Merge remote-tracking branch 'jamesagnew/master' into cleanup2

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/GenericClient.java

@@ -1889,8 +1889,12 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			}
 
 			for (Include next : myRevInclude) {
+				if (next.isRecurse()) {
+					addParam(params, Constants.PARAM_REVINCLUDE_RECURSE, next.getValue());
+				} else {
 					addParam(params, Constants.PARAM_REVINCLUDE, next.getValue());
 				}
+			}
 
 			if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU2)) {
 				SortSpec rootSs = null;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/Constants.java

@@ -40,11 +40,13 @@ public class Constants {
 	public static final String CT_HTML = "text/html";
 	public static final String CT_HTML_WITH_UTF8 = "text/html" + CHARSET_UTF8_CTSUFFIX;
 	public static final String CT_JSON = "application/json";
+	public static final String CT_JSON_PATCH = "application/json-patch+json";
 	public static final String CT_OCTET_STREAM = "application/octet-stream";
 	public static final String CT_TEXT = "text/plain";
 	public static final String CT_TEXT_WITH_UTF8 = CT_TEXT + CHARSET_UTF8_CTSUFFIX;
 	public static final String CT_X_FORM_URLENCODED = "application/x-www-form-urlencoded";
 	public static final String CT_XML = "application/xml";
+	public static final String CT_XML_PATCH = "application/xml-patch+xml";
 	public static final String ENCODING_GZIP = "gzip";
 	public static final String EXTOP_VALIDATE = "$validate";
 	public static final String EXTOP_VALIDATE_MODE = "mode";
@@ -61,10 +63,10 @@ public class Constants {
 	public static final String FORMATS_HTML_XML = "html/xml";
 	public static final String HEADER_ACCEPT = "Accept";
 	public static final String HEADER_ACCEPT_ENCODING = "Accept-Encoding";
+	public static final String HEADER_ACCEPT_VALUE_JSON_NON_LEGACY = CT_FHIR_JSON_NEW + ";q=1.0, " + CT_FHIR_JSON + ";q=0.9";
+	public static final String HEADER_ACCEPT_VALUE_XML_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_XML + ";q=0.9";
 	public static final String HEADER_ACCEPT_VALUE_XML_OR_JSON_LEGACY = CT_FHIR_XML + ";q=1.0, " + CT_FHIR_JSON + ";q=1.0";
 	public static final String HEADER_ACCEPT_VALUE_XML_OR_JSON_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_JSON_NEW + ";q=1.0, " + HEADER_ACCEPT_VALUE_XML_OR_JSON_LEGACY.replace("1.0", "0.9");
-	public static final String HEADER_ACCEPT_VALUE_XML_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_XML + ";q=0.9";
-	public static final String HEADER_ACCEPT_VALUE_JSON_NON_LEGACY = CT_FHIR_JSON_NEW + ";q=1.0, " + CT_FHIR_JSON + ";q=0.9";
 	public static final String HEADER_ALLOW = "Allow";
 	public static final String HEADER_AUTHORIZATION = "Authorization";
 	public static final String HEADER_AUTHORIZATION_VALPREFIX_BASIC = "Basic ";
@@ -127,10 +129,12 @@ public class Constants {
 	public static final String PARAM_PAGINGACTION = "_getpages";
 	public static final String PARAM_PAGINGOFFSET = "_getpagesoffset";
 	public static final String PARAM_PRETTY = "_pretty";
+	public static final String PARAM_PRETTY_VALUE_FALSE = "false";
 	public static final String PARAM_PRETTY_VALUE_TRUE = "true";
 	public static final String PARAM_PROFILE = "_profile";
 	public static final String PARAM_QUERY = "_query";
 	public static final String PARAM_REVINCLUDE = "_revinclude";
+	public static final String PARAM_REVINCLUDE_RECURSE = PARAM_REVINCLUDE+PARAM_INCLUDE_QUALIFIER_RECURSE;
 	public static final String PARAM_SEARCH = "_search";
 	public static final String PARAM_SECURITY = "_security";
 	public static final String PARAM_SINCE = "_since";
@@ -156,11 +160,11 @@ public class Constants {
 	public static final int STATUS_HTTP_401_CLIENT_UNAUTHORIZED = 401;
 	public static final int STATUS_HTTP_403_FORBIDDEN = 403;
 	public static final int STATUS_HTTP_404_NOT_FOUND = 404;
+	
 	public static final int STATUS_HTTP_405_METHOD_NOT_ALLOWED = 405;
 	public static final int STATUS_HTTP_409_CONFLICT = 409;
 	public static final int STATUS_HTTP_410_GONE = 410;
 	public static final int STATUS_HTTP_412_PRECONDITION_FAILED = 412;
-	
 	public static final int STATUS_HTTP_422_UNPROCESSABLE_ENTITY = 422;
 	public static final int STATUS_HTTP_500_INTERNAL_ERROR = 500;
 	public static final int STATUS_HTTP_501_NOT_IMPLEMENTED = 501;
@@ -168,9 +172,6 @@ public class Constants {
 	public static final String TAG_SUBSETTED_SYSTEM = "http://hl7.org/fhir/v3/ObservationValue";
 	public static final String URL_TOKEN_HISTORY = "_history";
 	public static final String URL_TOKEN_METADATA = "metadata";
-	public static final String CT_JSON_PATCH = "application/json-patch+json";
-	public static final String CT_XML_PATCH = "application/xml-patch+xml";
-	public static final String PARAM_PRETTY_VALUE_FALSE = "false";
 
 	static {
 		CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java

@@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
 
 import java.util.Collection;
 
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -84,6 +85,7 @@ public class ParametersUtil {
 	}
 
 	public static IBaseParameters newInstance(FhirContext theContext) {
+		Validate.notNull(theContext, "theContext must not be null");
 		return (IBaseParameters) theContext.getResourceDefinition("Parameters").newInstance();
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java

@@ -101,6 +101,7 @@ public class BaseDstu2Config extends BaseConfig {
 	public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 systemProviderDstu2() {
 		ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2();
 		retVal.setDao(systemDaoDstu2());
+		retVal.setContext(fhirContextDstu2());
 		return retVal;
 	}
 

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

@@ -22,29 +22,15 @@ package ca.uhn.fhir.jpa.dao;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
 import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeSet;
 
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
 
 import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.*;
-import org.hl7.fhir.instance.model.api.IBaseCoding;
-import org.hl7.fhir.instance.model.api.IBaseMetaType;
-import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-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.beans.factory.annotation.Required;
 import org.springframework.transaction.PlatformTransactionManager;
@@ -59,42 +45,21 @@ import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
-import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.entity.BaseTag;
-import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
-import ca.uhn.fhir.jpa.entity.ResourceLink;
-import ca.uhn.fhir.jpa.entity.ResourceTable;
-import ca.uhn.fhir.jpa.entity.TagDefinition;
-import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
-import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.*;
-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.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.method.MethodUtil;
+import ca.uhn.fhir.rest.method.*;
-import ca.uhn.fhir.rest.method.QualifiedParamList;
-import ca.uhn.fhir.rest.method.RequestDetails;
-import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
-import ca.uhn.fhir.rest.method.SearchMethodBinding;
 import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
 import ca.uhn.fhir.rest.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.*;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
-import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.FhirTerser;
@@ -110,14 +75,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired
 	private DaoConfig myDaoConfig;
 	@Autowired
-	protected IResourceTableDao myResourceTableDao;
-	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
 	private IResourceHistoryTableDao myResourceHistoryTableDao;
 	@Autowired()
 	protected IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
 	private String myResourceName;
+	@Autowired
+	protected IResourceTableDao myResourceTableDao;
 	private Class<T> myResourceType;
 	@Autowired(required = false)
 	protected IFulltextSearchSvc mySearchDao;
@@ -227,6 +192,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		validateOkToDelete(deleteConflicts, entity);
 		
+		preDelete(resourceToDelete);
+		
 		// Notify interceptors
 		if (theRequestDetails != null) {
 			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theId.getResourceType(), theId);
@@ -259,8 +226,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
+		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+		String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, w.getMillis());
+		String severity = "information";
+		String code = "informational";
+		OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
+
 		ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
-		return toMethodOutcome(savedEntity, null);
+		DaoMethodOutcome retVal = toMethodOutcome(savedEntity, null);
+		retVal.setOperationOutcome(oo);
+		return retVal;
 	}
 
 	@Override
@@ -320,7 +295,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
 		} else {
 			oo = OperationOutcomeUtil.newInstance(getContext());
-			String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", theUrl, deletedResources.size(), w.getMillis());
+			String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
 			String severity = "information";
 			String code = "informational";
 			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
@@ -553,6 +528,38 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
+	@Override
+	public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequestDetails) {
+		// Notify interceptors
+		ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId);
+		notifyInterceptors(RestOperationTypeEnum.META_DELETE, requestDetails);
+
+		StopWatch w = new StopWatch();
+		BaseHasResource entity = readEntity(theResourceId);
+		if (entity == null) {
+			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;
+	}
+
 	// @Override
 	// public IBundleProvider everything(IIdType theId) {
 	// Search search = new Search();
@@ -635,38 +642,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	// };
 	// }
 
-	@Override
-	public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequestDetails) {
-		// Notify interceptors
-		ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId);
-		notifyInterceptors(RestOperationTypeEnum.META_DELETE, requestDetails);
-
-		StopWatch w = new StopWatch();
-		BaseHasResource entity = readEntity(theResourceId);
-		if (entity == null) {
-			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;
-	}
-
 	@Override
 	public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequestDetails) {
 		// Notify interceptors
@@ -743,6 +718,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	}
 
+	/**
+	 * Subclasses may override to provide behaviour. Invoked within a delete
+	 * transaction with the resource that is about to be deleted. 
+	 */
+	protected void preDelete(T theResourceToDelete) {
+		// nothing by default
+	}
+
 	/**
 	 * May be overridden by subclasses to validate resources prior to storage
 	 * 

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

@@ -27,6 +27,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.locks.ReentrantLock;
 
 import javax.persistence.Query;
 import javax.persistence.Tuple;
@@ -64,15 +65,17 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class);
 
-	@Autowired
-	private PlatformTransactionManager myTxManager;
-
 	@Autowired
 	private IForcedIdDao myForcedIdDao;
 
+	private ReentrantLock myReindexLock = new ReentrantLock(false);
+
 	@Autowired
 	private ITermConceptDao myTermConceptDao;
 
+	@Autowired
+	private PlatformTransactionManager myTxManager;
+
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public void deleteAllTagsOnServer(RequestDetails theRequestDetails) {
@@ -205,8 +208,14 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 	@Transactional()
 	@Override
 	public int markAllResourcesForReindexing() {
+		
+		ourLog.info("Marking all resources as needing reindexing");
 		int retVal = myEntityManager.createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " t SET t.myIndexStatus = null").executeUpdate();
+		
+		ourLog.info("Marking all concepts as needing reindexing");
 		retVal += myTermConceptDao.markAllForReindexing();
+		
+		ourLog.info("Done marking reindexing");
 		return retVal;
 	}
 
@@ -270,12 +279,17 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 	@Override
 	@Transactional(propagation = Propagation.NOT_SUPPORTED)
 	public int performReindexingPass(final Integer theCount) {
+		if (!myReindexLock.tryLock()) {
+			return 0;
+		}
 		try {
 			return doPerformReindexingPass(theCount);
 		} catch (ReindexFailureException e) {
 			ourLog.warn("Reindexing failed for resource {}", e.getResourceId());
 			markResourceAsIndexingFailed(e.getResourceId());
 			return -1;
+		} finally {
+			myReindexLock.unlock();
 		}
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -492,7 +492,9 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
-			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, shouldUpdate, updateTime);
+			if (shouldUpdate) {
+				updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, true, updateTime);
+			}
 		}
 
 		myEntityManager.flush();

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

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.dao.data;
 
+import java.util.Collection;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -33,4 +35,7 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
 	@Modifying
 	void deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
 
+	@Query("SELECT t FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
+	Collection<TermConceptParentChildLink> findAllWithChild(@Param("child_pid") Long theConceptPid);
+	
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -41,6 +41,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@@ -187,6 +188,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 		return retVal;
 	}
 
+	@Autowired
+	private ITermCodeSystemVersionDao myCsvDao;
+	
 	@Override
 	protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 			boolean theUpdateVersion, Date theUpdateTime) {
@@ -198,12 +202,22 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 			String codeSystemUrl = cs.getUrl();
 			if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
 				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
-				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
+				
+				Long codeSystemResourcePid = retVal.getId();
+				TermCodeSystemVersion persCs = myCsvDao.findByCodeSystemResourceAndVersion(codeSystemResourcePid, retVal.getVersion());
+				if (persCs != null) {
+					ourLog.info("Code system version already exists in database");
+				} else {
+					
+					persCs = new TermCodeSystemVersion();
 					persCs.setResource(retVal);
 					persCs.setResourceVersionId(retVal.getVersion());
 					persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
+					ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
+					myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);
+					
+				}
 
-				myTerminologySvc.storeNewCodeSystemVersion(retVal.getId(), codeSystemUrl, persCs);
 			}
 		}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
+import java.util.List;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -33,6 +35,7 @@ import ca.uhn.fhir.jpa.dao.BaseSearchParamExtractor;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -45,12 +48,15 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 
 	private void markAffectedResources(SearchParameter theResource) {
-		String xpath = theResource.getXpath();
+		if (theResource != null) {
-		String resourceType = xpath.substring(0, xpath.indexOf('.'));
+			String expression = theResource.getExpression();
-		ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", xpath);
+			String resourceType = expression.substring(0, expression.indexOf('.'));
+			ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", expression);
 			int updatedCount = myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType);
 			ourLog.info("Marked {} resources for reindexing", updatedCount);
 		}
+	}
+
 
 	/**
 	 * This method is called once per minute to perform any required re-indexing. During most passes this will
@@ -77,13 +83,22 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 
 	}
 
+	@Override
+	protected void preDelete(SearchParameter theResourceToDelete) {
+		super.preDelete(theResourceToDelete);
+		markAffectedResources(theResourceToDelete);
+	}
+
+
 	@Override
 	protected void postPersist(ResourceTable theEntity, SearchParameter theResource) {
+		super.postPersist(theEntity, theResource);
 		markAffectedResources(theResource);
 	}
 
 	@Override
 	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource) {
+		super.postUpdate(theEntity, theResource);
 		markAffectedResources(theResource);
 	}
 
@@ -92,34 +107,34 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 		super.validateResourceForStorage(theResource, theEntityToSave);
 
 		if (theResource.getStatus() == null) {
-			throw new UnprocessableEntityException("Resource.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
+			throw new UnprocessableEntityException("SearchParameter.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
 		}
 
-		String xpath = theResource.getXpath();
+		String expression = theResource.getExpression();
-		if (isBlank(xpath)) {
+		if (isBlank(expression)) {
-			throw new UnprocessableEntityException("Resource.xpath is missing");
+			throw new UnprocessableEntityException("SearchParameter.expression is missing");
 		}
 
-		String[] xpathSplit = BaseSearchParamExtractor.SPLIT.split(xpath);
+		String[] expressionSplit = BaseSearchParamExtractor.SPLIT.split(expression);
 		String allResourceName = null;
-		for (String nextPath : xpathSplit) {
+		for (String nextPath : expressionSplit) {
 			int dotIdx = nextPath.indexOf('.');
 			if (dotIdx == -1) {
-				throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". Must start with a resource name");
+				throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\". Must start with a resource name");
 			}
 
 			String resourceName = nextPath.substring(0, dotIdx);
 			try {
 				getContext().getResourceDefinition(resourceName);
 			} catch (DataFormatException e) {
-				throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\": " + e.getMessage());
+				throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\": " + e.getMessage());
 			}
 
 			if (allResourceName == null) {
 				allResourceName = resourceName;
 			} else {
 				if (!allResourceName.equals(resourceName)) {
-					throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
+					throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
 				}
 			}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -383,7 +383,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
 				res.setId((String) null);
 				DaoMethodOutcome outcome;
-				outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails);
+				String matchUrl = nextReqEntry.getRequest().getIfNoneExist();
+				outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
 				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
 				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				if (outcome.getCreated() == false) {
@@ -489,7 +490,9 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 			IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
 			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
-			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, shouldUpdate, shouldUpdate, updateTime);
+			if (shouldUpdate) {
+				updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, shouldUpdate, true, updateTime);
+			}
 		}
 
 		myEntityManager.flush();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java

@@ -155,7 +155,7 @@ public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
 	private RuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
 		String name = theNextSp.getCode();
 		String description = theNextSp.getDescription();
-		String path = theNextSp.getXpath();
+		String path = theNextSp.getExpression();
 		RestSearchParameterTypeEnum paramType = null;
 		RuntimeSearchParamStatusEnum status = null;
 		switch (theNextSp.getType()) {

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

@@ -233,6 +233,7 @@ public class TermConcept implements Serializable {
 	@PreUpdate
 	@PrePersist
 	public void prePersist() {
+		if (myParentPids == null) {
 			Set<Long> parentPids = new HashSet<Long>();
 			TermConcept entity = this;
 			parentPids(entity, parentPids);
@@ -240,6 +241,7 @@ public class TermConcept implements Serializable {
 	
 			ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
 		}
+	}
 
 	public void setCode(String theCode) {
 		myCode = theCode;
@@ -280,6 +282,10 @@ public class TermConcept implements Serializable {
 		myParentPids = b.toString();
 	}
 
+	public void setParentPids(String theParentPids) {
+		myParentPids = theParentPids;
+	}
+
 	@Override
 	public String toString() {
 		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();

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

@@ -44,6 +44,9 @@ public class TermConceptParentChildLink implements Serializable {
 	@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
 	private TermConcept myChild;
 
+	@Column(name = "CHILD_PID", insertable = false, updatable = false)
+	private Long myChildPid;
+
 	@ManyToOne()
 	@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
 	private TermCodeSystemVersion myCodeSystem;
@@ -52,6 +55,9 @@ public class TermConceptParentChildLink implements Serializable {
 	@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
 	private TermConcept myParent;
 
+	@Column(name = "PARENT_PID", insertable = false, updatable = false)
+	private Long myParentPid;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_PC_PID", sequenceName = "SEQ_CONCEPT_PC_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PC_PID")
@@ -62,51 +68,6 @@ public class TermConceptParentChildLink implements Serializable {
 	@Column(name = "REL_TYPE", length = 5, nullable = true)
 	private RelationshipTypeEnum myRelationshipType;
 
-	public TermConcept getChild() {
-		return myChild;
-	}
-
-	public RelationshipTypeEnum getRelationshipType() {
-		return myRelationshipType;
-	}
-
-	public TermCodeSystemVersion getCodeSystem() {
-		return myCodeSystem;
-	}
-	
-	public TermConcept getParent() {
-		return myParent;
-	}
-
-	public void setChild(TermConcept theChild) {
-		myChild = theChild;
-	}
-	
-	public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
-		myCodeSystem = theCodeSystem;
-	}
-
-	public void setParent(TermConcept theParent) {
-		myParent = theParent;
-	}
-	
-	
-	public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
-		myRelationshipType = theRelationshipType;
-	}
-
-
-	@Override
-	public int hashCode() {
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
-		result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
-		result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
-		result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
-		return result;
-	}
-
 	@Override
 	public boolean equals(Object obj) {
 		if (this == obj)
@@ -136,15 +97,64 @@ public class TermConceptParentChildLink implements Serializable {
 		return true;
 	}
 
+	public TermConcept getChild() {
+		return myChild;
+	}
+
+	public Long getChildPid() {
+		return myChildPid;
+	}
+
+	public TermCodeSystemVersion getCodeSystem() {
+		return myCodeSystem;
+	}
+
+	public Long getId() {
+		return myPid;
+	}
+
+	public TermConcept getParent() {
+		return myParent;
+	}
+
+	public Long getParentPid() {
+		return myParentPid;
+	}
+
+	public RelationshipTypeEnum getRelationshipType() {
+		return myRelationshipType;
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
+		result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
+		result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
+		result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
+		return result;
+	}
+
+	public void setChild(TermConcept theChild) {
+		myChild = theChild;
+	}
+
+	public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
+		myCodeSystem = theCodeSystem;
+	}
+
+	public void setParent(TermConcept theParent) {
+		myParent = theParent;
+	}
+
+	public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
+		myRelationshipType = theRelationshipType;
+	}
 
 	public enum RelationshipTypeEnum {
 		// ********************************************
 		// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
 		ISA
 	}
-
-
-	public Long getId() {
-		return myPid;
-	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java

@@ -23,9 +23,11 @@ package ca.uhn.fhir.jpa.term;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
 
@@ -33,6 +35,7 @@ import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
@@ -45,7 +48,10 @@ import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Stopwatch;
+import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.Multimaps;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
@@ -66,6 +72,7 @@ import ca.uhn.fhir.util.ObjectUtil;
 import ca.uhn.fhir.util.ValidateUtil;
 
 public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
+	private static boolean ourForceSaveDeferredAlwaysForUnitTest;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvc.class);
 	private static final Object PLACEHOLDER_OBJECT = new Object();
 
@@ -94,8 +101,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
 	
-	private boolean myProcessDeferred = true;
 	private long myNextReindexPass;
+	private boolean myProcessDeferred = true;
+
+	@Autowired
+	private PlatformTransactionManager myTransactionMgr;
 
 	private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
 		boolean retVal = theSetToPopulate.add(theConcept);
@@ -108,6 +118,25 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return retVal;
 	}
 
+	private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
+		ourLog.trace("Checking {} parents", theParents.size());
+		int retVal = 0;
+		
+		for (TermConceptParentChildLink nextLink : theParents) {
+			if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
+				TermConcept nextParent = nextLink.getParent();
+				retVal += ensureParentsSaved(nextParent.getParents());
+				if (nextParent.getId() == null) {
+					myConceptDao.saveAndFlush(nextParent);
+					retVal++;
+					ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
+				}
+			}
+		}
+		
+		return retVal;
+	}
+
 	private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
 		for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
 			TermConcept nextChild = nextChildLink.getChild();
@@ -175,6 +204,15 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return retVal;
 	}
 
+	/**
+	 * Subclasses may override
+	 * @param theSystem The code system
+	 * @param theCode The code
+	 */
+	protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
+		return Collections.emptyList();
+	}
+
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
@@ -206,7 +244,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
 		return retVal;
 	}
-
 	/**
 	 * Subclasses may override
 	 * @param theSystem The code system
@@ -216,15 +253,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return Collections.emptyList();
 	}
 	
-	/**
-	 * Subclasses may override
-	 * @param theSystem The code system
-	 * @param theCode The code
-	 */
-	protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
-		return Collections.emptyList();
-	}
-
 	private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
 		TermCodeSystem cs = getCodeSystem(theCodeSystem);
 		if (cs == null || cs.getCurrentVersion() == null) {
@@ -233,6 +261,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		TermCodeSystemVersion csv = cs.getCurrentVersion();
 		return csv;
 	}
+
 	private TermCodeSystem getCodeSystem(String theSystem) {
 		TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
 		return cs;
@@ -271,15 +300,99 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		
 	}
 
-	private void saveConceptLink(TermConceptParentChildLink next) {
+	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
-		if (next.getId() == null) {
+		if (theNext.getCodeSystem() != null) {
-			myConceptParentChildLinkDao.save(next);
+			return;
 		}
+		theNext.setCodeSystem(theCodeSystemVersion);
+		for (TermConceptParentChildLink next : theNext.getChildren()) {
+			populateVersion(next.getChild(), theCodeSystemVersion);
+		}
+	}
+
+	private ArrayListMultimap<Long, Long> myChildToParentPidCache;
+	
+	private void processReindexing() {
+		if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
+			return;
+		}
+		
+		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
+		tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		tt.execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
+				int maxResult = 1000;
+				Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
+				if (concepts.hasContent() == false) {
+					myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
+					myChildToParentPidCache = null;
+					return;
+				}
+
+				if (myChildToParentPidCache == null) {
+					myChildToParentPidCache = ArrayListMultimap.create();
+				}
+				
+				ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
+
+				int count = 0;
+				StopWatch stopwatch = new StopWatch();
+
+				for (TermConcept nextConcept : concepts) {
+					
+					StringBuilder parentsBuilder = new StringBuilder();
+					createParentsString(parentsBuilder, nextConcept.getId());
+					nextConcept.setParentPids(parentsBuilder.toString());
+					
+					saveConcept(nextConcept);
+					count++;
+				}
+				
+				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
+			}
+
+			private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
+				Validate.notNull(theConceptPid, "theConceptPid must not be null");
+				List<Long> parents = myChildToParentPidCache.get(theConceptPid);
+				if (parents.contains(-1L)) {
+					return;
+				} else if (parents.isEmpty()) {
+					Collection<TermConceptParentChildLink> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
+					if (parentLinks.isEmpty()) {
+						myChildToParentPidCache.put(theConceptPid, -1L);
+						return;
+					} else {
+						for (TermConceptParentChildLink next : parentLinks) {
+							myChildToParentPidCache.put(theConceptPid, next.getParentPid());
+						}
+					}
+				}
+				
+				
+				for (Long nextParent : parents) {
+					if (theParentsBuilder.length() > 0) {
+						theParentsBuilder.append(' ');
+					}
+					theParentsBuilder.append(nextParent);
+					createParentsString(theParentsBuilder, nextParent);
+				}
+			}
+		});
+
 	}
 
 	private int saveConcept(TermConcept theConcept) {
 		int retVal = 0;
+	
+		/*
+		 * If the concept has an ID, we're reindexing, so there's no need to
+		 * save parent concepts first (it's way too slow to do that)
+		 */
+		if (theConcept.getId() == null) {
 			retVal += ensureParentsSaved(theConcept.getParents());
+		}
+		
 		if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
 			retVal++;
 			theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
@@ -290,32 +403,9 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return retVal;
 	}
 	
-	private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
+	private void saveConceptLink(TermConceptParentChildLink next) {
-		ourLog.trace("Checking {} parents", theParents.size());
+		if (next.getId() == null) {
-		int retVal = 0;
+			myConceptParentChildLinkDao.save(next);
-		
-		for (TermConceptParentChildLink nextLink : theParents) {
-			if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
-				TermConcept nextParent = nextLink.getParent();
-				retVal += ensureParentsSaved(nextParent.getParents());
-				if (nextParent.getId() == null) {
-					myConceptDao.saveAndFlush(nextParent);
-					retVal++;
-					ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
-				}
-			}
-		}
-		
-		return retVal;
-	}
-
-	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
-		if (theNext.getCodeSystem() != null) {
-			return;
-		}
-		theNext.setCodeSystem(theCodeSystemVersion);
-		for (TermConceptParentChildLink next : theNext.getChildren()) {
-			populateVersion(next.getChild(), theCodeSystemVersion);
 		}
 	}
 
@@ -369,42 +459,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		}
 	}
 	
-	@Autowired
-	private PlatformTransactionManager myTransactionMgr;
-	
-	private void processReindexing() {
-		if (System.currentTimeMillis() < myNextReindexPass) {
-			return;
-		}
-		
-		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
-		tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
-		tt.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
-				int maxResult = 1000;
-				Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
-				if (resources.hasContent() == false) {
-					myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
-					return;
-				}
-
-				ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
-
-				int count = 0;
-				StopWatch stopwatch = new StopWatch();
-
-				for (TermConcept resourceTable : resources) {
-					saveConcept(resourceTable);
-					count++;
-				}
-				
-				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
-			}
-		});
-
-	}
-
 	@Override
 	public void setProcessDeferred(boolean theProcessDeferred) {
 		myProcessDeferred = theProcessDeferred;
@@ -470,7 +524,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 			totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
 		}
 
-		ourLog.info("Saving version");
+		ourLog.info("Saving version containing {} concepts", totalCodeCount);
 
 		TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
 
@@ -547,4 +601,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		return retVal;
 	}
 
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting
+	public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
+		ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.term;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
@@ -64,6 +65,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -159,7 +161,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 	}
 
 	private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
-		//@formatter:off
 		Query textQuery = qb
 				.phrase()
 				.withSlop(2)
@@ -169,7 +170,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 				// .andField("myDisplayPhonetic").boostedTo(0.5f)
 				.sentence(nextFilter.getValue().toLowerCase()).createQuery();
 		bool.must(textQuery);
-		//@formatter:on
 	}
 
 	@Override
@@ -216,10 +216,18 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 			bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
 
 			for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
-				if (isNotBlank(nextFilter.getValue())) {
+				if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
+					continue;
+				}
+
+				if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
+					throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
+				}
+				
+				
 				if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
 					addDisplayFilterExact(qb, bool, nextFilter);
-					} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
+				} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
 					if (nextFilter.getValue().trim().contains(" ")) {
 						addDisplayFilterExact(qb, bool, nextFilter);
 					} else {
@@ -237,14 +245,18 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 					throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
 				}
 			}
-			}
 
 			Query luceneQuery = bool.createQuery();
 			FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
 			jpaQuery.setMaxResults(1000);
 
+			StopWatch sw = new StopWatch();
+			
 			@SuppressWarnings("unchecked")
 			List<TermConcept> result = jpaQuery.getResultList();
+			
+			ourLog.info("Expansion completed in {}ms", sw.getMillis());
+			
 			for (TermConcept nextConcept : result) {
 				addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
 			}
@@ -259,7 +271,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
 			}
 		}
 
-
 		return retVal;
 	}
 

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

@@ -19,10 +19,12 @@ import static org.mockito.Mockito.verify;
 
 import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Test;
@@ -73,6 +75,43 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
 
+	/**
+	 * Per a message on the mailing list
+	 */
+	@Test
+	public void testTransactionWithPostDoesntUpdate() throws Exception {
+
+		// First bundle (name is Joshua)
+		
+		String input = IOUtils.toString(getClass().getResource("/dstu3-post1.xml"), StandardCharsets.UTF_8);
+		Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
+		Bundle response = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
+		
+		assertEquals(1, response.getEntry().size());
+		assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
+		assertEquals("1", response.getEntry().get(0).getResponse().getEtag());
+		String id = response.getEntry().get(0).getResponse().getLocation();
+		
+		// Now the second (name is Adam, shouldn't get used)
+		
+		input = IOUtils.toString(getClass().getResource("/dstu3-post2.xml"), StandardCharsets.UTF_8);
+		request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
+		response = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
+		
+		assertEquals(1, response.getEntry().size());
+		assertEquals("200 OK", response.getEntry().get(0).getResponse().getStatus());
+		assertEquals("1", response.getEntry().get(0).getResponse().getEtag());
+		String id2 = response.getEntry().get(0).getResponse().getLocation();
+		assertEquals(id, id2);
+		
+		Patient patient = myPatientDao.read(new IdType(id), mySrd);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
+		assertEquals("Joshua", patient.getNameFirstRep().getGivenAsSingleString());
+	}
+
+	
 	@Test
 	public void testReindexing() {
 		Patient p = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java

@@ -0,0 +1,44 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import static org.junit.Assert.assertNotEquals;
+
+import java.nio.charset.StandardCharsets;
+
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
+import ca.uhn.fhir.util.TestUtil;
+
+public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3CodeSystemTest.class);
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+		BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
+	}
+
+	
+	@Test
+	public void testIndexContained() throws Exception {
+		BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
+		
+		String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
+		CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
+		myCodeSystemDao.create(cs, mySrd);
+
+		
+		mySystemDao.markAllResourcesForReindexing();
+
+		int outcome = mySystemDao.performReindexingPass(100);
+		assertNotEquals(-1, outcome); // -1 means there was a failure
+		
+		myTermSvc.saveDeferred();
+		
+	}
+
+	
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java

@@ -1,8 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.junit.Assert.assertThat;
-
 import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Reference;
@@ -11,9 +8,6 @@ import org.junit.AfterClass;
 import org.junit.Test;
 
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.param.TokenParamModifier;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
@@ -18,6 +19,7 @@ import org.junit.Test;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 
@@ -30,14 +32,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("PatientFoo.gender");
+		fooSp.setExpression("PatientFoo.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		try {
 			mySearchParameterDao.create(fooSp, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Invalid path value \"PatientFoo.gender\": Unknown resource name \"PatientFoo\" (this name is not known in FHIR version \"DSTU3\")", e.getMessage());
+			assertEquals("Invalid SearchParameter.expression value \"PatientFoo.gender\": Unknown resource name \"PatientFoo\" (this name is not known in FHIR version \"DSTU3\")", e.getMessage());
 		}
 	}
 
@@ -47,14 +49,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender or Observation.code");
+		fooSp.setExpression("Patient.gender or Observation.code");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		try {
 			mySearchParameterDao.create(fooSp, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Invalid path value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
+			assertEquals("Invalid SearchParameter.expression value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
 		}
 	}
 
@@ -70,7 +72,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 			mySearchParameterDao.create(fooSp, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Resource.xpath is missing", e.getMessage());
+			assertEquals("SearchParameter.expression is missing", e.getMessage());
 		}
 	}
 
@@ -80,14 +82,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("gender");
+		fooSp.setExpression("gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		try {
 			mySearchParameterDao.create(fooSp, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Invalid path value \"gender\". Must start with a resource name", e.getMessage());
+			assertEquals("Invalid SearchParameter.expression value \"gender\". Must start with a resource name", e.getMessage());
 		}
 	}
 
@@ -98,14 +100,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(null);
 		try {
 			mySearchParameterDao.create(fooSp, mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("Resource.status is missing or invalid: null", e.getMessage());
+			assertEquals("SearchParameter.status is missing or invalid: null", e.getMessage());
 		}
 
 	}
@@ -117,10 +119,10 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
-		mySearchParameterDao.create(fooSp, mySrd);
+		IIdType spId = mySearchParameterDao.create(fooSp, mySrd).getId().toUnqualifiedVersionless();
 
 		mySearchParamRegsitry.forceRefresh();
 
@@ -150,6 +152,17 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		foundResources = toUnqualifiedVersionlessIdValues(results);
 		assertThat(foundResources, contains(patId.getValue()));
 
+		// Delete the param
+		mySearchParameterDao.delete(spId, mySrd);
+		
+		mySearchParamRegsitry.forceRefresh();
+		mySystemDao.performReindexingPass(100);
+
+		// Try with custom gender SP
+		map = new SearchParameterMap();
+		map.add("foo", new TokenParam(null, "male"));
+		IBundleProvider res = myPatientDao.search(map);
+		assertEquals(0, res.size());
 	}
 
 	@Test
@@ -159,7 +172,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.DRAFT);
 		mySearchParameterDao.create(fooSp, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -26,7 +26,9 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
@@ -34,6 +36,8 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
@@ -52,6 +56,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 	@After
 	public void after() {
 		myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
+		
+		BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
 	}
 
 	@Before
@@ -318,6 +324,71 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testExpandWithIsAInExternalValueSet() {
+		createExternalCsAndLocalVs();
+
+		ValueSet vs = new ValueSet();
+		ConceptSetComponent include = vs.getCompose().addInclude();
+		include.setSystem(URL_MY_CODE_SYSTEM);
+		include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
+
+		ValueSet result = myValueSetDao.expand(vs, null);
+		logAndValidateValueSet(result);
+
+		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
+		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+
+	}
+
+	@Autowired
+	private IHapiTerminologySvc myHapiTerminologySvc;
+	
+	@Test
+	public void testExpandWithIsAInExternalValueSetReindex() {
+		BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
+		
+		createExternalCsAndLocalVs();
+
+		mySystemDao.markAllResourcesForReindexing();
+
+		mySystemDao.performReindexingPass(100);
+		mySystemDao.performReindexingPass(100);
+		myHapiTerminologySvc.saveDeferred();
+		myHapiTerminologySvc.saveDeferred();
+		myHapiTerminologySvc.saveDeferred();
+		
+		ValueSet vs = new ValueSet();
+		ConceptSetComponent include = vs.getCompose().addInclude();
+		include.setSystem(URL_MY_CODE_SYSTEM);
+		include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
+
+		ValueSet result = myValueSetDao.expand(vs, null);
+		logAndValidateValueSet(result);
+
+		ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
+		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
+
+	}
+
+	@Test
+	public void testExpandInvalid() {
+		createExternalCsAndLocalVs();
+
+		ValueSet vs = new ValueSet();
+		ConceptSetComponent include = vs.getCompose().addInclude();
+		include.setSystem(URL_MY_CODE_SYSTEM);
+		include.addFilter();
+		include.addFilter().setOp(FilterOperator.ISA).setValue("childAA");
+
+		try {
+			myValueSetDao.expand(vs, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid filter, must have fields populated: property op value", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testExpandWithSystemAndCodesInExternalValueSet() {
 		createExternalCsAndLocalVs();

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

@@ -382,6 +382,42 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
+	/**
+	 * Per a message on the mailing list
+	 */
+	@Test
+	public void testTransactionWithPostDoesntUpdate() throws Exception {
+
+		// First bundle (name is Joshua)
+		
+		String input = IOUtils.toString(getClass().getResource("/dstu3-post1.xml"), StandardCharsets.UTF_8);
+		Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
+		Bundle response = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
+		
+		assertEquals(1, response.getEntry().size());
+		assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
+		assertEquals("1", response.getEntry().get(0).getResponse().getEtag());
+		String id = response.getEntry().get(0).getResponse().getLocation();
+		
+		// Now the second (name is Adam, shouldn't get used)
+		
+		input = IOUtils.toString(getClass().getResource("/dstu3-post2.xml"), StandardCharsets.UTF_8);
+		request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
+		response = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
+		
+		assertEquals(1, response.getEntry().size());
+		assertEquals("200 OK", response.getEntry().get(0).getResponse().getStatus());
+		assertEquals("1", response.getEntry().get(0).getResponse().getEtag());
+		String id2 = response.getEntry().get(0).getResponse().getLocation();
+		assertEquals(id, id2);
+		
+		Patient patient = myPatientDao.read(new IdType(id), mySrd);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
+		assertEquals("Joshua", patient.getNameFirstRep().getGivenAsSingleString());
+	}
+
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -10,6 +10,7 @@ import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
@@ -139,7 +140,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		get.addHeader("Accept", "application/xml, text/html");
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
-			String response = IOUtils.toString(http.getEntity().getContent());
+			String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(response);
 			assertThat(response, (containsString("_format=json")));
 			assertEquals(200, http.getStatusLine().getStatusCode());
@@ -167,7 +168,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		get.addHeader("Accept", "application/xml+fhir");
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
-			String response = IOUtils.toString(http.getEntity().getContent());
+			String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(response);
 			assertThat(response, not(containsString("_format")));
 			assertEquals(200, http.getStatusLine().getStatusCode());
@@ -216,7 +217,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
 			assertEquals(200, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			
 			Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@@ -246,7 +247,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'context' must be provided"));
 		} finally {
@@ -257,7 +258,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'searchParam' must be provided"));
 		} finally {
@@ -268,7 +269,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'text' must be provided"));
 		} finally {
@@ -286,7 +287,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	@Test
 	public void testTransactionFromBundle() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 	}
@@ -295,7 +296,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	public void testTransactionFromBundle2() throws Exception {
 
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 
@@ -311,7 +312,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		 */
 
 		bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
-		bundle = IOUtils.toString(bundleRes);
+		bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 
@@ -335,7 +336,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	public void testTransactionFromBundle3() throws Exception {
 
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/grahame-transaction.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 	}
@@ -343,7 +344,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	@Test
 	public void testTransactionFromBundle4() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 		Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@@ -358,7 +359,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	@Test
 	public void testTransactionFromBundle5() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle2.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		try {
 			ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 			fail();
@@ -372,7 +373,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	@Test
 	public void testTransactionFromBundle6() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		// try {
 		// fail();
@@ -427,5 +428,18 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		assertEquals(0, respSub.getEntry().size());
 	}
 
+	@Test
+	public void testMarkResourcesForReindexing() throws Exception {
+		HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(output);
+			assertEquals(200, http.getStatusLine().getStatusCode());
+		} finally {
+			IOUtils.closeQuietly(http);;
+		}
+	}
+
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java

@@ -58,7 +58,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 	public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
 		SearchParameter sp = new SearchParameter();
 		sp.setCode("foo");
-		sp.setXpath("Patient.gender");
+		sp.setExpression("Patient.gender");
 		sp.setXpathUsage(XPathUsageType.NORMAL);
 		sp.setTitle("Foo Param");
 
@@ -66,7 +66,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 			ourClient.create().resource(sp).execute();
 			fail();
 		} catch (UnprocessableEntityException e) {
-			assertEquals("HTTP 422 Unprocessable Entity: Resource.status is missing or invalid: null", e.getMessage());
+			assertEquals("HTTP 422 Unprocessable Entity: SearchParameter.status is missing or invalid: null", e.getMessage());
 		}
 	}
 
@@ -100,7 +100,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -110,7 +110,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("gender");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("Gender");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -152,7 +152,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -162,7 +162,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("gender");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("Gender");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -206,7 +206,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -232,6 +232,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 				.where(new TokenClientParam("foo").exactly().code("male"))
 				.returnBundle(Bundle.class)
 				.execute();
+		
 		foundResources = toUnqualifiedVersionlessIdValues(result);
 		assertThat(foundResources, contains(patId.getValue()));
 
@@ -256,7 +257,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Patient.gender");
+		fooSp.setExpression("Patient.gender");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(fooSp, mySrd);
@@ -276,7 +277,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 		fooSp.setCode("foo");
 		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.REFERENCE);
 		fooSp.setTitle("FOO SP");
-		fooSp.setXpath("Observation.subject");
+		fooSp.setExpression("Observation.subject");
 		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
 		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
 		mySearchParameterDao.create(fooSp, mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -161,7 +161,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		myDaoConfig.setAllowMultipleDelete(true);
 	}
 
-	
 	private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
 		HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
 		CloseableHttpResponse resp = ourHttpClient.execute(get);
@@ -674,7 +673,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		String encoded = myFhirCtx.newXmlParser().encodeResourceToString(response);
 		ourLog.info(encoded);
 		assertThat(encoded, containsString(
-				"<issue><severity value=\"information\"/><code value=\"informational\"/><diagnostics value=\"Successfully deleted Patient?identifier=testDeleteConditionalMultiple resource(s) in 2ms\"/></issue>"));
+				"<issue><severity value=\"information\"/><code value=\"informational\"/><diagnostics value=\"Successfully deleted 2 resource(s) in "));
 		try {
 			ourClient.read().resource("Patient").withId(id1).execute();
 			fail();
@@ -726,7 +725,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 	 * Test for #345
 	 */
 	@Test
-	public void testDeleteNormal() throws IOException {
+	public void testDeleteNormal() {
 		Patient p = new Patient();
 		p.addName().setFamily("FAM");
 		IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
@@ -743,6 +742,17 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 	}
 
+	@Test
+	public void testDeleteReturnsOperationOutcome() {
+		Patient p = new Patient();
+		p.addName().setFamily("FAM");
+		IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+
+		IBaseOperationOutcome resp = ourClient.delete().resourceById(id).execute();
+		OperationOutcome oo = (OperationOutcome) resp;
+		assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
+	}
+
 	@Test
 	public void testDeleteResourceConditional1() throws IOException {
 		String methodName = "testDeleteResourceConditional1";
@@ -768,6 +778,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		response = ourHttpClient.execute(delete);
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
 		} finally {
 			response.close();
 		}
@@ -777,6 +791,24 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		try {
 			ourLog.info(response.toString());
 			assertEquals(Constants.STATUS_HTTP_410_GONE, response.getStatusLine().getStatusCode());
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Resource was deleted at"));
+		} finally {
+			response.close();
+		}
+
+		// Delete should now have no matches
+		
+		delete = new HttpDelete(ourServerBase + "/Patient?name=" + methodName);
+		response = ourHttpClient.execute(delete);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
+			assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Unable to find resource matching URL \"Patient?name=testDeleteResourceConditional1\". Deletion failed."));
 		} finally {
 			response.close();
 		}
@@ -1781,7 +1813,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info("Response: {}", respString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, respString);
-			assertEquals("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"AAA\" does not match URL ID of \"" + id.getIdPart() + "\"", oo.getIssue().get(0).getDiagnostics());
+			assertEquals(
+					"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"AAA\" does not match URL ID of \""
+							+ id.getIdPart() + "\"",
+					oo.getIssue().get(0).getDiagnostics());
 		} finally {
 			response.close();
 		}
@@ -1814,7 +1849,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		p.getManagingOrganization().setReference("http://example.com/Organization/123");
 		ourClient.create().resource(p).execute();
 
-		
 		Bundle b = ourClient.search().forResource("Patient").include(Patient.INCLUDE_ORGANIZATION).returnBundle(Bundle.class).execute();
 		assertEquals(1, b.getEntry().size());
 	}
@@ -1834,7 +1868,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 	}
 
-	
 	@Test
 	public void testMetadataSuperParamsAreIncluded() throws IOException {
 		StructureDefinition p = new StructureDefinition();
@@ -2102,7 +2135,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		String respString = ourClient.transaction().withBundle(input).prettyPrint().execute();
 		ourLog.info(respString);
 
-		ourHttpClient.execute(new HttpGet("http://localhost:" + ourPort + "/QuestionnaireResponse?patient=QR3295&questionnaire=profile&_sort:desc=authored&_count=5&_include=QuestionnaireResponse:questionnaire&_include=QuestionnaireResponse:subject"));
+		ourHttpClient.execute(new HttpGet("http://localhost:" + ourPort
+				+ "/QuestionnaireResponse?patient=QR3295&questionnaire=profile&_sort:desc=authored&_count=5&_include=QuestionnaireResponse:questionnaire&_include=QuestionnaireResponse:subject"));
 		// Bundle bundle =
 	}
 
@@ -3445,7 +3479,9 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
-			assertEquals("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"A2\"", oo.getIssue().get(0).getDiagnostics());
+			assertEquals(
+					"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"A2\"",
+					oo.getIssue().get(0).getDiagnostics());
 		} finally {
 			response.close();
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java

@@ -129,7 +129,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		
 		CloseableHttpResponse resp = ourHttpClient.execute(req);
 		try {
-			String encoded = IOUtils.toString(resp.getEntity().getContent());
+			String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(encoded);
 
 			assertThat(encoded, containsString("transaction-response")); 
@@ -162,7 +162,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		
 		CloseableHttpResponse resp = ourHttpClient.execute(req);
 		try {
-			String encoded = IOUtils.toString(resp.getEntity().getContent());
+			String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(encoded);
 
 			assertThat(encoded, containsString("transaction-response"));
@@ -271,14 +271,14 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		try {
 	
 			InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
-			String bundleStr = IOUtils.toString(bundleRes);
+			String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 	
 			HttpPost req = new HttpPost(ourServerBase);
 			req.setEntity(new StringEntity(bundleStr, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
 			
 			CloseableHttpResponse resp = ourHttpClient.execute(req);
 			try {
-				String encoded = IOUtils.toString(resp.getEntity().getContent());
+				String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
 				ourLog.info(encoded);
 	
 				//@formatter:off
@@ -314,7 +314,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 
 		try {
-			String response = IOUtils.toString(http.getEntity().getContent());
+			String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(response);
 			assertThat(response, containsString("_format=json"));
 			assertEquals(200, http.getStatusLine().getStatusCode());
@@ -342,7 +342,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		get.addHeader("Accept", "application/xml+fhir");
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
-			String response = IOUtils.toString(http.getEntity().getContent());
+			String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(response);
 			assertThat(response, not(containsString("_format")));
 			assertEquals(200, http.getStatusLine().getStatusCode());
@@ -373,7 +373,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertEquals(200, http.getStatusLine().getStatusCode());
 		} finally {
@@ -404,7 +404,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
 			assertEquals(200, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 
 			Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@@ -434,7 +434,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		CloseableHttpResponse http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'context' must be provided"));
 		} finally {
@@ -445,7 +445,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'searchParam' must be provided"));
 		} finally {
@@ -456,7 +456,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		http = ourHttpClient.execute(get);
 		try {
 			assertEquals(400, http.getStatusLine().getStatusCode());
-			String output = IOUtils.toString(http.getEntity().getContent());
+			String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 			assertThat(output, containsString("Parameter 'text' must be provided"));
 		} finally {
@@ -500,7 +500,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 	public void testTransactionFromBundle2() throws Exception {
 
 		InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 
@@ -516,7 +516,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		 */
 
 		bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
-		bundle = IOUtils.toString(bundleRes);
+		bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 
@@ -540,7 +540,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 	public void testTransactionFromBundle3() throws Exception {
 
 		InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/grahame-transaction.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 	}
@@ -548,7 +548,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 	@Test
 	public void testTransactionFromBundle4() throws Exception {
 		InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
 		Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@@ -563,7 +563,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 	@Test
 	public void testTransactionFromBundle5() throws Exception {
 		InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle2.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		try {
 			ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 			fail();
@@ -577,7 +577,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 	@Test
 	public void testTransactionFromBundle6() throws Exception {
 		InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle3.xml");
-		String bundle = IOUtils.toString(bundleRes);
+		String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
 		ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		// try {
 		// fail();

hapi-fhir-jpaserver-base/src/test/resources/dstu3-post1.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Bundle xmlns="http://hl7.org/fhir">
+    <type value="transaction"/>
+    <entry>
+        <resource>
+           <Patient>
+                <id value="ID613876"/>
+                <identifier>
+                    <value value="ID613876"/>
+                </identifier>
+                <name>
+                    <given value="Joshua"/>
+                </name>
+            </Patient>
+        </resource>      
+	<request>
+		<method value="POST"/>
+		<url value="Patient/ID613876"/>
+		<ifNoneExist value="identifier=ID613876"/>
+	</request>
+    </entry>
+</Bundle>

hapi-fhir-jpaserver-base/src/test/resources/dstu3-post2.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Bundle xmlns="http://hl7.org/fhir">
+    <type value="transaction"/>
+    <entry>
+        <resource>
+           <Patient>
+                <id value="ID613876"/>
+                <identifier>
+                    <value value="ID613876"/>
+                </identifier>
+                <name>
+                    <given value="Adam"/>
+                </name>
+            </Patient>
+        </resource>      
+	<request>
+		<method value="POST"/>
+		<url value="Patient/ID613876"/>
+		<ifNoneExist value="identifier=ID613876"/>
+	</request>
+    </entry>
+</Bundle>

hapi-fhir-jpaserver-base/src/test/resources/dstu3_codesystem_complete.json

@@ -0,0 +1,27 @@
+{
+	"resourceType": "CodeSystem",
+	"id": "22472",
+	"meta": {
+		"versionId": "3",
+		"lastUpdated": "2017-01-27T10:53:39.457-05:00"
+	},
+	"url": "xvalue://dedalus.eu/mci/CodeSystem/AddressUse",
+	"name": "AddressUse",
+	"status": "active",
+	"publisher": "x1v1-mci",
+	"date": "2016-04-07",
+	"description": "AddressUse",
+	"caseSensitive": true,
+	"compositional": false,
+	"versionNeeded": false,
+	"content": "complete",
+	"concept": {
+		"code": "work",
+		"display": "Work",
+		"definition": "An office address. First choice for business related contacts during business hours.",
+		"designation": {
+			"language": "IT",
+			"value": "Lavoro"
+		}
+	}
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -25,7 +25,9 @@ import java.nio.charset.StandardCharsets;
 import java.text.SimpleDateFormat;
 import java.util.*;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
 import org.custommonkey.xmlunit.Diff;
 import org.custommonkey.xmlunit.XMLUnit;
 import org.hamcrest.collection.IsEmptyCollection;
@@ -76,6 +78,24 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
+	/**
+	 * See #551
+	 */
+	@Test
+	public void testXmlLargeAttribute() {
+		String largeString = StringUtils.leftPad("", (int) FileUtils.ONE_MB, 'A');
+		
+		Patient p = new Patient();
+		p.addName().setFamily(largeString);
+		
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
+		
+		p = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+		
+		assertEquals(largeString, p.getNameFirstRep().getFamily());
+	}
+	
+	
 	/**
 	 * See #544
 	 */

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java

@@ -120,6 +120,26 @@ public class GenericClientDstu3Test {
 		return capt;
 	}
 
+	@Test
+	public void testRevIncludeRecursive() throws ClientProtocolException, IOException {
+		ArgumentCaptor<HttpUriRequest> capt = prepareClientForSearchResponse();
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+		int idx = 0;
+
+		client.search()
+				.forResource(EpisodeOfCare.class)
+				.where(EpisodeOfCare.PATIENT.hasId("123"))
+				.revInclude(Encounter.INCLUDE_EPISODEOFCARE)
+				.revInclude(Observation.INCLUDE_ENCOUNTER.asRecursive())
+				.returnBundle(Bundle.class)
+				.execute();
+
+		assertEquals("http://example.com/fhir/EpisodeOfCare?patient=123&_revinclude=Encounter%3Aepisodeofcare&_revinclude%3Arecurse=Observation%3Aencounter", capt.getAllValues().get(idx).getURI().toString());
+		idx++;
+
+	}
+
 	@Test
 	public void testPatchJsonByIdString() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -157,6 +177,7 @@ public class GenericClientDstu3Test {
 		OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
+
 	@Test
 	public void testPatchJsonByIdType() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -194,6 +215,7 @@ public class GenericClientDstu3Test {
 		OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
+
 	@Test
 	public void testPatchJsonByConditionalString() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -231,6 +253,7 @@ public class GenericClientDstu3Test {
 		OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
+
 	@Test
 	public void testPatchJsonByConditionalParam() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -269,6 +292,7 @@ public class GenericClientDstu3Test {
 		OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
+
 	@Test
 	public void testPatchJsonByConditionalParamResourceType() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -307,6 +331,7 @@ public class GenericClientDstu3Test {
 		OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
 		assertThat(oo.getText().getDivAsString(), containsString("OK!"));
 	}
+
 	@Test
 	public void testPatchXmlByIdString() throws Exception {
 		OperationOutcome conf = new OperationOutcome();
@@ -481,8 +506,6 @@ public class GenericClientDstu3Test {
 
 	}
 
-	
-	
 	@SuppressWarnings("unchecked")
 	@Test
 	public void testClientFailures() throws Exception {
@@ -1743,7 +1766,6 @@ public class GenericClientDstu3Test {
 			assertEquals("Unable to determing encoding of request (body does not appear to be valid XML or JSON)", e.getMessage());
 		}
 
-
 	}
 
 	@Test
@@ -2051,7 +2073,6 @@ public class GenericClientDstu3Test {
 		patient.getText().setDivAsString("OK!");
 		b.addEntry().setResource(patient);
 
-		
 		final String respString = p.encodeResourceToString(b);
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
@@ -2082,8 +2103,6 @@ public class GenericClientDstu3Test {
 		assertEquals(expectedUserAgent(), capt.getAllValues().get(0).getHeaders("User-Agent")[0].getValue());
 	}
 
-	
-	
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/SearchDefaultMethodDstu3Test.java

@@ -1,8 +1,7 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.either;
-import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.oneOf;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
@@ -65,7 +64,7 @@ public class SearchDefaultMethodDstu3Test {
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
 
-			assertThat(ourLastMethod, either(equalTo("search01")).or(equalTo("search02")));
+			assertThat(ourLastMethod, oneOf("search01", "search02", "search03"));
 			assertEquals(null, ourLastParam1);
 			assertEquals(null, ourLastParam2);
 			assertEquals(null, ourLastAdditionalParams);

src/changes/changes.xml

@@ -123,6 +123,21 @@
 				Clean up dependencies and remove Eclipse project files from git. Thanks to
 				@sekaijin for the pull request!
 			</action>
+			<action type="fix">
+				When performing a conditional create in a transaction in JPA server, 
+				if a resource already existed matching the conditional expression, the 
+				server did not change the version of the resource but did update the body
+				with the passed in body. Thanks to Artem Sopin for reporting and providing a test
+				case for this!
+			</action>
+			<action type="fix">
+				Client revincludes did not include the :recurse modifier. Thanks to
+				Jenny Meinsma for pointing this out on Zulip!
+			</action>
+			<action type="add">
+				JPA server did not return an OperationOutcome in the response for
+				a normal delete operation.
+			</action>
 		</release>
 		<release version="2.2" date="2016-12-20">
 			<action type="add">