 +2154,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 						for (IQueryParameterType next : nextValue) {
 							String value = next.getValueAsQueryToken();
 							IIdType valueId = new IdDt(value);
+							
 							try {
-								long valueLong = translateForcedIdToPid(valueId);
+								BaseHasResource entity = readEntity(valueId);
-								joinPids.add(valueLong);
+								if (entity.getDeleted() != null) {
+									continue;
+								}
+								joinPids.add(entity.getId());
 							} catch (ResourceNotFoundException e) {
 								// This isn't an error, just means no result found
 							}
 						}
 						if (joinPids.isEmpty()) {
-							continue;
+							return new HashSet<Long>();
 						}
 					}
 
+					
 					pids = addPredicateId(pids, joinPids);
 					if (pids.isEmpty()) {
 						return new HashSet<Long>();
@@ -2250,9 +2283,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	}
 
 	private DaoMethodOutcome toMethodOutcome(final ResourceTable theEntity, IResource theResource) {
+		DaoMethodOutcome retVal = toMethodOutcome((BaseHasResource)theEntity, theResource);
+		retVal.setEntity(theEntity);
+		return retVal;
+	}
+
+	private DaoMethodOutcome toMethodOutcome(final BaseHasResource theEntity, IResource theResource) {
 		DaoMethodOutcome outcome = new DaoMethodOutcome();
 		outcome.setId(theEntity.getIdDt());
-		outcome.setEntity(theEntity);
 		outcome.setResource(theResource);
 		if (theResource != null) {
 			theResource.setId(theEntity.getIdDt());

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

@@ -90,6 +90,10 @@ public class SearchParameterMap extends HashMap<String, List<List<? extends IQue
 		getIncludes().add(theInclude);
 	}
 
+	public void addRevInclude(Include theInclude) {
+		getRevIncludes().add(theInclude);
+	}
+
 	public Integer getCount() {
 		return myCount;
 	}
@@ -106,6 +110,9 @@ public class SearchParameterMap extends HashMap<String, List<List<? extends IQue
 	}
 
 	public Set<Include> getRevIncludes() {
+		if (myRevIncludes == null) {
+			myRevIncludes = new HashSet<Include>();
+		}
 		return myRevIncludes;
 	}
 

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

@@ -41,16 +41,15 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.server.Constants;
 
 @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 = { @UniqueConstraint(name = "IDX_RES_VER_ALL", columnNames = { "RES_ID", "RES_TYPE", "RES_VER" }) })
-@org.hibernate.annotations.Table(appliesTo="HFJ_RES_VER", indexes= {@Index(name="IDX_RES_VER_DATE", columnNames= {"RES_UPDATED"})})
+@org.hibernate.annotations.Table(appliesTo = "HFJ_RES_VER", indexes = { @Index(name = "IDX_RES_VER_DATE", columnNames = { "RES_UPDATED" }) })
 public class ResourceHistoryTable extends BaseHasResource implements Serializable {
 
 	private static final long serialVersionUID = 1L;
 
-
 	@Id
-	@GeneratedValue(strategy=GenerationType.AUTO)
+	@GeneratedValue(strategy = GenerationType.AUTO)
-	@Column(name="PID")
+	@Column(name = "PID")
 	private Long myId;
 
 	@Column(name = "RES_ID")
@@ -87,13 +86,14 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return historyTag;
 	}
 
+	@Override
 	public Long getId() {
 		return myId;
 	}
 
 	@Override
 	public IdDt getIdDt() {
-		Object id = getForcedId()==null? getResourceId() : getForcedId().getForcedId();
+		Object id = getForcedId() == null ? getResourceId() : getForcedId().getForcedId();
 		return new IdDt(getResourceType() + '/' + id + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
 	}
 
@@ -101,11 +101,12 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return myResourceId;
 	}
 
+	@Override
 	public String getResourceType() {
 		return myResourceType;
 	}
 
-
+	@Override
 	public Collection<ResourceHistoryTag> getTags() {
 		if (myTags == null) {
 			myTags = new ArrayList<ResourceHistoryTag>();
@@ -132,11 +133,11 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	}
 
 	public void setResourceType(String theResourceType) {
-		myResourceType=theResourceType;
+		myResourceType = theResourceType;
 	}
 
 	public void setVersion(long theVersion) {
-		myResourceVersion=theVersion;
+		myResourceVersion = theVersion;
 	}
 
 }

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

@@ -46,7 +46,7 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
 	public ResourceIndexedSearchParamCoords() {
 	}
 
-	public ResourceIndexedSearchParamCoords(String theName, String theUri, double theLatitude, double theLongitude) {
+	public ResourceIndexedSearchParamCoords(String theName, double theLatitude, double theLongitude) {
 		setParamName(theName);
 		setLatitude(theLatitude);
 		setLongitude(theLongitude);

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

@@ -141,16 +141,19 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@Column(name = "RES_VER")
 	private long myVersion;
 
+	@Override
 	public ResourceTag addTag(TagDefinition theTag) {
 		ResourceTag tag = new ResourceTag(this, theTag);
 		getTags().add(tag);
 		return tag;
 	}
 
+	@Override
 	public Long getId() {
 		return myId;
 	}
 
+	@Override
 	public IdDt getIdDt() {
 		Object id = getForcedId() == null ? myId : getForcedId().getForcedId();
 		return new IdDt(myResourceType + '/' + id + '/' + Constants.PARAM_HISTORY + '/' + myVersion);
@@ -224,10 +227,12 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return myResourceLinks;
 	}
 
+	@Override
 	public String getResourceType() {
 		return myResourceType;
 	}
 
+	@Override
 	public Collection<ResourceTag> getTags() {
 		if (myTags == null) {
 			myTags = new HashSet<ResourceTag>();
@@ -235,6 +240,7 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return myTags;
 	}
 
+	@Override
 	public long getVersion() {
 		return myVersion;
 	}
@@ -428,4 +434,5 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 
 		return retVal;
 	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaDstu2Test.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.dao;
 
 import static org.mockito.Mockito.mock;
 
+import java.util.List;
+
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 
@@ -34,6 +36,7 @@ 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.TagDefinition;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
@@ -46,6 +49,7 @@ import ca.uhn.fhir.model.dstu2.resource.Practitioner;
 import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
 import ca.uhn.fhir.model.dstu2.resource.QuestionnaireResponse;
 import ca.uhn.fhir.model.dstu2.resource.ValueSet;
+import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 //@formatter:off
@@ -57,6 +61,8 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 //@formatter:on
 public class BaseJpaDstu2Test extends BaseJpaTest {
 
+	@Autowired
+	protected DaoConfig myDaoConfig;
 	@Autowired
 	@Qualifier("myDeviceDaoDstu2")
 	protected IFhirResourceDao<Device> myDeviceDao;
@@ -66,6 +72,8 @@ public class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myEncounterDaoDstu2")
 	protected IFhirResourceDao<Encounter> myEncounterDao;
+	@PersistenceContext()
+	protected EntityManager myEntityManager;
 	@Autowired
 	protected FhirContext myFhirCtx;
 	protected IServerInterceptor myInterceptor;
@@ -79,9 +87,6 @@ public class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myOrganizationDaoDstu2")
 	protected IFhirResourceDao<Organization> myOrganizationDao;
 	@Autowired
-	@Qualifier("myValueSetDaoDstu2")
-	protected IFhirResourceDao<ValueSet> myValueSetDao;
-	@Autowired
 	@Qualifier("myPatientDaoDstu2")
 	protected IFhirResourceDao<Patient> myPatientDao;
 	@Autowired
@@ -94,14 +99,32 @@ public class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myQuestionnaireResponseDaoDstu2")
 	protected IFhirResourceDao<QuestionnaireResponse> myQuestionnaireResponseDao;
 	@Autowired
+	@Qualifier("myResourceProvidersDstu2")
+	protected Object myResourceProviders;
+	@Autowired
 	@Qualifier("mySystemDaoDstu2")
 	protected IFhirSystemDao<Bundle> mySystemDao;
 	@Autowired
-	protected DaoConfig myDaoConfig;
+	@Qualifier("mySystemProviderDstu2")
+	protected JpaSystemProviderDstu2 mySystemProvider;
 	@Autowired
 	protected PlatformTransactionManager myTxManager;
-	@PersistenceContext()
+	@Autowired
-	protected EntityManager myEntityManager;
+	@Qualifier("myValueSetDaoDstu2")
+	protected IFhirResourceDao<ValueSet> myValueSetDao;
+
+	@Before
+	public void beforeCreateInterceptor() {
+		myInterceptor = mock(IServerInterceptor.class);
+		myDaoConfig.setInterceptors(myInterceptor);
+	}
+
+	@Before
+	@Transactional()
+	public void beforePurgeDatabase() {
+		final EntityManager entityManager = this.myEntityManager;
+		purgeDatabase(entityManager, myTxManager);
+	}
 
 	/**
 	 * Just so that JUnit doesn't complain about no test methods in this class
@@ -111,52 +134,43 @@ public class BaseJpaDstu2Test extends BaseJpaTest {
 		// nothing
 	}
 
-	@Before
+	public static void purgeDatabase(final EntityManager entityManager, PlatformTransactionManager theTxManager) {
-	@Transactional()
+		TransactionTemplate txTemplate = new TransactionTemplate(theTxManager);
-	public void beforePurgeDatabase() {
-		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
 		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
 		txTemplate.execute(new TransactionCallback<Void>() {
 			@Override
 			public Void doInTransaction(TransactionStatus theStatus) {
-				myEntityManager.createQuery("UPDATE " + ResourceHistoryTable.class.getSimpleName() + " d SET d.myForcedId = null").executeUpdate();
+				entityManager.createQuery("UPDATE " + ResourceHistoryTable.class.getSimpleName() + " d SET d.myForcedId = null").executeUpdate();
-				myEntityManager.createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " d SET d.myForcedId = null").executeUpdate();
+				entityManager.createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " d SET d.myForcedId = null").executeUpdate();
 				return null;
 			}
 		});
 		txTemplate.execute(new TransactionCallback<Void>() {
 			@Override
 			public Void doInTransaction(TransactionStatus theStatus) {
-				myEntityManager.createQuery("DELETE from " + ForcedId.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ForcedId.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamDate.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamDate.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamNumber.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamNumber.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamQuantity.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamQuantity.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamString.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamString.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamToken.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamToken.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamUri.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamUri.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceIndexedSearchParamCoords.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceIndexedSearchParamCoords.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceLink.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceLink.class.getSimpleName() + " d").executeUpdate();
 				return null;
 			}
 		});
 		txTemplate.execute(new TransactionCallback<Void>() {
 			@Override
 			public Void doInTransaction(TransactionStatus theStatus) {
-				myEntityManager.createQuery("DELETE from " + ResourceHistoryTag.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceHistoryTag.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceTag.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceTag.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + TagDefinition.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + TagDefinition.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceHistoryTable.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceHistoryTable.class.getSimpleName() + " d").executeUpdate();
-				myEntityManager.createQuery("DELETE from " + ResourceTable.class.getSimpleName() + " d").executeUpdate();
+				entityManager.createQuery("DELETE from " + ResourceTable.class.getSimpleName() + " d").executeUpdate();
 				return null;
 			}
 		});
 	}
 
-
-	@Before
-	public void beforeCreateInterceptor() {
-		myInterceptor = mock(IServerInterceptor.class);
-		myDaoConfig.setInterceptors(myInterceptor);
-	}
-
 }

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

@@ -4,6 +4,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.endsWith;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.hasItem;
@@ -42,6 +43,7 @@ import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
@@ -67,6 +69,7 @@ import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
 import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
 import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
 import ca.uhn.fhir.model.dstu2.valueset.QuantityComparatorEnum;
+import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -107,45 +110,43 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		return retVal;
 	}
 
-	@Test
+	private void sort(TagList thePublished) {
-	public void testReadWithDeletedResource() {
+		ArrayList<Tag> tags = new ArrayList<Tag>(thePublished);
-		String methodName = "testReadWithDeletedResource";
+		Collections.sort(tags, new Comparator<Tag>() {
-
+			@Override
-		Patient patient = new Patient();
+			public int compare(Tag theO1, Tag theO2) {
-		patient.addName().addFamily(methodName);
+				int retVal = defaultString(theO1.getScheme()).compareTo(defaultString(theO2.getScheme()));
-		IIdType id = myPatientDao.create(patient).getId().toVersionless();
+				if (retVal == 0) {
-		myPatientDao.delete(id);
+					retVal = defaultString(theO1.getTerm()).compareTo(defaultString(theO2.getTerm()));
-
+				}
-		try {
+				return retVal;
-			myPatientDao.read(id);
+			}
-			fail();
+		});
-		} catch (ResourceGoneException e) {
+		thePublished.clear();
-			// good
+		for (Tag next : tags) {
+			thePublished.add(next);
+		}
 	}
 
-		patient.setId(id);
+	private void sortCodings(List<BaseCodingDt> theSecLabels) {
-		patient.addAddress().addLine("AAA");
+		Collections.sort(theSecLabels, new Comparator<BaseCodingDt>() {
-		myPatientDao.update(patient);
+			@Override
-		
+			public int compare(BaseCodingDt theO1, BaseCodingDt theO2) {
-		Patient p;
+				return theO1.getSystemElement().getValue().compareTo(theO2.getSystemElement().getValue());
-
+			}
-		p = myPatientDao.read(id);
+		});
-		assertEquals(1, (p).getName().size());
-
-		p = myPatientDao.read(id.withVersion("1"));
-		assertEquals(1, (p).getName().size());
-
-		try {
-			myPatientDao.read(id.withVersion("2"));
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
 	}
 
-		p = myPatientDao.read(id.withVersion("3"));
+	private List<IdDt> sortIds(List<IdDt> theProfiles) {
-		assertEquals(1, (p).getName().size());
+		ArrayList<IdDt> retVal = new ArrayList<IdDt>(theProfiles);
+		Collections.sort(retVal, new Comparator<IdDt>() {
+			@Override
+			public int compare(IdDt theO1, IdDt theO2) {
+				return theO1.getValue().compareTo(theO2.getValue());
+			}
+		});
+		return retVal;
 	}
-
 
 	@Test
 	public void testChoiceParamConcept() {
@@ -314,48 +315,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
-	@Test
-	public void testCreateWithInvalidReferenceNoId() {
-		Patient p = new Patient();
-		p.addName().addFamily("Hello");
-		p.getManagingOrganization().setReference("Organization/");
-
-		try {
-			myPatientDao.create(p);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Does not contain resource ID"));
-		}
-	}
-
-	@Test
-	public void testCreateWithReferenceBadType() {
-		Patient p = new Patient();
-		p.addName().addFamily("Hello");
-		p.getManagingOrganization().setReference("Blah/123");
-
-		try {
-			myPatientDao.create(p);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Invalid resource reference"));
-		}
-	}
-
-	@Test
-	public void testCreateWithReferenceNoType() {
-		Patient p = new Patient();
-		p.addName().addFamily("Hello");
-		p.getManagingOrganization().setReference("123");
-
-		try {
-			myPatientDao.create(p);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Does not contain resource type"));
-		}
-	}
-
 	@Test
 	public void testCreateWithIfNoneExistBasic() {
 		String methodName = "testCreateWithIfNoneExistBasic";
@@ -422,6 +381,48 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	@Test
+	public void testCreateWithInvalidReferenceNoId() {
+		Patient p = new Patient();
+		p.addName().addFamily("Hello");
+		p.getManagingOrganization().setReference("Organization/");
+
+		try {
+			myPatientDao.create(p);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Does not contain resource ID"));
+		}
+	}
+
+	@Test
+	public void testCreateWithReferenceBadType() {
+		Patient p = new Patient();
+		p.addName().addFamily("Hello");
+		p.getManagingOrganization().setReference("Blah/123");
+
+		try {
+			myPatientDao.create(p);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Invalid resource reference"));
+		}
+	}
+
+	@Test
+	public void testCreateWithReferenceNoType() {
+		Patient p = new Patient();
+		p.addName().addFamily("Hello");
+		p.getManagingOrganization().setReference("123");
+
+		try {
+			myPatientDao.create(p);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Does not contain resource type"));
+		}
+	}
+
 	@Test
 	public void testDatePeriodParamEndOnly() {
 		{
@@ -623,6 +624,81 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	@Test
+	public void testCantSearchForDeletedResourceByLanguageOrTag() {
+		String methodName = "testCantSearchForDeletedResourceByLanguageOrTag";
+		Organization org = new Organization();
+		org.setLanguage(new CodeDt("EN_ca"));
+		org.setName(methodName);
+
+		TagList tl = new TagList();
+		tl.add(new Tag(methodName, methodName));
+		ResourceMetadataKeyEnum.TAG_LIST.put(org, tl);
+
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.add("_language", new StringParam("EN_ca"));
+		assertEquals(1, myOrganizationDao.search(map).size());
+
+		map = new SearchParameterMap();
+		map.add("_tag", new TokenParam(methodName, methodName));
+		assertEquals(1, myOrganizationDao.search(map).size());
+
+		myOrganizationDao.delete(orgId);
+
+		map = new SearchParameterMap();
+		map.add("_language", new StringParam("EN_ca"));
+		assertEquals(0, myOrganizationDao.search(map).size());
+
+		map = new SearchParameterMap();
+		map.add("_tag", new TokenParam(methodName, methodName));
+		assertEquals(0, myOrganizationDao.search(map).size());
+	}
+
+	@Test
+	public void testDeleteFailsIfIncomingLinks() {
+		String methodName = "testDeleteFailsIfIncomingLinks";
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		Patient patient = new Patient();
+		patient.addName().addFamily(methodName);
+		patient.getManagingOrganization().setReference(orgId);
+		IIdType patId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.add("_id", new StringParam(orgId.getIdPart()));
+		map.addRevInclude(new Include("*"));
+		List<IIdType> found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
+		assertThat(found, contains(orgId, patId));
+
+		try {
+			myOrganizationDao.delete(orgId);
+			fail();
+		} catch (PreconditionFailedException e) {
+			assertThat(e.getMessage(), containsString("Unable to delete Organization/" + orgId.getIdPart() + " because at least one resource has a reference to this resource. First reference found was resource Patient/" + patId.getIdPart() + " in path Patient.managingOrganization"));
+		}
+
+		myPatientDao.delete(patId);
+
+		map = new SearchParameterMap();
+		map.add("_id", new StringParam(orgId.getIdPart()));
+		map.addRevInclude(new Include("*"));
+		found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
+		assertThat(found, contains(orgId));
+
+		myOrganizationDao.delete(orgId);
+
+		map = new SearchParameterMap();
+		map.add("_id", new StringParam(orgId.getIdPart()));
+		map.addRevInclude(new Include("*"));
+		found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
+		assertThat(found, empty());
+
+	}
+
 	@Test
 	public void testDeleteThenUndelete() {
 		Patient patient = new Patient();
@@ -717,6 +793,155 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertNotEquals(idv1, idv2);
 	}
 
+	@Test
+	public void testHistoryOverMultiplePages() throws Exception {
+		String methodName = "testHistoryOverMultiplePages";
+
+		Patient patient = new Patient();
+		patient.addName().addFamily(methodName);
+		IIdType id = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Date middleDate = null;
+		int halfSize = 50;
+		int fullSize = 100;
+		for (int i = 0; i < fullSize; i++) {
+			if (i == halfSize) {
+				Thread.sleep(fullSize);
+				middleDate = new Date();
+				Thread.sleep(fullSize);
+			}
+			patient.setId(id);
+			patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");
+			myPatientDao.update(patient);
+		}
+
+		// By instance
+		IBundleProvider history = myPatientDao.history(id, null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By type
+		history = myPatientDao.history(null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By server
+		history = mySystemDao.history(null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		/*
+		 * With since date
+		 */
+
+		// By instance
+		history = myPatientDao.history(id, middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By type
+		history = myPatientDao.history(middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By server
+		history = mySystemDao.history(middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		/*
+		 * Now delete the most recent version and make sure everything still works
+		 */
+
+		myPatientDao.delete(id.toVersionless());
+
+		fullSize++;
+		halfSize++;
+
+		// By instance
+		history = myPatientDao.history(id, null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By type
+		history = myPatientDao.history(null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By server
+		history = mySystemDao.history(null);
+		assertEquals(fullSize + 1, history.size());
+		for (int i = 0; i < fullSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		/*
+		 * With since date
+		 */
+
+		// By instance
+		history = myPatientDao.history(id, middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By type
+		history = myPatientDao.history(middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+		// By server
+		history = mySystemDao.history(middleDate);
+		assertEquals(halfSize, history.size());
+		for (int i = 0; i < halfSize; i++) {
+			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
+			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
+			assertEquals(expected, actual);
+		}
+
+	}
+
 	@Test
 	public void testHistoryWithDeletedResource() throws Exception {
 		String methodName = "testHistoryWithDeletedResource";
@@ -745,80 +970,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) entries.get(2)));
 	}
 
-	@Test
-	public void testHistoryOverMultiplePages() throws Exception {
-		String methodName = "testHistoryOverMultiplePages";
-
-		Patient patient = new Patient();
-		patient.addName().addFamily(methodName);
-		IIdType id = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
-
-		Date middleDate = null;
-		for (int i = 0; i < 100; i++) {
-			if (i == 50) {
-				Thread.sleep(100);
-				middleDate = new Date();
-				Thread.sleep(100);
-			}
-			patient.setId(id);
-			patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");
-			myPatientDao.update(patient);
-		}
-
-		// By instance
-		IBundleProvider history = myPatientDao.history(id, null);
-		for (int i = 0; i < 100; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-		// By type
-		history = myPatientDao.history(null);
-		for (int i = 0; i < 100; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-		// By server
-		history = mySystemDao.history(null);
-		for (int i = 0; i < 100; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-		/*
-		 * With since date
-		 */
-
-		// By instance
-		history = myPatientDao.history(id, middleDate);
-		for (int i = 0; i < 50; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-		// By type
-		history = myPatientDao.history(middleDate);
-		for (int i = 0; i < 50; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-		// By server
-		history = mySystemDao.history(middleDate);
-		for (int i = 0; i < 50; i++) {
-			String expected = id.withVersion(Integer.toString(101 - i)).getValue();
-			String actual = history.getResources(i, i + 1).get(0).getIdElement().getValue();
-			assertEquals(expected, actual);
-		}
-
-	}
-
 	@Test
 	public void testIdParam() {
 		Patient patient = new Patient();
@@ -891,6 +1042,141 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
+	@Test
+	public void testInstanceMetaOperations() {
+		String methodName = "testMetaRead";
+		IIdType id;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue(methodName);
+			TagList tagList = new TagList();
+			tagList.addTag("tag_scheme1", "tag_code1", "tag_display1");
+			tagList.addTag("tag_scheme2", "tag_code2", "tag_display2");
+			ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
+
+			List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
+			securityLabels.add(new CodingDt().setSystem("seclabel_sys1").setCode("seclabel_code1").setDisplay("seclabel_dis1"));
+			securityLabels.add(new CodingDt().setSystem("seclabel_sys2").setCode("seclabel_code2").setDisplay("seclabel_dis2"));
+			ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
+
+			ArrayList<IdDt> profiles = new ArrayList<IdDt>();
+			profiles.add(new IdDt("http://profile/1"));
+			profiles.add(new IdDt("http://profile/2"));
+			ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
+
+			id = myPatientDao.create(patient).getId();
+		}
+
+		assertTrue(id.hasVersionIdPart());
+
+		/*
+		 * Create a second version
+		 */
+
+		Patient pt = myPatientDao.read(id);
+		pt.addName().addFamily("anotherName");
+		myPatientDao.update(pt);
+
+		/*
+		 * Meta-Delete on previous version
+		 */
+
+		MetaDt meta = new MetaDt();
+		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
+		meta.addProfile("http://profile/1");
+		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
+		MetaDt newMeta = myPatientDao.metaDeleteOperation(id.withVersion("1"), meta);
+		assertEquals(1, newMeta.getProfile().size());
+		assertEquals(1, newMeta.getSecurity().size());
+		assertEquals(1, newMeta.getTag().size());
+		assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
+		assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
+		assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
+
+		/*
+		 * Meta Read on Version
+		 */
+
+		meta = myPatientDao.metaGetOperation(id.withVersion("1"));
+		assertEquals(1, meta.getProfile().size());
+		assertEquals(1, meta.getSecurity().size());
+		assertEquals(1, meta.getTag().size());
+		assertEquals("tag_code2", meta.getTag().get(0).getCode());
+		assertEquals("http://profile/2", meta.getProfile().get(0).getValue());
+		assertEquals("seclabel_code2", meta.getSecurity().get(0).getCode());
+
+		/*
+		 * Meta-read on Version 2
+		 */
+		meta = myPatientDao.metaGetOperation(id.withVersion("2"));
+		assertEquals(2, meta.getProfile().size());
+		assertEquals(2, meta.getSecurity().size());
+		assertEquals(2, meta.getTag().size());
+
+		/*
+		 * Meta-read on latest version
+		 */
+		meta = myPatientDao.metaGetOperation(id.toVersionless());
+		assertEquals(2, meta.getProfile().size());
+		assertEquals(2, meta.getSecurity().size());
+		assertEquals(2, meta.getTag().size());
+		assertEquals("2", meta.getVersionId());
+
+		/*
+		 * Meta-Add on previous version
+		 */
+
+		meta = new MetaDt();
+		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
+		meta.addProfile("http://profile/1");
+		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
+		newMeta = myPatientDao.metaAddOperation(id.withVersion("1"), meta);
+		assertEquals(2, newMeta.getProfile().size());
+		assertEquals(2, newMeta.getSecurity().size());
+		assertEquals(2, newMeta.getTag().size());
+
+		/*
+		 * Meta Read on Version
+		 */
+
+		meta = myPatientDao.metaGetOperation(id.withVersion("1"));
+		assertEquals(2, meta.getProfile().size());
+		assertEquals(2, meta.getSecurity().size());
+		assertEquals(2, meta.getTag().size());
+		assertEquals("1", meta.getVersionId());
+
+		/*
+		 * Meta delete on latest
+		 */
+
+		meta = new MetaDt();
+		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
+		meta.addProfile("http://profile/1");
+		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
+		newMeta = myPatientDao.metaDeleteOperation(id.toVersionless(), meta);
+		assertEquals(1, newMeta.getProfile().size());
+		assertEquals(1, newMeta.getSecurity().size());
+		assertEquals(1, newMeta.getTag().size());
+		assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
+		assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
+		assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
+
+		/*
+		 * Meta-Add on latest version
+		 */
+
+		meta = new MetaDt();
+		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
+		meta.addProfile("http://profile/1");
+		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
+		newMeta = myPatientDao.metaAddOperation(id.toVersionless(), meta);
+		assertEquals(2, newMeta.getProfile().size());
+		assertEquals(2, newMeta.getSecurity().size());
+		assertEquals(2, newMeta.getTag().size());
+		assertEquals("2", newMeta.getVersionId());
+
+	}
+
 	/**
 	 * See #196
 	 */
@@ -1217,138 +1503,42 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	@Test
-	public void testInstanceMetaOperations() {
+	public void testReadWithDeletedResource() {
-		String methodName = "testMetaRead";
+		String methodName = "testReadWithDeletedResource";
-		IIdType id;
+
-		{
 		Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue(methodName);
+		patient.addName().addFamily(methodName);
-			TagList tagList = new TagList();
+		IIdType id = myPatientDao.create(patient).getId().toVersionless();
-			tagList.addTag("tag_scheme1", "tag_code1", "tag_display1");
+		myPatientDao.delete(id);
-			tagList.addTag("tag_scheme2", "tag_code2", "tag_display2");
-			ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
 
-			List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
+		try {
-			securityLabels.add(new CodingDt().setSystem("seclabel_sys1").setCode("seclabel_code1").setDisplay("seclabel_dis1"));
+			myPatientDao.read(id);
-			securityLabels.add(new CodingDt().setSystem("seclabel_sys2").setCode("seclabel_code2").setDisplay("seclabel_dis2"));
+			fail();
-			ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
+		} catch (ResourceGoneException e) {
-
+			// good
-			ArrayList<IdDt> profiles = new ArrayList<IdDt>();
-			profiles.add(new IdDt("http://profile/1"));
-			profiles.add(new IdDt("http://profile/2"));
-			ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
-
-			id = myPatientDao.create(patient).getId();
 		}
 
-		assertTrue(id.hasVersionIdPart());
+		patient.setId(id);
+		patient.addAddress().addLine("AAA");
+		myPatientDao.update(patient);
 
-		/*
+		Patient p;
-		 * Create a second version
-		 */
 
-		Patient pt = myPatientDao.read(id);
+		p = myPatientDao.read(id);
-		pt.addName().addFamily("anotherName");
+		assertEquals(1, (p).getName().size());
-		myPatientDao.update(pt);
 
-		/*
+		p = myPatientDao.read(id.withVersion("1"));
-		 * Meta-Delete on previous version
+		assertEquals(1, (p).getName().size());
-		 */
 
-		MetaDt meta = new MetaDt();
+		try {
-		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
+			myPatientDao.read(id.withVersion("2"));
-		meta.addProfile("http://profile/1");
+			fail();
-		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
+		} catch (ResourceGoneException e) {
-		MetaDt newMeta = myPatientDao.metaDeleteOperation(id.withVersion("1"), meta);
+			// good
-		assertEquals(1, newMeta.getProfile().size());
+		}
-		assertEquals(1, newMeta.getSecurity().size());
-		assertEquals(1, newMeta.getTag().size());
-		assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
-		assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
-		assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
-
-		/*
-		 * Meta Read on Version
-		 */
-
-		meta = myPatientDao.metaGetOperation(id.withVersion("1"));
-		assertEquals(1, meta.getProfile().size());
-		assertEquals(1, meta.getSecurity().size());
-		assertEquals(1, meta.getTag().size());
-		assertEquals("tag_code2", meta.getTag().get(0).getCode());
-		assertEquals("http://profile/2", meta.getProfile().get(0).getValue());
-		assertEquals("seclabel_code2", meta.getSecurity().get(0).getCode());
-
-		/*
-		 * Meta-read on Version 2
-		 */
-		meta = myPatientDao.metaGetOperation(id.withVersion("2"));
-		assertEquals(2, meta.getProfile().size());
-		assertEquals(2, meta.getSecurity().size());
-		assertEquals(2, meta.getTag().size());
-
-		/*
-		 * Meta-read on latest version
-		 */
-		meta = myPatientDao.metaGetOperation(id.toVersionless());
-		assertEquals(2, meta.getProfile().size());
-		assertEquals(2, meta.getSecurity().size());
-		assertEquals(2, meta.getTag().size());
-		assertEquals("2", meta.getVersionId());
-
-		/*
-		 * Meta-Add on previous version
-		 */
-
-		meta = new MetaDt();
-		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
-		meta.addProfile("http://profile/1");
-		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
-		newMeta = myPatientDao.metaAddOperation(id.withVersion("1"), meta);
-		assertEquals(2, newMeta.getProfile().size());
-		assertEquals(2, newMeta.getSecurity().size());
-		assertEquals(2, newMeta.getTag().size());
-
-		/*
-		 * Meta Read on Version
-		 */
-
-		meta = myPatientDao.metaGetOperation(id.withVersion("1"));
-		assertEquals(2, meta.getProfile().size());
-		assertEquals(2, meta.getSecurity().size());
-		assertEquals(2, meta.getTag().size());
-		assertEquals("1", meta.getVersionId());
-
-		/*
-		 * Meta delete on latest
-		 */
-
-		meta = new MetaDt();
-		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
-		meta.addProfile("http://profile/1");
-		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
-		newMeta = myPatientDao.metaDeleteOperation(id.toVersionless(), meta);
-		assertEquals(1, newMeta.getProfile().size());
-		assertEquals(1, newMeta.getSecurity().size());
-		assertEquals(1, newMeta.getTag().size());
-		assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
-		assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
-		assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
-
-		/*
-		 * Meta-Add on latest version
-		 */
-
-		meta = new MetaDt();
-		meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
-		meta.addProfile("http://profile/1");
-		meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
-		newMeta = myPatientDao.metaAddOperation(id.toVersionless(), meta);
-		assertEquals(2, newMeta.getProfile().size());
-		assertEquals(2, newMeta.getSecurity().size());
-		assertEquals(2, newMeta.getTag().size());
-		assertEquals("2", newMeta.getVersionId());
 
+		p = myPatientDao.read(id.withVersion("3"));
+		assertEquals(1, (p).getName().size());
 	}
 
 	@Test
@@ -1989,6 +2179,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals("Cat", published.get(1).getTerm());
 		assertEquals("Kittens", published.get(1).getLabel());
 		assertEquals("http://foo", published.get(1).getScheme());
+
 		List<BaseCodingDt> secLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(retrieved);
 		sortCodings(secLabels);
 		assertEquals(2, secLabels.size());
@@ -2001,19 +2192,24 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		profiles = ResourceMetadataKeyEnum.PROFILES.get(retrieved);
 		profiles = sortIds(profiles);
 		assertEquals(2, profiles.size());
-		assertEquals("http://profile/1", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(0).getValue());
+		assertEquals("http://profile/1", profiles.get(0).getValue());
-		assertEquals("http://profile/2", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(1).getValue());
+		assertEquals("http://profile/2", profiles.get(1).getValue());
 
 		List<Patient> search = toList(myPatientDao.search(Patient.SP_IDENTIFIER, patient.getIdentifierFirstRep()));
 		assertEquals(1, search.size());
 		retrieved = search.get(0);
+
 		published = (TagList) retrieved.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
+		sort(published);
 		assertEquals("Dog", published.get(0).getTerm());
 		assertEquals("Puppies", published.get(0).getLabel());
 		assertEquals(null, published.get(0).getScheme());
 		assertEquals("Cat", published.get(1).getTerm());
 		assertEquals("Kittens", published.get(1).getLabel());
 		assertEquals("http://foo", published.get(1).getScheme());
+
+		secLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(retrieved);
+		sortCodings(secLabels);
 		assertEquals(2, secLabels.size());
 		assertEquals("seclabel:sys:1", secLabels.get(0).getSystemElement().getValue());
 		assertEquals("seclabel:code:1", secLabels.get(0).getCodeElement().getValue());
@@ -2021,25 +2217,32 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals("seclabel:sys:2", secLabels.get(1).getSystemElement().getValue());
 		assertEquals("seclabel:code:2", secLabels.get(1).getCodeElement().getValue());
 		assertEquals("seclabel:dis:2", secLabels.get(1).getDisplayElement().getValue());
-		assertEquals(2, ResourceMetadataKeyEnum.PROFILES.get(retrieved).size());
+
-		assertEquals("http://profile/1", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(0).getValue());
+		profiles = ResourceMetadataKeyEnum.PROFILES.get(retrieved);
-		assertEquals("http://profile/2", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(1).getValue());
+		profiles = sortIds(profiles);
+		assertEquals(2, profiles.size());
+		assertEquals("http://profile/1", profiles.get(0).getValue());
+		assertEquals("http://profile/2", profiles.get(1).getValue());
 
 		myPatientDao.addTag(patientId, TagTypeEnum.TAG, "http://foo", "Cat", "Kittens");
 		myPatientDao.addTag(patientId, TagTypeEnum.TAG, "http://foo", "Cow", "Calves");
 
 		retrieved = myPatientDao.read(patientId);
 		published = (TagList) retrieved.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
+		sort(published);
 		assertEquals(3, published.size());
-		assertEquals("Dog", published.get(0).getTerm());
+		assertEquals(published.toString(), "Dog", published.get(0).getTerm());
-		assertEquals("Puppies", published.get(0).getLabel());
+		assertEquals(published.toString(), "Puppies", published.get(0).getLabel());
-		assertEquals(null, published.get(0).getScheme());
+		assertEquals(published.toString(), null, published.get(0).getScheme());
-		assertEquals("Cat", published.get(1).getTerm());
+		assertEquals(published.toString(), "Cat", published.get(1).getTerm());
-		assertEquals("Kittens", published.get(1).getLabel());
+		assertEquals(published.toString(), "Kittens", published.get(1).getLabel());
-		assertEquals("http://foo", published.get(1).getScheme());
+		assertEquals(published.toString(), "http://foo", published.get(1).getScheme());
-		assertEquals("Cow", published.get(2).getTerm());
+		assertEquals(published.toString(), "Cow", published.get(2).getTerm());
-		assertEquals("Calves", published.get(2).getLabel());
+		assertEquals(published.toString(), "Calves", published.get(2).getLabel());
-		assertEquals("http://foo", published.get(2).getScheme());
+		assertEquals(published.toString(), "http://foo", published.get(2).getScheme());
+
+		secLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(retrieved);
+		sortCodings(secLabels);
 		assertEquals(2, secLabels.size());
 		assertEquals("seclabel:sys:1", secLabels.get(0).getSystemElement().getValue());
 		assertEquals("seclabel:code:1", secLabels.get(0).getCodeElement().getValue());
@@ -2047,41 +2250,13 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals("seclabel:sys:2", secLabels.get(1).getSystemElement().getValue());
 		assertEquals("seclabel:code:2", secLabels.get(1).getCodeElement().getValue());
 		assertEquals("seclabel:dis:2", secLabels.get(1).getDisplayElement().getValue());
-		assertEquals(2, ResourceMetadataKeyEnum.PROFILES.get(retrieved).size());
-		assertEquals("http://profile/1", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(0).getValue());
-		assertEquals("http://profile/2", ResourceMetadataKeyEnum.PROFILES.get(retrieved).get(1).getValue());
 
-	}
+		profiles = ResourceMetadataKeyEnum.PROFILES.get(retrieved);
+		profiles = sortIds(profiles);
+		assertEquals(2, profiles.size());
+		assertEquals("http://profile/1", profiles.get(0).getValue());
+		assertEquals("http://profile/2", profiles.get(1).getValue());
 
-	private List<IdDt> sortIds(List<IdDt> theProfiles) {
-		ArrayList<IdDt> retVal = new ArrayList<IdDt>(theProfiles);
-		Collections.sort(retVal, new Comparator<IdDt>() {
-			@Override
-			public int compare(IdDt theO1, IdDt theO2) {
-				return theO1.getValue().compareTo(theO2.getValue());
-			}});
-		return retVal;
-	}
-
-	private void sortCodings(List<BaseCodingDt> theSecLabels) {
-		Collections.sort(theSecLabels, new Comparator<BaseCodingDt>() {
-			@Override
-			public int compare(BaseCodingDt theO1, BaseCodingDt theO2) {
-				return theO1.getSystemElement().getValue().compareTo(theO2.getSystemElement().getValue());
-			}});
-	}
-
-	private void sort(TagList thePublished) {
-		ArrayList<Tag> tags = new ArrayList<Tag>(thePublished);
-		Collections.sort(tags, new Comparator<Tag>() {
-			@Override
-			public int compare(Tag theO1, Tag theO2) {
-				return defaultString(theO1.getScheme()).compareTo(defaultString(theO2.getScheme()));
-			}});
-		thePublished.clear();
-		for (Tag next : tags) {
-			thePublished.add(next);
-		}
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -49,16 +49,12 @@ import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
 import org.junit.AfterClass;
-import org.junit.BeforeClass;
+import org.junit.Before;
 import org.junit.Test;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
 
-import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
-import ca.uhn.fhir.jpa.dao.BaseJpaTest;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;
@@ -105,26 +101,18 @@ import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.gclient.IQuery;
-import ca.uhn.fhir.rest.gclient.StringClientParam;
-import ca.uhn.fhir.rest.gclient.TokenClientParam;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
-import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
-public class ResourceProviderDstu2Test extends BaseJpaTest {
+public class ResourceProviderDstu2Test extends BaseJpaDstu2Test {
 
-	private static ClassPathXmlApplicationContext ourAppCtx;
 	private static IGenericClient ourClient;
-	private static FhirContext ourCtx = FhirContext.forDstu2();
-	private static DaoConfig ourDaoConfig;
 	private static CloseableHttpClient ourHttpClient;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu2Test.class);
-	private static IFhirResourceDao<Organization> ourOrganizationDao;
 	private static int ourPort;
 	private static Server ourServer;
 	private static String ourServerBase;
@@ -138,28 +126,30 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		assertEquals(200, resp.getStatusLine().getStatusCode());
 	}
 
-	private void delete(String theResourceType, String theParamName, String theParamValue) {
+	// private void delete(String theResourceType, String theParamName, String theParamValue) {
-		Bundle resources;
+	// Bundle resources;
-		do {
+	// do {
-			IQuery<Bundle> forResource = ourClient.search().forResource(theResourceType);
+	// IQuery<Bundle> forResource = ourClient.search().forResource(theResourceType);
-			if (theParamName != null) {
+	// if (theParamName != null) {
-				forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
+	// forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
-			}
+	// }
-			resources = forResource.execute();
+	// resources = forResource.execute();
-			for (IResource next : resources.toListOfResources()) {
+	// for (IResource next : resources.toListOfResources()) {
-				ourLog.info("Deleting resource: {}", next.getId());
+	// ourLog.info("Deleting resource: {}", next.getId());
-				ourClient.delete().resource(next).execute();
+	// ourClient.delete().resource(next).execute();
-			}
+	// }
-		} while (resources.size() > 0);
+	// } while (resources.size() > 0);
-	}
+	// }
-
+	//
-	private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue) {
+	// private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue)
-		Bundle resources = ourClient.search().forResource(theResourceType).where(new TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
+	// {
-		for (IResource next : resources.toListOfResources()) {
+	// Bundle resources = ourClient.search().forResource(theResourceType).where(new
-			ourLog.info("Deleting resource: {}", next.getId());
+	// TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
-			ourClient.delete().resource(next).execute();
+	// for (IResource next : resources.toListOfResources()) {
-		}
+	// ourLog.info("Deleting resource: {}", next.getId());
-	}
+	// ourClient.delete().resource(next).execute();
+	// }
+	// }
 
 	@Test
 	public void testBundleCreate() throws Exception {
@@ -172,7 +162,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = client.read().resource(ca.uhn.fhir.model.dstu2.resource.Bundle.class).withId(id).execute();
 
-		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 	}
 
 	@Test
@@ -192,7 +182,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	@Test
 	public void testCountParam() throws Exception {
 		// NB this does not get used- The paging provider has its own limits built in
-		ourDaoConfig.setHardSearchLimit(100);
+		myDaoConfig.setHardSearchLimit(100);
 
 		List<IBaseResource> resources = new ArrayList<IBaseResource>();
 		for (int i = 0; i < 100; i++) {
@@ -250,7 +240,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
-		String resource = ourCtx.newXmlParser().encodeResourceToString(pt);
+		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
 		post.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?name=" + methodName);
@@ -322,10 +312,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testDeepChaining() {
-		delete("Location", Location.SP_NAME, "testDeepChainingL1");
-		delete("Location", Location.SP_NAME, "testDeepChainingL2");
-		deleteToken("Encounter", Encounter.SP_IDENTIFIER, "urn:foo", "testDeepChainingE1");
-
 		Location l1 = new Location();
 		l1.getNameElement().setValue("testDeepChainingL1");
 		IIdType l1id = ourClient.create().resource(l1).execute().getId();
@@ -365,7 +351,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
-		String resource = ourCtx.newXmlParser().encodeResourceToString(pt);
+		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
@@ -409,7 +395,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
 		pt.addIdentifier().setSystem("http://ghh.org/patient").setValue(methodName);
-		String resource = ourCtx.newXmlParser().encodeResourceToString(pt);
+		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
@@ -491,8 +477,8 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	 */
 	@Test
 	public void testDocumentManifestResources() throws Exception {
-		ourCtx.getResourceDefinition(Practitioner.class);
+		myFhirCtx.getResourceDefinition(Practitioner.class);
-		ourCtx.getResourceDefinition(ca.uhn.fhir.model.dstu.resource.DocumentManifest.class);
+		myFhirCtx.getResourceDefinition(ca.uhn.fhir.model.dstu.resource.DocumentManifest.class);
 
 		IGenericClient client = ourClient;
 
@@ -531,7 +517,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	@Test
 	public void testEverythingDoesntRepeatPatient() throws Exception {
 		ca.uhn.fhir.model.dstu2.resource.Bundle b;
-		b = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/bug147-bundle.json")));
+		b = myFhirCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/bug147-bundle.json")));
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle resp = ourClient.transaction().withBundle(b).execute();
 		List<IdDt> ids = new ArrayList<IdDt>();
@@ -600,7 +586,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle resp = ourClient.transaction().withBundle(b).execute();
 
-		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
 
 		IdDt patientId = new IdDt(resp.getEntry().get(0).getResponse().getLocation());
 		assertEquals("Patient", patientId.getResourceType());
@@ -794,17 +780,28 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	}
 
 	@Test
-	public void testSaveAndRetrieveExistingNarrative() {
+	public void testSaveAndRetrieveExistingNarrativeJson() {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSaveAndRetrieveExistingNarrative01");
-
 		Patient p1 = new Patient();
 		p1.getText().setStatus(ca.uhn.fhir.model.dstu2.valueset.NarrativeStatusEnum.GENERATED);
 		p1.getText().getDiv().setValueAsString("<div>HELLO WORLD</div>");
 		p1.addIdentifier().setSystem("urn:system").setValue("testSaveAndRetrieveExistingNarrative01");
 
-		IIdType newId = ourClient.create().resource(p1).execute().getId();
+		IIdType newId = ourClient.create().resource(p1).encodedJson().execute().getId();
 
-		Patient actual = ourClient.read(Patient.class, (UriDt) newId);
+		Patient actual = ourClient.read().resource(Patient.class).withId(newId).encodedJson().execute();
+		assertEquals("<div>HELLO WORLD</div>", actual.getText().getDiv().getValueAsString());
+	}
+
+	@Test
+	public void testSaveAndRetrieveExistingNarrativeXml() {
+		Patient p1 = new Patient();
+		p1.getText().setStatus(ca.uhn.fhir.model.dstu2.valueset.NarrativeStatusEnum.GENERATED);
+		p1.getText().getDiv().setValueAsString("<div>HELLO WORLD</div>");
+		p1.addIdentifier().setSystem("urn:system").setValue("testSaveAndRetrieveExistingNarrative01");
+
+		IIdType newId = ourClient.create().resource(p1).encodedXml().execute().getId();
+
+		Patient actual = ourClient.read().resource(Patient.class).withId(newId).encodedXml().execute();
 		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">HELLO WORLD</div>", actual.getText().getDiv().getValueAsString());
 	}
 
@@ -856,9 +853,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testSearchByIdentifier() {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByIdentifier01");
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByIdentifier02");
-
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByIdentifier01");
 		p1.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven01");
@@ -888,7 +882,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testSearchByIdentifierWithoutSystem() {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "", "testSearchByIdentifierWithoutSystem01");
 
 		Patient p1 = new Patient();
 		p1.addIdentifier().setValue("testSearchByIdentifierWithoutSystem01");
@@ -902,8 +895,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testSearchByResourceChain() {
-		delete("Organization", Organization.SP_NAME, "testSearchByResourceChainName01");
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByResourceChain01");
 
 		Organization o1 = new Organization();
 		o1.setName("testSearchByResourceChainName01");
@@ -1036,7 +1027,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		String resp = IOUtils.toString(response.getEntity().getContent());
 		IOUtils.closeQuietly(response.getEntity().getContent());
 		ourLog.info(resp);
-		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, resp);
+		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = myFhirCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, resp);
 		matches = bundle.getTotal();
 
 		assertThat(matches, greaterThan(0));
@@ -1104,8 +1095,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	public void testSearchWithMissing() throws Exception {
 		ourLog.info("Starting testSearchWithMissing");
 
-		delete("Organization", null, null);
-
 		String methodName = "testSearchWithMissing";
 
 		Organization org = new Organization();
@@ -1334,15 +1323,15 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		// Read back directly from the DAO
 		{
-			Organization returned = ourOrganizationDao.read(orgId);
+			Organization returned = myOrganizationDao.read(orgId);
-			String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
+			String val = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
 			ourLog.info(val);
 			assertThat(val, containsString("<name value=\"測試醫院\"/>"));
 		}
 		// Read back through the HTTP API
 		{
 			Organization returned = ourClient.read(Organization.class, orgId);
-			String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
+			String val = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
 			ourLog.info(val);
 			assertThat(val, containsString("<name value=\"測試醫院\"/>"));
 		}
@@ -1350,8 +1339,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testTryToCreateResourceWithReferenceThatDoesntExist() {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testTryToCreateResourceWithReferenceThatDoesntExist01");
-
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testTryToCreateResourceWithReferenceThatDoesntExist01");
 		p1.addName().addFamily("testTryToCreateResourceWithReferenceThatDoesntExistFamily01").addGiven("testTryToCreateResourceWithReferenceThatDoesntExistGiven01");
@@ -1366,9 +1353,9 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	}
 
+
 	@Test
 	public void testUpdateRejectsInvalidTypes() throws InterruptedException {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testUpdateRejectsInvalidTypes");
 
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
@@ -1399,7 +1386,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
-		String resource = ourCtx.newXmlParser().encodeResourceToString(pt);
+		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient?name=" + methodName);
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
@@ -1434,7 +1421,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
-		String resource = ourCtx.newXmlParser().encodeResourceToString(pt);
+		String resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
@@ -1461,7 +1448,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 			String responseString = IOUtils.toString(response.getEntity().getContent());
 			IOUtils.closeQuietly(response.getEntity().getContent());
 
-			Patient respPt = ourCtx.newXmlParser().parseResource(Patient.class, responseString);
+			Patient respPt = myFhirCtx.newXmlParser().parseResource(Patient.class, responseString);
 			assertEquals("2", respPt.getId().getVersionIdPart());
 
 			InstantDt updateTime = ResourceMetadataKeyEnum.UPDATED.get(respPt);
@@ -1475,8 +1462,6 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 
 	@Test
 	public void testUpdateWithClientSuppliedIdWhichDoesntExist() {
-		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2");
-
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2");
 		MethodOutcome outcome = ourClient.update().resource(p1).withId("testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2").execute();
@@ -1501,7 +1486,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		Parameters input = new Parameters();
 		input.addParameter().setName("resource").setResource(patient);
 
-		String inputStr = ourCtx.newXmlParser().encodeResourceToString(input);
+		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(input);
 		ourLog.info(inputStr);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
@@ -1529,7 +1514,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		Parameters input = new Parameters();
 		input.addParameter().setName("resource").setResource(patient);
 
-		String inputStr = ourCtx.newXmlParser().encodeResourceToString(input);
+		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(input);
 		ourLog.info(inputStr);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
@@ -1556,7 +1541,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 		Parameters input = new Parameters();
 		input.addParameter().setName("resource").setResource(patient);
 
-		String inputStr = ourCtx.newXmlParser().encodeResourceToString(input);
+		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(input);
 		ourLog.info(inputStr);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/123/$validate");
@@ -1576,7 +1561,7 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	@Test
 	public void testValueSetExpandOperation() throws IOException {
 
-		ValueSet upload = ourCtx.newXmlParser().parseResource(ValueSet.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/extensional-case-2.xml")));
+		ValueSet upload = myFhirCtx.newXmlParser().parseResource(ValueSet.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/extensional-case-2.xml")));
 		IIdType vsid = ourClient.create().resource(upload).execute().getId().toUnqualifiedVersionless();
 
 		HttpGet get = new HttpGet(ourServerBase + "/ValueSet/" + vsid.getIdPart() + "/$expand");
@@ -1673,42 +1658,40 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 	@AfterClass
 	public static void afterClass() throws Exception {
 		ourServer.stop();
-		ourAppCtx.stop();
 		ourHttpClient.close();
 	}
 
-	@SuppressWarnings("unchecked")
+	@After
-	@BeforeClass
+	public void after() {
-	public static void beforeClass() throws Exception {
+		myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
+	}
+
+	@SuppressWarnings({ "unchecked", "rawtypes" })
+	@Before
+	public void before() throws Exception {
+		myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		myFhirCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+
+		if (ourServer == null) {
 			ourPort = RandomServerPortProvider.findFreePort();
 
-		RestfulServer restServer = new RestfulServer(ourCtx);
+			RestfulServer restServer = new RestfulServer(myFhirCtx);
-		restServer.setFhirContext(ourCtx);
 
 			ourServerBase = "http://localhost:" + ourPort + "/fhir/context";
 
-		ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu2.xml", "fhir-jpabase-spring-test-config.xml");
+			restServer.setResourceProviders((List)myResourceProviders);
-
-		ourDaoConfig = (DaoConfig) ourAppCtx.getBean(DaoConfig.class);
-
-		ourOrganizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDaoDstu2", IFhirResourceDao.class);
-
-		List<IResourceProvider> rpsDev = (List<IResourceProvider>) ourAppCtx.getBean("myResourceProvidersDstu2", List.class);
-		restServer.setResourceProviders(rpsDev);
 
 			restServer.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 
-		JpaSystemProviderDstu2 systemProv = ourAppCtx.getBean(JpaSystemProviderDstu2.class, "mySystemProviderDstu2");
+			restServer.setPlainProviders(mySystemProvider);
-		restServer.setPlainProviders(systemProv);
 
-		IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle> systemDao = ourAppCtx.getBean(IFhirSystemDao.class);
+			JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(restServer, mySystemDao);
-		JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(restServer, systemDao);
 			confProvider.setImplementationDescription("THIS IS THE DESC");
 			restServer.setServerConformanceProvider(confProvider);
 
 			restServer.setPagingProvider(new FifoMemoryPagingProvider(10));
 
-		ourServer = new Server(ourPort);
+			Server server = new Server(ourPort);
 
 			ServletContextHandler proxyHandler = new ServletContextHandler();
 			proxyHandler.setContextPath("/");
@@ -1717,12 +1700,10 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 			servletHolder.setServlet(restServer);
 			proxyHandler.addServlet(servletHolder, "/fhir/context/*");
 
-		ourServer.setHandler(proxyHandler);
+			server.setHandler(proxyHandler);
-		ourServer.start();
+			server.start();
 
-		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+			ourClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
-		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
 			ourClient.registerInterceptor(new LoggingInterceptor(true));
 
 			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
@@ -1730,6 +1711,8 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
 			builder.setConnectionManager(connectionManager);
 			ourHttpClient = builder.build();
 
+			ourServer = server;
+		}
 	}
 
 }

src/changes/changes.xml

@@ -186,6 +186,9 @@
 				JPA server now correctly suppresses contents of deleted resources
 				in history
 			</action>
+			<action type="fix" issue="222">
+				JPA server returned deleted resources in search results when using the _tag, _id, _profile, or _security search parameters
+			</action>
 		</release>
 		<release version="1.1" date="2015-07-13">
 			<action type="add">

src/site/xdoc/doc_validation.xml

@@ -26,7 +26,7 @@
 				<li>
 					<b>Resource Validation</b>
 					is validation of the parsed (or constructed) resource against
-					the official FHIR validation rules (e.g. Schema/Schematron).
+					the official FHIR validation rules (e.g. Schema/Schematron/Profile/StructureDefinition/ValueSet).
 				</li>
 			</ul>