Remove duplicate resource body creation (Merge branch 'optimize_jpa')

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  * http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -913,104 +913,123 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	/**
 	 * Returns true if the resource has changed (either the contents or the tags)
 	 */
-	protected boolean populateResourceIntoEntity(IBaseResource theResource, ResourceTable theEntity, boolean theUpdateHash) {
-		theEntity.setResourceType(toResourceName(theResource));
+	protected EncodedResource populateResourceIntoEntity(IBaseResource theResource, ResourceTable theEntity, boolean theUpdateHash) {
+		if (theEntity.getResourceType() == null) {
+			theEntity.setResourceType(toResourceName(theResource));
+		}
 
-		List<BaseResourceReferenceDt> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class);
-		for (BaseResourceReferenceDt nextRef : refs) {
-			if (nextRef.getReference().isEmpty() == false) {
-				if (nextRef.getReference().hasVersionIdPart()) {
-					nextRef.setReference(nextRef.getReference().toUnqualifiedVersionless());
+		if (theResource != null) {
+			List<BaseResourceReferenceDt> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class);
+			for (BaseResourceReferenceDt nextRef : refs) {
+				if (nextRef.getReference().isEmpty() == false) {
+					if (nextRef.getReference().hasVersionIdPart()) {
+						nextRef.setReference(nextRef.getReference().toUnqualifiedVersionless());
+					}
 				}
 			}
 		}
 
-		ResourceEncodingEnum encoding = myConfig.getResourceEncoding();
-
-		IParser parser = encoding.newParser(myContext);
-		parser.setDontEncodeElements(EXCLUDE_ELEMENTS_IN_ENCODED);
-		String encoded = parser.encodeResourceToString(theResource);
-
-		theEntity.setEncoding(encoding);
-		theEntity.setFhirVersion(myContext.getVersion().getVersion());
 		byte[] bytes;
-		switch (encoding) {
-			case JSON:
-				bytes = encoded.getBytes(Charsets.UTF_8);
-				break;
-			default:
-			case JSONC:
-				bytes = GZipUtil.compress(encoded);
-				break;
-		}
-
-		ourLog.debug("Encoded {} chars of resource body as {} bytes", encoded.length(), bytes.length);
-
+		ResourceEncodingEnum encoding;
 		boolean changed = false;
 
-		if (theUpdateHash) {
-			HashFunction sha256 = Hashing.sha256();
-			String hashSha256 = sha256.hashBytes(bytes).toString();
-			if (hashSha256.equals(theEntity.getHashSha256()) == false) {
+		if (theEntity.getDeleted() == null) {
+
+			encoding = myConfig.getResourceEncoding();
+			IParser parser = encoding.newParser(myContext);
+			parser.setDontEncodeElements(EXCLUDE_ELEMENTS_IN_ENCODED);
+			String encoded = parser.encodeResourceToString(theResource);
+
+			theEntity.setFhirVersion(myContext.getVersion().getVersion());
+			switch (encoding) {
+				case JSON:
+					bytes = encoded.getBytes(Charsets.UTF_8);
+					break;
+				default:
+				case JSONC:
+					bytes = GZipUtil.compress(encoded);
+					break;
+			}
+
+			ourLog.debug("Encoded {} chars of resource body as {} bytes", encoded.length(), bytes.length);
+
+			if (theUpdateHash) {
+				HashFunction sha256 = Hashing.sha256();
+				String hashSha256 = sha256.hashBytes(bytes).toString();
+				if (hashSha256.equals(theEntity.getHashSha256()) == false) {
+					changed = true;
+				}
+				theEntity.setHashSha256(hashSha256);
+			}
+
+			Set<TagDefinition> allDefs = new HashSet<>();
+
+			theEntity.setHasTags(false);
+
+			Set<TagDefinition> allTagsOld = getAllTagDefinitions(theEntity);
+
+			if (theResource instanceof IResource) {
+				extractTagsHapi((IResource) theResource, theEntity, allDefs);
+			} else {
+				extractTagsRi((IAnyResource) theResource, theEntity, allDefs);
+			}
+
+			RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
+			if (def.isStandardType() == false) {
+				String profile = def.getResourceProfile("");
+				if (isNotBlank(profile)) {
+					TagDefinition tag = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
+					if (tag != null) {
+						allDefs.add(tag);
+						theEntity.addTag(tag);
+						theEntity.setHasTags(true);
+					}
+				}
+			}
+
+			ArrayList<ResourceTag> existingTags = new ArrayList<>();
+			if (theEntity.isHasTags()) {
+				existingTags.addAll(theEntity.getTags());
+			}
+			for (ResourceTag next : existingTags) {
+				TagDefinition nextDef = next.getTag();
+				if (!allDefs.contains(nextDef)) {
+					if (shouldDroppedTagBeRemovedOnUpdate(theEntity, next)) {
+						theEntity.getTags().remove(next);
+					}
+				}
+			}
+
+			Set<TagDefinition> allTagsNew = getAllTagDefinitions(theEntity);
+			if (!allTagsOld.equals(allTagsNew)) {
 				changed = true;
 			}
-			theEntity.setHashSha256(hashSha256);
+
+		} else {
+			theEntity.setHashSha256(null);
+			bytes = null;
+			encoding = ResourceEncodingEnum.DEL;
 		}
 
 		if (changed == false) {
-			if (theEntity.getResource() == null) {
+			if (theEntity.getId() == null) {
 				changed = true;
 			} else {
-				changed = !Arrays.equals(theEntity.getResource(), bytes);
-			}
-		}
-
-		theEntity.setResource(bytes);
-
-		Set<TagDefinition> allDefs = new HashSet<>();
-
-		theEntity.setHasTags(false);
-
-		Set<TagDefinition> allTagsOld = getAllTagDefinitions(theEntity);
-
-		if (theResource instanceof IResource) {
-			extractTagsHapi((IResource) theResource, theEntity, allDefs);
-		} else {
-			extractTagsRi((IAnyResource) theResource, theEntity, allDefs);
-		}
-
-		RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
-		if (def.isStandardType() == false) {
-			String profile = def.getResourceProfile("");
-			if (isNotBlank(profile)) {
-				TagDefinition tag = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
-				if (tag != null) {
-					allDefs.add(tag);
-					theEntity.addTag(tag);
-					theEntity.setHasTags(true);
+				ResourceHistoryTable currentHistoryVersion = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
+				if (currentHistoryVersion == null || currentHistoryVersion.getResource() == null) {
+					changed = true;
+				} else {
+					changed = !Arrays.equals(currentHistoryVersion.getResource(), bytes);
 				}
 			}
 		}
 
-		ArrayList<ResourceTag> existingTags = new ArrayList<>();
-		if (theEntity.isHasTags()) {
-			existingTags.addAll(theEntity.getTags());
-		}
-		for (ResourceTag next : existingTags) {
-			TagDefinition nextDef = next.getTag();
-			if (!allDefs.contains(nextDef)) {
-				if (shouldDroppedTagBeRemovedOnUpdate(theEntity, next)) {
-					theEntity.getTags().remove(next);
-				}
-			}
-		}
+		EncodedResource retVal = new EncodedResource();
+		retVal.setEncoding(encoding);
+		retVal.setResource(bytes);
+		retVal.setChanged(changed);
 
-		Set<TagDefinition> allTagsNew = getAllTagDefinitions(theEntity);
-		if (!allTagsOld.equals(allTagsNew)) {
-			changed = true;
-		}
-
-		return changed;
+		return retVal;
 	}
 
 	@SuppressWarnings("unchecked")
@@ -1183,6 +1202,17 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		throw new NotImplementedException("");
 	}
 
+	private <T> Collection<T> removeCommon(Collection<T> theInput, Collection<T> theToRemove) {
+		assert theInput != theToRemove;
+
+		if (theInput.isEmpty()) {
+			return theInput;
+		}
+
+		ArrayList<T> retVal = new ArrayList<>(theInput);
+		retVal.removeAll(theToRemove);
+		return retVal;
+	}
 	private void setUpdatedTime(Collection<? extends BaseResourceIndexedSearchParam> theParams, Date theUpdateTime) {
 		for (BaseResourceIndexedSearchParam nextSearchParam : theParams) {
 			nextSearchParam.setUpdated(theUpdateTime);
@@ -1219,17 +1249,34 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@SuppressWarnings("unchecked")
 	@Override
 	public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
+
+		ResourceHistoryTable history;
+		if (theEntity instanceof ResourceHistoryTable) {
+			history = (ResourceHistoryTable) theEntity;
+		} else {
+			history = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
+		}
+
+		if (history == null) {
+			return null;
+		}
+
+		byte[] resourceBytes = history.getResource();
+		ResourceEncodingEnum resourceEncoding = history.getEncoding();
+
 		String resourceText = null;
-		switch (theEntity.getEncoding()) {
+		switch (resourceEncoding) {
 			case JSON:
 				try {
-					resourceText = new String(theEntity.getResource(), "UTF-8");
+					resourceText = new String(resourceBytes, "UTF-8");
 				} catch (UnsupportedEncodingException e) {
 					throw new Error("Should not happen", e);
 				}
 				break;
 			case JSONC:
-				resourceText = GZipUtil.decompress(theEntity.getResource());
+				resourceText = GZipUtil.decompress(resourceBytes);
+				break;
+			case DEL:
 				break;
 		}
 
@@ -1253,27 +1300,34 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 		}
 
-		IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
-		parser.setParserErrorHandler(new LenientErrorHandler(false).setErrorOnInvalidValue(false));
-
 		R retVal;
-		try {
-			retVal = parser.parseResource(resourceType, resourceText);
-		} catch (Exception e) {
-			StringBuilder b = new StringBuilder();
-			b.append("Failed to parse database resource[");
-			b.append(resourceType);
-			b.append("/");
-			b.append(theEntity.getIdDt().getIdPart());
-			b.append(" (pid ");
-			b.append(theEntity.getId());
-			b.append(", version ");
-			b.append(theEntity.getFhirVersion().name());
-			b.append("): ");
-			b.append(e.getMessage());
-			String msg = b.toString();
-			ourLog.error(msg, e);
-			throw new DataFormatException(msg, e);
+		if (resourceEncoding != ResourceEncodingEnum.DEL) {
+			IParser parser = resourceEncoding.newParser(getContext(theEntity.getFhirVersion()));
+			parser.setParserErrorHandler(new LenientErrorHandler(false).setErrorOnInvalidValue(false));
+
+			try {
+				retVal = parser.parseResource(resourceType, resourceText);
+			} catch (Exception e) {
+				StringBuilder b = new StringBuilder();
+				b.append("Failed to parse database resource[");
+				b.append(resourceType);
+				b.append("/");
+				b.append(theEntity.getIdDt().getIdPart());
+				b.append(" (pid ");
+				b.append(theEntity.getId());
+				b.append(", version ");
+				b.append(theEntity.getFhirVersion().name());
+				b.append("): ");
+				b.append(e.getMessage());
+				String msg = b.toString();
+				ourLog.error(msg, e);
+				throw new DataFormatException(msg, e);
+			}
+
+		} else {
+
+			retVal = (R) myContext.getResourceDefinition(theEntity.getResourceType()).newInstance();
+
 		}
 
 		if (retVal instanceof IResource) {
@@ -1283,6 +1337,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			IAnyResource res = (IAnyResource) retVal;
 			retVal = populateResourceMetadataRi(resourceType, theEntity, theForHistoryOperation, res);
 		}
+
+
 		return retVal;
 	}
 
@@ -1290,11 +1346,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return myContext.getResourceDefinition(theResourceType).getName();
 	}
 
-	protected String toResourceName(IBaseResource theResource) {
+	String toResourceName(IBaseResource theResource) {
 		return myContext.getResourceDefinition(theResource).getName();
 	}
 
-	protected Long translateForcedIdToPid(String theResourceName, String theResourceId) {
+	Long translateForcedIdToPid(String theResourceName, String theResourceId) {
 		return translateForcedIdToPids(new IdDt(theResourceName, theResourceId), myForcedIdDao).get(0);
 	}
 
@@ -1302,7 +1358,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return translateForcedIdToPids(theId, myForcedIdDao);
 	}
 
-	protected String translatePidIdToForcedId(String theResourceType, Long theId) {
+	private String translatePidIdToForcedId(String theResourceType, Long theId) {
 		ForcedId forcedId = myForcedIdDao.findByResourcePid(theId);
 		if (forcedId != null) {
 			return forcedId.getResourceType() + '/' + forcedId.getForcedId();
@@ -1385,7 +1441,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		Set<ResourceLink> links = null;
 
 		Set<String> populatedResourceLinkParameters = Collections.emptySet();
-		boolean changed;
+		EncodedResource changed;
 		if (theDeletedTimestampOrNull != null) {
 
 			stringParams = Collections.emptySet();
@@ -1403,7 +1459,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			theEntity.setNarrativeTextParsedIntoWords(null);
 			theEntity.setContentTextParsedIntoWords(null);
 			theEntity.setHashSha256(null);
-			changed = true;
+			changed = populateResourceIntoEntity(theResource, theEntity, true);
 
 		} else {
 
@@ -1555,7 +1611,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 		}
 
-		if (!changed && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
+		if (!changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
 			ourLog.info("Resource {} has not changed", theEntity.getIdDt().toUnqualified().getValue());
 			if (theResource != null) {
 				populateResourceIdFromEntity(theEntity, theResource);
@@ -1586,6 +1642,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			postUpdate(theEntity, (T) theResource);
 		}
 
+		/*
+		 * Create history entry
+		 */
+		if (theCreateNewHistoryEntry) {
+			final ResourceHistoryTable historyEntry = theEntity.toHistory();
+//			if (theEntity.getVersion() > 1) {
+//				existing = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
+//				ourLog.warn("Reusing existing history entry entity {}", theEntity.getIdDt().getValue());
+//			}
+			historyEntry.setEncoding(changed.getEncoding());
+			historyEntry.setResource(changed.getResource());
+
+			ourLog.info("Saving history entry {}", historyEntry.getIdDt());
+			myResourceHistoryTableDao.save(historyEntry);
+		}
+
 		/*
 		 * Update the "search param present" table which is used for the
 		 * ?foo:missing=true queries
@@ -1612,22 +1684,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			mySearchParamPresenceSvc.updatePresence(theEntity, presentSearchParams);
 		}
 
-		/*
-		 * Create history entry
-		 */
-		if (theCreateNewHistoryEntry) {
-
-			ResourceHistoryTable existing = null;
-//			if (theEntity.getVersion() > 1) {
-//				existing = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
-//				ourLog.warn("Reusing existing history entry entity {}", theEntity.getIdDt().getValue());
-//			}
-			final ResourceHistoryTable historyEntry = theEntity.toHistory(existing);
-
-			ourLog.info("Saving history entry {}", historyEntry.getIdDt());
-			myResourceHistoryTableDao.save(historyEntry);
-		}
-
 		/*
 		 * Indexing
 		 */
@@ -1728,19 +1784,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return theEntity;
 	}
 
-	private <T> Collection<T> removeCommon(Collection<T> theInput, Collection<T> theToRemove) {
-		assert theInput != theToRemove;
-
-		if (theInput.isEmpty()) {
-			return theInput;
-		}
-
-		ArrayList<T> retVal = new ArrayList<>(theInput);
-		retVal.removeAll(theToRemove);
-		return retVal;
-	}
-
-
 	protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable entity, Date theDeletedTimestampOrNull, Date theUpdateTime) {
 		return updateEntity(theResource, entity, theDeletedTimestampOrNull, true, true, theUpdateTime, false, true);
 	}
@@ -1883,19 +1926,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	 * parameters across a set of search parameters. An example of why
 	 * this is needed:
 	 * <p>
-	 *    Let's say we have a unique index on (Patient:gender AND Patient:name).
-	 *    Then we pass in <code>SMITH, John</code> with a gender of <code>male</code>.
+	 * Let's say we have a unique index on (Patient:gender AND Patient:name).
+	 * Then we pass in <code>SMITH, John</code> with a gender of <code>male</code>.
 	 * </p>
 	 * <p>
-	 *		In this case, because the name parameter matches both first and last name,
-	 *		we now need two unique indexes:
-	 *	<ul>
-	 *	   <li>Patient?gender=male&amp;name=SMITH</li>
-	 *	   <li>Patient?gender=male&amp;name=JOHN</li>
-	 *	</ul>
+	 * In this case, because the name parameter matches both first and last name,
+	 * we now need two unique indexes:
+	 * <ul>
+	 * <li>Patient?gender=male&amp;name=SMITH</li>
+	 * <li>Patient?gender=male&amp;name=JOHN</li>
+	 * </ul>
 	 * </p>
 	 * <p>
-	 *    So this recursive algorithm calculates those
+	 * So this recursive algorithm calculates those
 	 * </p>
 	 *
 	 * @param theResourceType E.g. <code>Patient
@@ -1921,8 +1964,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		Collections.sort(thePartsChoices, new Comparator<List<String>>() {
 			@Override
 			public int compare(List<String> o1, List<String> o2) {
-				String str1=null;
-				String str2=null;
+				String str1 = null;
+				String str2 = null;
 				if (o1.size() > 0) {
 					str1 = o1.get(0);
 				}
@@ -2007,10 +2050,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		/*
 		 * The following block of code is used to strip out diacritical marks from latin script
 		 * and also convert to upper case. E.g. "j?mes" becomes "JAMES".
-		 * 
+		 *
 		 * See http://www.unicode.org/charts/PDF/U0300.pdf for the logic
 		 * behind stripping 0300-036F
-		 * 
+		 *
 		 * See #454 for an issue where we were completely stripping non latin characters
 		 * See #832 for an issue where we normalize korean characters, which are decomposed
 		 */

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -51,6 +51,7 @@ import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ObjectUtil;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
+import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.*;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -75,6 +76,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
+	private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
@@ -84,7 +86,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired()
 	protected ISearchResultDao mySearchResultDao;
 	@Autowired
-	private DaoConfig myDaoConfig;
+	protected DaoConfig myDaoConfig;
 	@Autowired
 	private IResourceHistoryTableDao myResourceHistoryTableDao;
 	@Autowired
@@ -92,7 +94,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	private String myResourceName;
 	private Class<T> myResourceType;
 	private String mySecondaryPrimaryKeyParamName;
-
 	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
 
@@ -192,6 +193,25 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			throw new ResourceVersionConflictException("Trying to delete " + theId + " but this is not the current version");
 		}
 
+		// Don't delete again if it's already deleted
+		if (entity.getDeleted() != null) {
+			DaoMethodOutcome outcome = new DaoMethodOutcome();
+			outcome.setEntity(entity);
+
+			IIdType id = getContext().getVersion().newIdType();
+			id.setValue(entity.getIdDt().getValue());
+			outcome.setId(id);
+
+			IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+			String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, 0);
+			String severity = "information";
+			String code = "informational";
+			OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
+			outcome.setOperationOutcome(oo);
+
+			return outcome;
+		}
+
 		StopWatch w = new StopWatch();
 
 		T resourceToDelete = toResource(myResourceType, entity, false);
@@ -206,7 +226,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
-		validateOkToDelete(theDeleteConflicts, entity);
+		validateOkToDelete(theDeleteConflicts, entity, false);
 
 		preDelete(resourceToDelete, entity);
 
@@ -288,7 +308,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				}
 			}
 
-			validateOkToDelete(deleteConflicts, entity);
+			validateOkToDelete(deleteConflicts, entity, false);
 
 			// Notify interceptors
 			IdDt idToDelete = entity.getIdDt();
@@ -300,7 +320,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			// Perform delete
 			Date updateTime = new Date();
 			updateEntity(null, entity, updateTime, updateTime);
-	        resourceToDelete.setId(entity.getIdDt());
+			resourceToDelete.setId(entity.getIdDt());
 
 			// Notify JPA interceptors
 			if (theRequestDetails != null) {
@@ -1223,12 +1243,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		// Perform update
 		ResourceTable savedEntity = updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, new Date(), theForceUpdateVersion, thePerformIndexing);
 
-		/* 
+		/*
 		 * If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
 		 * we'll manually increase the version. This is important because we want the updated version number
 		 * to be reflected in the resource shared with interceptors
 		 */
-		if (!thePerformIndexing && !savedEntity.isUnchangedInCurrentOperation()) {
+		if (!thePerformIndexing && !savedEntity.isUnchangedInCurrentOperation() && !ourDisableIncrementOnUpdateForUnitTest) {
 			if (resourceId.hasVersionIdPart() == false) {
 				resourceId = resourceId.withVersion(Long.toString(savedEntity.getVersion()));
 			}
@@ -1260,7 +1280,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return outcome;
 	}
 
-
 	@Override
 	public DaoMethodOutcome update(T theResource, String theMatchUrl, boolean thePerformIndexing, RequestDetails theRequestDetails) {
 		return update(theResource, theMatchUrl, thePerformIndexing, false, theRequestDetails);
@@ -1304,7 +1323,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
-	protected void validateOkToDelete(List<DeleteConflict> theDeleteConflicts, ResourceTable theEntity) {
+	protected void validateOkToDelete(List<DeleteConflict> theDeleteConflicts, ResourceTable theEntity, boolean theForValidate) {
 		TypedQuery<ResourceLink> query = myEntityManager.createQuery("SELECT l FROM ResourceLink l WHERE l.myTargetResourcePid = :target_pid", ResourceLink.class);
 		query.setParameter("target_pid", theEntity.getId());
 		query.setMaxResults(1);
@@ -1313,7 +1332,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			return;
 		}
 
-		if (myDaoConfig.isEnforceReferentialIntegrityOnDelete() == false) {
+		if (myDaoConfig.isEnforceReferentialIntegrityOnDelete() == false && !theForValidate) {
 			ourLog.info("Deleting {} resource dependencies which can no longer be satisfied", resultList.size());
 			myResourceLinkDao.delete(resultList);
 			return;
@@ -1337,4 +1356,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 	}
 
+	@VisibleForTesting
+	public static void setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest) {
+		ourDisableIncrementOnUpdateForUnitTest = theDisableIncrementOnUpdateForUnitTest;
+	}
+
 }

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

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.dao;
+
+import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
+
+class EncodedResource {
+
+	private boolean myChanged;
+	private byte[] myResource;
+	private ResourceEncodingEnum myEncoding;
+
+	public ResourceEncodingEnum getEncoding() {
+		return myEncoding;
+	}
+
+	public void setEncoding(ResourceEncodingEnum theEncoding) {
+		myEncoding = theEncoding;
+	}
+
+	public byte[] getResource() {
+		return myResource;
+	}
+
+	public void setResource(byte[] theResource) {
+		myResource = theResource;
+	}
+
+	public boolean isChanged() {
+		return myChanged;
+	}
+
+	public void setChanged(boolean theChanged) {
+		myChanged = theChanged;
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java

@@ -80,7 +80,9 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
 			// Validate that there are no resources pointing to the candidate that
 			// would prevent deletion
 			List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
-			validateOkToDelete(deleteConflicts, entity);
+			if (myDaoConfig.isEnforceReferentialIntegrityOnDelete()) {
+				validateOkToDelete(deleteConflicts, entity, true);
+			}
 			validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
 			OperationOutcome oo = new OperationOutcome();

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

@@ -1587,6 +1587,10 @@ public class SearchBuilder implements ISearchBuilder {
 		for (ResourceTable next : resultList) {
 			Class<? extends IBaseResource> resourceType = context.getResourceDefinition(next.getResourceType()).getImplementingClass();
 			IBaseResource resource = theDao.toResource(resourceType, next, theForHistoryOperation);
+			if (resource == null) {
+				ourLog.warn("Unable to find resource {}/{}/_history/{} in database", next.getResourceType(), next.getIdDt().getIdPart(), next.getVersion());
+				continue;
+			}
 			Integer index = position.get(next.getId());
 			if (index == null) {
 				ourLog.warn("Got back unexpected resource PID {}", next.getId());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java

@@ -85,7 +85,9 @@ public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirRe
 			// Validate that there are no resources pointing to the candidate that
 			// would prevent deletion
 			List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
-			validateOkToDelete(deleteConflicts, entity);
+			if (myDaoConfig.isEnforceReferentialIntegrityOnDelete()) {
+				validateOkToDelete(deleteConflicts, entity, true);
+			}
 			validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
 			OperationOutcome oo = new OperationOutcome();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4.java

@@ -85,7 +85,9 @@ public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResou
 			// Validate that there are no resources pointing to the candidate that
 			// would prevent deletion
 			List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
-			validateOkToDelete(deleteConflicts, entity);
+			if (myDaoConfig.isEnforceReferentialIntegrityOnDelete()) {
+				validateOkToDelete(deleteConflicts, entity, true);
+			}
 			validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
 			OperationOutcome oo = new OperationOutcome();

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -36,11 +36,6 @@ public abstract class BaseHasResource {
 	@Temporal(TemporalType.TIMESTAMP)
 	private Date myDeleted;
 
-	@Column(name = "RES_ENCODING", nullable = false, length = 5)
-	@Enumerated(EnumType.STRING)
-	@OptimisticLock(excluded = true)
-	private ResourceEncodingEnum myEncoding;
-
 	@Column(name = "RES_VERSION", nullable = true, length = 7)
 	@Enumerated(EnumType.STRING)
 	@OptimisticLock(excluded = true)
@@ -60,11 +55,6 @@ public abstract class BaseHasResource {
 	@OptimisticLock(excluded = true)
 	private Date myPublished;
 
-	@Column(name = "RES_TEXT", length = Integer.MAX_VALUE - 1, nullable = false)
-	@Lob()
-	@OptimisticLock(excluded = true)
-	private byte[] myResource;
-
 	@Temporal(TemporalType.TIMESTAMP)
 	@Column(name = "RES_UPDATED", nullable = false)
 	@OptimisticLock(excluded = true)
@@ -80,13 +70,6 @@ public abstract class BaseHasResource {
 		myDeleted = theDate;
 	}
 
-	public ResourceEncodingEnum getEncoding() {
-		return myEncoding;
-	}
-
-	public void setEncoding(ResourceEncodingEnum theEncoding) {
-		myEncoding = theEncoding;
-	}
 
 	public FhirVersionEnum getFhirVersion() {
 		return myFhirVersion;
@@ -116,16 +99,8 @@ public abstract class BaseHasResource {
 		}
 	}
 
-	public void setPublished(InstantDt thePublished) {
-		myPublished = thePublished.getValue();
-	}
-
-	public byte[] getResource() {
-		return myResource;
-	}
-
-	public void setResource(byte[] theResource) {
-		myResource = theResource;
+	public void setPublished(Date thePublished) {
+		myPublished = thePublished;
 	}
 
 	public abstract String getResourceType();
@@ -136,8 +111,8 @@ public abstract class BaseHasResource {
 		return new InstantDt(myUpdated);
 	}
 
-	public void setUpdated(InstantDt theUpdated) {
-		myUpdated = theUpdated.getValue();
+	public void setUpdated(Date theUpdated) {
+		myUpdated = theUpdated;
 	}
 
 	public Date getUpdatedDate() {
@@ -154,12 +129,12 @@ public abstract class BaseHasResource {
 		myHasTags = theHasTags;
 	}
 
-	public void setPublished(Date thePublished) {
-		myPublished = thePublished;
+	public void setPublished(InstantDt thePublished) {
+		myPublished = thePublished.getValue();
 	}
 
-	public void setUpdated(Date theUpdated) {
-		myUpdated = theUpdated;
+	public void setUpdated(InstantDt theUpdated) {
+		myUpdated = theUpdated.getValue();
 	}
 
 }

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

@@ -25,11 +25,22 @@ import ca.uhn.fhir.parser.IParser;
 
 public enum ResourceEncodingEnum {
 
+	/*
+	 * NB: Constants in this enum must be 5 chars long or less!!!
+	 *
+	 * See ResourceHistoryTable RES_ENCODING column
+	 */
+
 	/** Json */
 	JSON,
 	
 	/** Json Compressed */
-	JSONC;
+	JSONC,
+
+	/**
+	 * Resource was deleted - No contents expected
+	 */
+	DEL;
 
 	public IParser newParser(FhirContext theContext) {
 		return theContext.newJsonParser();

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -20,23 +20,23 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.api.Constants;
+import org.hibernate.annotations.OptimisticLock;
+
+import javax.persistence.*;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
-import javax.persistence.*;
-
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.Constants;
-
 //@formatter:off
 @Entity
 @Table(name = "HFJ_RES_VER", uniqueConstraints = {
-	@UniqueConstraint(name="IDX_RESVER_ID_VER", columnNames = { "RES_ID", "RES_VER" }) 
-}, indexes= {
-	@Index(name="IDX_RESVER_TYPE_DATE", columnList="RES_TYPE,RES_UPDATED"), 
-	@Index(name="IDX_RESVER_ID_DATE", columnList="RES_ID,RES_UPDATED"), 
-	@Index(name="IDX_RESVER_DATE", columnList="RES_UPDATED") 
+	@UniqueConstraint(name = "IDX_RESVER_ID_VER", columnNames = {"RES_ID", "RES_VER"})
+}, indexes = {
+	@Index(name = "IDX_RESVER_TYPE_DATE", columnList = "RES_TYPE,RES_UPDATED"),
+	@Index(name = "IDX_RESVER_ID_DATE", columnList = "RES_ID,RES_UPDATED"),
+	@Index(name = "IDX_RESVER_DATE", columnList = "RES_UPDATED")
 })
 //@formatter:on
 public class ResourceHistoryTable extends BaseHasResource implements Serializable {
@@ -61,11 +61,20 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	@OneToMany(mappedBy = "myResourceHistory", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
 	private Collection<ResourceHistoryTag> myTags;
 
+	@Column(name = "RES_TEXT", length = Integer.MAX_VALUE - 1, nullable = true)
+	@Lob()
+	@OptimisticLock(excluded = true)
+	private byte[] myResource;
+
+	@Column(name = "RES_ENCODING", nullable = false, length = 5)
+	@Enumerated(EnumType.STRING)
+	@OptimisticLock(excluded = true)
+	private ResourceEncodingEnum myEncoding;
+
 	public ResourceHistoryTable() {
 		super();
 	}
-	
-	
+
 	public void addTag(ResourceHistoryTag theTag) {
 		for (ResourceHistoryTag next : getTags()) {
 			if (next.getTag().equals(theTag)) {
@@ -93,11 +102,23 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return historyTag;
 	}
 
+	public ResourceEncodingEnum getEncoding() {
+		return myEncoding;
+	}
+
+	public void setEncoding(ResourceEncodingEnum theEncoding) {
+		myEncoding = theEncoding;
+	}
+
 	@Override
 	public Long getId() {
 		return myId;
 	}
 
+	public void setId(Long theId) {
+		myId = theId;
+	}
+
 	@Override
 	public IdDt getIdDt() {
 		if (getForcedId() == null) {
@@ -108,15 +129,31 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		}
 	}
 
+	public byte[] getResource() {
+		return myResource;
+	}
+
+	public void setResource(byte[] theResource) {
+		myResource = theResource;
+	}
+
 	public Long getResourceId() {
 		return myResourceId;
 	}
 
+	public void setResourceId(Long theResourceId) {
+		myResourceId = theResourceId;
+	}
+
 	@Override
 	public String getResourceType() {
 		return myResourceType;
 	}
 
+	public void setResourceType(String theResourceType) {
+		myResourceType = theResourceType;
+	}
+
 	@Override
 	public Collection<ResourceHistoryTag> getTags() {
 		if (myTags == null) {
@@ -130,6 +167,10 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return myResourceVersion;
 	}
 
+	public void setVersion(long theVersion) {
+		myResourceVersion = theVersion;
+	}
+
 	public boolean hasTag(String theTerm, String theScheme) {
 		for (ResourceHistoryTag next : getTags()) {
 			if (next.getTag().getSystem().equals(theScheme) && next.getTag().getCode().equals(theTerm)) {
@@ -139,20 +180,4 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return false;
 	}
 
-	public void setId(Long theId) {
-		myId = theId;
-	}
-
-	public void setResourceId(Long theResourceId) {
-		myResourceId = theResourceId;
-	}
-
-	public void setResourceType(String theResourceType) {
-		myResourceType = theResourceType;
-	}
-
-	public void setVersion(long theVersion) {
-		myResourceVersion = theVersion;
-	}
-
 }

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.search.IndexNonDeletedInterceptor;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.annotations.OptimisticLock;
@@ -39,7 +40,6 @@ import java.util.Set;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
-//@formatter:off
 @Indexed(interceptor = IndexNonDeletedInterceptor.class)
 @Entity
 @Table(name = "HFJ_RESOURCE", uniqueConstraints = {}, indexes = {
@@ -49,13 +49,18 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 	@Index(name = "IDX_RES_TYPE", columnList = "RES_TYPE"),
 	@Index(name = "IDX_INDEXSTATUS", columnList = "SP_INDEX_STATUS")
 })
-//@formatter:on
 public class ResourceTable extends BaseHasResource implements Serializable {
 	static final int RESTYPE_LEN = 30;
 	private static final int MAX_LANGUAGE_LENGTH = 20;
 	private static final int MAX_PROFILE_LENGTH = 200;
 	private static final long serialVersionUID = 1L;
 
+//	@Transient
+//	private transient byte[] myResource;
+//
+//	@Transient
+//	private transient ResourceEncodingEnum myEncoding;
+
 	/**
 	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
 	 */
@@ -214,6 +219,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return tag;
 	}
 
+//	public ResourceEncodingEnum getEncoding() {
+//		Validate.notNull(myEncoding, "myEncoding is null");
+//		return myEncoding;
+//	}
+//
+//	public void setEncoding(ResourceEncodingEnum theEncoding) {
+//		myEncoding = theEncoding;
+//	}
+
 	public String getHashSha256() {
 		return myHashSha256;
 	}
@@ -387,6 +401,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myProfile = theProfile;
 	}
 
+//	public byte[] getResource() {
+//		Validate.notNull(myEncoding, "myEncoding is null");
+//		return myResource;
+//	}
+//
+//	public void setResource(byte[] theResource) {
+//		myResource = theResource;
+//	}
+
 	public Collection<ResourceLink> getResourceLinks() {
 		if (myResourceLinks == null) {
 			myResourceLinks = new ArrayList<>();
@@ -527,8 +550,8 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myNarrativeText = theNarrativeText;
 	}
 
-	public ResourceHistoryTable toHistory(ResourceHistoryTable theResourceHistoryTable) {
-		ResourceHistoryTable retVal = theResourceHistoryTable != null ? theResourceHistoryTable : new ResourceHistoryTable();
+	public ResourceHistoryTable toHistory() {
+		ResourceHistoryTable retVal = new ResourceHistoryTable();
 
 		retVal.setResourceId(myId);
 		retVal.setResourceType(myResourceType);
@@ -536,9 +559,9 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 
 		retVal.setPublished(getPublished());
 		retVal.setUpdated(getUpdated());
-		retVal.setEncoding(getEncoding());
+//		retVal.setEncoding(getEncoding());
 		retVal.setFhirVersion(getFhirVersion());
-		retVal.setResource(getResource());
+//		retVal.setResource(getResource());
 		retVal.setDeleted(getDeleted());
 		retVal.setForcedId(getForcedId());
 

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

@@ -22,6 +22,7 @@ import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.mockito.Mockito;
@@ -57,6 +58,11 @@ public abstract class BaseJpaTest {
 		when(mySrd.getUserData()).thenReturn(new HashMap<>());
 	}
 
+	@After
+	public final void afterPerformCleanup() {
+		BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
+	}
+
 	protected abstract FhirContext getContext();
 
 	/**

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -8,10 +8,13 @@ import java.util.List;
 
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
+import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@@ -24,6 +27,7 @@ import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.util.TestUtil;
+import org.springframework.transaction.support.TransactionTemplate;
 
 public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 
@@ -392,13 +396,14 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 	 */
 	@Test
 	public void testSearchDontReindexForUpdateWithIndexDisabled() {
+		BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(true);
 		Patient patient;
 		SearchParameterMap map;
 
 		patient = new Patient();
 		patient.getText().setDiv("<div>DIVAAA</div>");
 		patient.addName().addGiven("NAMEAAA");
-		IIdType pId1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		final IIdType pId1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));

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

@@ -45,41 +45,13 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2Test.class);
 
-	@Before
-	public void beforeDisableResultReuse() {
-		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
-	}
-
 	@After
 	public final void after() {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(new DaoConfig().isEnforceReferentialIntegrityOnDelete());
 	}
 
-	/**
-	 * See #773
-	 */
-	@Test
-	public void testDeleteResourceWithOutboundDeletedResources() {
-		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
-
-		Organization org = new Organization();
-		org.setId("ORG");
-		org.setName("ORG");
-		myOrganizationDao.update(org);
-
-		Patient pat = new Patient();
-		pat.setId("PAT");
-		pat.setActive(true);
-		pat.setManagingOrganization(new ResourceReferenceDt("Organization/ORG"));
-		myPatientDao.update(pat);
-
-		myOrganizationDao.delete(new IdDt("Organization/ORG"));
-
-		myPatientDao.delete(new IdDt("Patient/PAT"));
-	}
-
-
 	private void assertGone(IIdType theId) {
 		try {
 			assertNotGone(theId);
@@ -102,6 +74,11 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
+	@Before
+	public void beforeDisableResultReuse() {
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
+	}
+
 	private List<String> extractNames(IBundleProvider theSearch) {
 		ArrayList<String> retVal = new ArrayList<String>();
 		for (IBaseResource next : theSearch.getResources(0, theSearch.size())) {
@@ -865,6 +842,29 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new ResourceReferenceDt("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdDt("Organization/ORG"));
+
+		myPatientDao.delete(new IdDt("Patient/PAT"));
+	}
+
 	@Test
 	public void testDeleteThenUndelete() {
 		Patient patient = new Patient();

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

@@ -134,78 +134,6 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 	}
 
 	
-	@Test
-	public void testReindexing() {
-		Patient p = new Patient();
-		p.addName().addFamily("family");
-		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
-
-		ValueSet vs = new ValueSet();
-		vs.setUrl("http://foo");
-		myValueSetDao.create(vs, mySrd);
-
-		ResourceTable entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(1), entity.getIndexStatus());
-
-		mySystemDao.markAllResourcesForReindexing();
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(null, entity.getIndexStatus());
-
-		mySystemDao.performReindexingPass(null);
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(1), entity.getIndexStatus());
-
-		// Just make sure this doesn't cause a choke
-		mySystemDao.performReindexingPass(100000);
-
-		// Try making the resource unparseable
-
-		TransactionTemplate template = new TransactionTemplate(myTxManager);
-		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
-		template.execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				ResourceTable table = myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-				table.setEncoding(ResourceEncodingEnum.JSON);
-				table.setIndexStatus(null);
-				try {
-					table.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
-				} catch (UnsupportedEncodingException e) {
-					throw new Error(e);
-				}
-				myEntityManager.merge(table);
-				return null;
-			}
-		});
-
-		mySystemDao.performReindexingPass(null);
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(2), entity.getIndexStatus());
-
-	}
 
 	@Test
 	public void testSystemMetaOperation() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchFtTest.java

@@ -8,6 +8,8 @@ import java.util.List;
 
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -19,6 +21,9 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 
 public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	
@@ -473,13 +478,14 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	 */
 	@Test
 	public void testSearchDontReindexForUpdateWithIndexDisabled() {
+		BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(true);
 		Patient patient;
 		SearchParameterMap map;
 
 		patient = new Patient();
 		patient.getText().setDivAsString("<div>DIVAAA</div>");
 		patient.addName().addGiven("NAMEAAA");
-		IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
+		final IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));

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

@@ -2508,36 +2508,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
-	/**
-	 * Can we handle content that was previously saved containing vocabulary that
-	 * is no longer valid
-	 */
-	@Test
-	public void testResourceInDatabaseContainsInvalidVocabulary() {
-		final Patient p = new Patient();
-		p.setGender(AdministrativeGender.MALE);
-		final IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
-		
-		TransactionTemplate tx = new TransactionTemplate(myTxManager);
-		tx.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
-		tx.execute(new TransactionCallbackWithoutResult() {
-			@Override
-			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
-				ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
-				String newContent = myFhirCtx.newJsonParser().encodeResourceToString(p);
-				newContent = newContent.replace("male", "foo");
-				table.setResource(newContent.getBytes(Charsets.UTF_8));
-				table.setEncoding(ResourceEncodingEnum.JSON);
-				myResourceTableDao.save(table);
-			}
-		});
-		
-		Patient read = myPatientDao.read(id);
-		String string = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(read);
-		ourLog.info(string);
-		assertThat(string, containsString("value=\"foo\""));
-	}
-
 	@Test
 	public void testResourceInstanceMetaOperation() {
 

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

@@ -3,8 +3,6 @@ package ca.uhn.fhir.jpa.dao.dstu3;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
-import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.ResourceTag;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
@@ -26,15 +24,12 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
-import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.math.BigDecimal;
 import java.nio.charset.StandardCharsets;
 import java.util.HashSet;
@@ -444,79 +439,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
-	@Test
-	public void testReindexing() {
-		Patient p = new Patient();
-		p.addName().setFamily("family");
-		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
-
-		ValueSet vs = new ValueSet();
-		vs.setUrl("http://foo");
-		myValueSetDao.create(vs, mySrd);
-
-		ResourceTable entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(1), entity.getIndexStatus());
-
-		mySystemDao.markAllResourcesForReindexing();
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(null, entity.getIndexStatus());
-
-		mySystemDao.performReindexingPass(null);
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(1), entity.getIndexStatus());
-
-		// Just make sure this doesn't cause a choke
-		mySystemDao.performReindexingPass(100000);
-
-		// Try making the resource unparseable
-
-		TransactionTemplate template = new TransactionTemplate(myTxManager);
-		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
-		template.execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				ResourceTable table = myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-				table.setEncoding(ResourceEncodingEnum.JSON);
-				table.setIndexStatus(null);
-				try {
-					table.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
-				} catch (UnsupportedEncodingException e) {
-					throw new Error(e);
-				}
-				myEntityManager.merge(table);
-				return null;
-			}
-		});
-
-		mySystemDao.performReindexingPass(null);
-
-		entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback<ResourceTable>() {
-			@Override
-			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-			}
-		});
-		assertEquals(Long.valueOf(2), entity.getIndexStatus());
-
-	}
-
 	@Test
 	public void testSystemMetaOperation() {
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -180,6 +180,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Autowired
 	protected IResourceTableDao myResourceTableDao;
 	@Autowired
+	protected IResourceHistoryTableDao myResourceHistoryTableDao;
+	@Autowired
 	protected IResourceTagDao myResourceTagDao;
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@@ -234,6 +236,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@After()
 	public void afterCleanupDao() {
 		myDaoConfig.setExpireSearchResults(new DaoConfig().isExpireSearchResults());
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(new DaoConfig().isEnforceReferentialIntegrityOnDelete());
 		myDaoConfig.setExpireSearchResultsAfterMillis(new DaoConfig().getExpireSearchResultsAfterMillis());
 		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
 		myDaoConfig.setSuppressUpdatesWithNoChange(new DaoConfig().isSuppressUpdatesWithNoChange());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -74,7 +74,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testTransactionCreateWithUuidResourceStrategy() throws Exception {
+	public void testTransactionCreateWithUuidResourceStrategy() {
 		myDaoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
 
 		Organization org = new Organization();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java

@@ -8,6 +8,8 @@ import java.util.List;
 
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -19,6 +21,9 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.*;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 
 public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
 	
@@ -488,13 +493,14 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
 	 */
 	@Test
 	public void testSearchDontReindexForUpdateWithIndexDisabled() {
+		BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(true);
 		Patient patient;
 		SearchParameterMap map;
 
 		patient = new Patient();
 		patient.getText().setDivAsString("<div>DIVAAA</div>");
 		patient.addName().addGiven("NAMEAAA");
-		IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
+		final IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -1108,9 +1108,52 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testDeleteTwicePerformsNoOp() {
+		Patient patient = new Patient();
+		patient.setActive(true);
+
+		IIdType id = myPatientDao.create(patient, mySrd).getId();
+		assertNotNull(id.getIdPartAsLong());
+		assertEquals("1", id.getVersionIdPart());
+
+		IIdType id2 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id2.getIdPart());
+		assertEquals("2", id2.getVersionIdPart());
+
+		IIdType id3 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id3.getIdPart());
+		assertEquals("2", id3.getVersionIdPart());
+
+		IIdType id4 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id4.getIdPart());
+		assertEquals("2", id4.getVersionIdPart());
+
+		patient = new Patient();
+		patient.setId(id.getIdPart());
+		patient.setActive(false);
+		IIdType id5 = myPatientDao.update(patient).getId();
+		assertEquals(id.getIdPart(), id5.getIdPart());
+		assertEquals("3", id5.getVersionIdPart());
+
+		patient = myPatientDao.read(id.withVersion("1"));
+		assertEquals(true, patient.getActive());
+
+		try {
+			myPatientDao.read(id.withVersion("2"));
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		patient = myPatientDao.read(id.withVersion("3"));
+		assertEquals(false, patient.getActive());
+
+	}
+
 	@Test
 	public void testDeleteResource() {
-		int initialHistory = myPatientDao.history((Date) null, null, mySrd).size();
+		int initialHistory = myPatientDao.history(null, null, mySrd).size();
 
 		IIdType id1;
 		IIdType id2;
@@ -1132,7 +1175,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ");
 			id2b = myPatientDao.update(patient, mySrd).getId();
 		}
-		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", new Object[] { id1, id2, id2b });
+		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", id1, id2, id2b);
 
 		SearchParameterMap params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
@@ -1153,7 +1196,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			// good
 		}
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(4 + initialHistory, history.size().intValue());
 		List<IBaseResource> resources = history.getResources(0, 4);
 		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) resources.get(0)));
@@ -1525,7 +1568,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 
 		// By type
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(fullSize + 1, history.size().intValue());
 		for (int i = 0; i < fullSize; i++) {
 			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
@@ -1592,7 +1635,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 
 		// By type
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(fullSize + 1, history.size().intValue());
 		for (int i = 0; i < fullSize; i++) {
 			String expected = id.withVersion(Integer.toString(fullSize + 1 - i)).getValue();
@@ -1643,13 +1686,13 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testHistoryReflectsMetaOperations() throws Exception {
+	public void testHistoryReflectsMetaOperations() {
 		Patient inPatient = new Patient();
 		inPatient.addName().setFamily("version1");
 		inPatient.getMeta().addProfile("http://example.com/1");
 		IIdType id = myPatientDao.create(inPatient, mySrd).getId().toUnqualifiedVersionless();
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		Patient outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1663,7 +1706,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		inPatient.getMeta().addProfile("http://example.com/2");
 		myPatientDao.metaAddOperation(id, inPatient.getMeta(), mySrd);
 
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1679,7 +1722,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		inPatient.getName().get(0).setFamily("version2");
 		myPatientDao.update(inPatient, mySrd);
 
-		history = myPatientDao.history((Date) null, null, mySrd);
+		history = myPatientDao.history(null, null, mySrd);
 		assertEquals(2, history.size().intValue());
 		outPatient = (Patient) history.getResources(0, 2).get(0);
 		assertEquals("version2", outPatient.getName().get(0).getFamily());
@@ -1694,7 +1737,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testHistoryWithDeletedResource() throws Exception {
+	public void testHistoryWithDeletedResource() {
 		String methodName = "testHistoryWithDeletedResource";
 
 		Patient patient = new Patient();
@@ -1707,9 +1750,9 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		IBundleProvider history = myPatientDao.history(id, null, null, mySrd);
 		List<IBaseResource> entries = history.getResources(0, 3);
-		ourLog.info(((IAnyResource) entries.get(0)).getIdElement() + " - " + ((IAnyResource) entries.get(0)).getMeta().getLastUpdated());
-		ourLog.info(((IAnyResource) entries.get(1)).getIdElement() + " - " + ((IAnyResource) entries.get(1)).getMeta().getLastUpdated());
-		ourLog.info(((IAnyResource) entries.get(2)).getIdElement() + " - " + ((IAnyResource) entries.get(2)).getMeta().getLastUpdated());
+		ourLog.info(entries.get(0).getIdElement() + " - " + entries.get(0).getMeta().getLastUpdated());
+		ourLog.info(entries.get(1).getIdElement() + " - " + entries.get(1).getMeta().getLastUpdated());
+		ourLog.info(entries.get(2).getIdElement() + " - " + entries.get(2).getMeta().getLastUpdated());
 		assertEquals(3, history.size().intValue());
 
 		assertEquals(id.withVersion("3"), entries.get(0).getIdElement());
@@ -1773,7 +1816,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		// No since
 
-		IBundleProvider history = myPatientDao.history((Date) null, null, mySrd);
+		IBundleProvider history = myPatientDao.history(null, null, mySrd);
 		assertEquals(1, history.size().intValue());
 		Patient outPatient = (Patient) history.getResources(0, 1).get(0);
 		assertEquals("version1", inPatient.getName().get(0).getFamily());
@@ -1797,7 +1840,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testHistoryWithInvalidId() throws Exception {
+	public void testHistoryWithInvalidId() {
 		try {
 			myPatientDao.history(new IdType("Patient/FOOFOOFOO"), null, null, mySrd);
 			fail();
@@ -2175,7 +2218,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		dr01.setSubject(new Reference(patientId01));
 		IIdType drId01 = myDiagnosticReportDao.create(dr01, mySrd).getId();
 
-		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[] { patientId01, patientId02, obsId01, obsId02, drId01 });
+		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", patientId01, patientId02, obsId01, obsId02, drId01);
 
 		List<Observation> result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam(patientId01.getIdPart())).setLoadSynchronous(true)));
 		assertEquals(1, result.size());
@@ -2185,7 +2228,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertEquals(1, result.size());
 		assertEquals(obsId02.getIdPart(), result.get(0).getIdElement().getIdPart());
 
-		result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));;
+		result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));
 		assertEquals(0, result.size());
 
 	}
@@ -2268,7 +2311,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		long id = outcome.getId().getIdPartAsLong();
 
 		TokenParam value = new TokenParam("urn:system", "001testPersistSearchParams");
-		List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));;
+		List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));
 		assertEquals(1, found.size());
 		assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue());
 
@@ -2380,7 +2423,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testReadInvalidVersion() throws Exception {
+	public void testReadInvalidVersion() {
 		String methodName = "testReadInvalidVersion";
 
 		Patient pat = new Patient();
@@ -2565,12 +2608,12 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		tx.execute(new TransactionCallbackWithoutResult() {
 			@Override
 			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
-				ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+				ResourceHistoryTable table = myResourceHistoryTableDao.findForIdAndVersion(id.getIdPartAsLong(), 1L);
 				String newContent = myFhirCtx.newJsonParser().encodeResourceToString(p);
 				newContent = newContent.replace("male", "foo");
 				table.setResource(newContent.getBytes(Charsets.UTF_8));
 				table.setEncoding(ResourceEncodingEnum.JSON);
-				myResourceTableDao.save(table);
+				myResourceHistoryTableDao.save(table);
 			}
 		});
 		
@@ -2592,7 +2635,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			id1 = myPatientDao.create(patient, mySrd).getId();
 
 			Meta metaAdd = new Meta();
-			metaAdd.addTag().setSystem((String) null).setCode("Dog").setDisplay("Puppies");
+			metaAdd.addTag().setSystem(null).setCode("Dog").setDisplay("Puppies");
 			metaAdd.addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1");
 			metaAdd.addProfile("http://profile/1");
 			myPatientDao.metaAddOperation(id1, metaAdd, mySrd);
@@ -2662,7 +2705,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		{
 			Meta metaDel = new Meta();
-			metaDel.addTag().setSystem((String) null).setCode("Dog");
+			metaDel.addTag().setSystem(null).setCode("Dog");
 			metaDel.addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1");
 			metaDel.addProfile("http://profile/1");
 			myPatientDao.metaDeleteOperation(id1, metaDel, mySrd);
@@ -3387,7 +3430,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	 * Test for issue #60
 	 */
 	@Test
-	public void testStoreUtf8Characters() throws Exception {
+	public void testStoreUtf8Characters() {
 		Organization org = new Organization();
 		org.setName("測試醫院");
 		org.addIdentifier().setSystem("urn:system").setValue("testStoreUtf8Characters_01");
@@ -3547,7 +3590,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testTimingSearchParams() throws Exception {
+	public void testTimingSearchParams() {
 		Date before = new DateTimeType("2011-01-01T10:00:00Z").getValue();
 		Date middle = new DateTimeType("2011-01-02T10:00:00Z").getValue();
 		Date after = new DateTimeType("2011-01-03T10:00:00Z").getValue();
@@ -3613,7 +3656,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testUpdateRejectsIdWhichPointsToForcedId() throws InterruptedException {
+	public void testUpdateRejectsIdWhichPointsToForcedId() {
 		Patient p1 = new Patient();
 		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsIdWhichPointsToForcedId01");
 		p1.addName().setFamily("Tester").addGiven("testUpdateRejectsIdWhichPointsToForcedId01");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -270,6 +270,46 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testValidateForDeleteWithReferentialIntegrityDisabled() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+		String methodName = "testValidateForDelete";
+
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient pat = new Patient();
+		pat.addName().setFamily(methodName);
+		pat.getManagingOrganization().setReference(orgId.getValue());
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		myOrganizationDao.validate(null, orgId, null, null, ValidationModeEnum.DELETE, null, mySrd);
+
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(true);
+		try {
+			myOrganizationDao.validate(null, orgId, null, null, ValidationModeEnum.DELETE, null, mySrd);
+			fail();
+		} catch (ResourceVersionConflictException e) {
+			// good
+		}
+
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+
+		myOrganizationDao.read(orgId);
+
+		myOrganizationDao.delete(orgId);
+
+		try {
+			myOrganizationDao.read(orgId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+	}
+
 	private IBaseResource findResourceByIdInBundle(Bundle vss, String name) {
 		IBaseResource retVal = null;
 		for (BundleEntryComponent next : vss.getEntry()) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -3,10 +3,8 @@ package ca.uhn.fhir.jpa.dao.r4;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
-import ca.uhn.fhir.jpa.entity.ResourceTable;
-import ca.uhn.fhir.jpa.entity.ResourceTag;
-import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -26,6 +24,7 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -443,7 +442,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 	public void testReindexing() {
 		Patient p = new Patient();
 		p.addName().setFamily("family");
-		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualified();
 
 		ValueSet vs = new ValueSet();
 		vs.setUrl("http://foo");
@@ -487,15 +486,19 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 		template.execute(new TransactionCallback<ResourceTable>() {
 			@Override
 			public ResourceTable doInTransaction(TransactionStatus theStatus) {
-				ResourceTable table = myEntityManager.find(ResourceTable.class, id.getIdPartAsLong());
-				table.setEncoding(ResourceEncodingEnum.JSON);
-				table.setIndexStatus(null);
+				ResourceHistoryTable resourceHistoryTable = myResourceHistoryTableDao.findForIdAndVersion(id.getIdPartAsLong(), id.getVersionIdPartAsLong());
+				resourceHistoryTable.setEncoding(ResourceEncodingEnum.JSON);
 				try {
-					table.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
+					resourceHistoryTable.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
 				} catch (UnsupportedEncodingException e) {
 					throw new Error(e);
 				}
-				myEntityManager.merge(table);
+				myResourceHistoryTableDao.save(resourceHistoryTable);
+
+				ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+				table.setIndexStatus(null);
+				myResourceTableDao.save(table);
+
 				return null;
 			}
 		});

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTransactionSearchDstu2Test.java

@@ -1,45 +1,48 @@
 package ca.uhn.fhir.jpa.provider;
 
-import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletContextHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
-import org.junit.*;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
-import ca.uhn.fhir.jpa.rp.dstu2.*;
+import ca.uhn.fhir.jpa.rp.dstu2.ObservationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu2.OrganizationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu2.valueset.*;
+import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.TestUtil;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
 
 public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu2Test.class);
 	private static RestfulServer myRestServer;
 	private static IGenericClient ourClient;
 	private static FhirContext ourCtx;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu2Test.class);
 	private static Server ourServer;
 	private static String ourServerBase;
 	private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
-	
 
 
-	
 	@SuppressWarnings("deprecation")
 	@After
 	public void after() {
@@ -53,7 +56,7 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 		mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
 		ourClient.registerInterceptor(mySimpleHeaderInterceptor);
 	}
-	
+
 	@Before
 	public void beforeStartServer() throws Exception {
 		if (myRestServer == null) {
@@ -96,11 +99,11 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 			ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
 			myRestServer = restServer;
 		}
-		
+
 		myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
 		myRestServer.setPagingProvider(myPagingProvider);
 	}
-	
+
 
 	private List<String> create20Patients() {
 		List<String> ids = new ArrayList<String>();
@@ -108,7 +111,7 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 			Patient patient = new Patient();
 			patient.setGender(AdministrativeGenderEnum.MALE);
 			patient.addIdentifier().setSystem("urn:foo").setValue("A");
-			patient.addName().addFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
+			patient.addName().addFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i + 1));
 			String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
 			ids.add(id);
 		}
@@ -116,9 +119,9 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	@Test
-	public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testBatchWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.BATCH);
 		input
@@ -126,12 +129,12 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 			.getRequest()
 			.setMethod(HTTPVerbEnum.GET)
 			.setUrl("Patient?_count=5&_sort=name");
-		
+
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(1, output.getEntry().size());
 		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
 		assertEquals(5, respBundle.getEntry().size());
@@ -139,11 +142,11 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 		List<String> actualIds = toIds(respBundle);
 		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
 	}
-	
+
 	@Test
-	public void testBatchWithGetNormalSearch() throws Exception {
+	public void testBatchWithGetNormalSearch() {
 		List<String> ids = create20Patients();
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.BATCH);
 		input
@@ -151,16 +154,16 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 			.getRequest()
 			.setMethod(HTTPVerbEnum.GET)
 			.setUrl("Patient?_count=5&_sort=name");
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(1, output.getEntry().size());
 		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
 		assertEquals(5, respBundle.getEntry().size());
 		List<String> actualIds = toIds(respBundle);
 		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
-		
+
 		String nextPageLink = respBundle.getLink("next").getUrl();
 		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
 		respBundle = output;
@@ -173,10 +176,10 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 	 * 30 searches in one batch! Whoa!
 	 */
 	@Test
-	public void testBatchWithManyGets() throws Exception {
+	public void testBatchWithManyGets() {
 		List<String> ids = create20Patients();
 
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.BATCH);
 		for (int i = 0; i < 30; i++) {
@@ -186,10 +189,10 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 				.setMethod(HTTPVerbEnum.GET)
 				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
 		}
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(30, output.getEntry().size());
 		for (int i = 0; i < 30; i++) {
 			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
@@ -201,22 +204,22 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	@Test
-	public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testTransactionWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.TRANSACTION);
 		input
 			.addEntry()
 			.getRequest()
 			.setMethod(HTTPVerbEnum.GET)
-			.setUrl("Patient?_count=5");
-		
+			.setUrl("Patient?_count=5&_sort=_id");
+
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(1, output.getEntry().size());
 		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
 		assertEquals(5, respBundle.getEntry().size());
@@ -224,11 +227,11 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 		List<String> actualIds = toIds(respBundle);
 		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
 	}
-	
+
 	@Test
-	public void testTransactionWithGetNormalSearch() throws Exception {
+	public void testTransactionWithGetNormalSearch() {
 		List<String> ids = create20Patients();
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.TRANSACTION);
 		input
@@ -236,16 +239,16 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 			.getRequest()
 			.setMethod(HTTPVerbEnum.GET)
 			.setUrl("Patient?_count=5&_sort=name");
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(1, output.getEntry().size());
 		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
 		assertEquals(5, respBundle.getEntry().size());
 		List<String> actualIds = toIds(respBundle);
 		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
-		
+
 		String nextPageLink = respBundle.getLink("next").getUrl();
 		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
 		respBundle = output;
@@ -258,10 +261,10 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 	 * 30 searches in one Transaction! Whoa!
 	 */
 	@Test
-	public void testTransactionWithManyGets() throws Exception {
+	public void testTransactionWithManyGets() {
 		List<String> ids = create20Patients();
 
-		
+
 		Bundle input = new Bundle();
 		input.setType(BundleTypeEnum.TRANSACTION);
 		for (int i = 0; i < 30; i++) {
@@ -271,10 +274,10 @@ public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
 				.setMethod(HTTPVerbEnum.GET)
 				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
 		}
-		
+
 		Bundle output = ourClient.transaction().withBundle(input).execute();
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
-		
+
 		assertEquals(30, output.getEntry().size());
 		for (int i = 0; i < 30; i++) {
 			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java

@@ -126,7 +126,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	@Test
-	public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testBatchWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -135,7 +135,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 			.addEntry()
 			.getRequest()
 			.setMethod(HTTPVerb.GET)
-			.setUrl("Patient?_count=5");
+			.setUrl("Patient?_count=5&_sort=_id");
 		
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
 		
@@ -151,7 +151,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	}
 	
 	@Test
-	public void testBatchWithGetNormalSearch() throws Exception {
+	public void testBatchWithGetNormalSearch() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -183,7 +183,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	 * 30 searches in one batch! Whoa!
 	 */
 	@Test
-	public void testBatchWithManyGets() throws Exception {
+	public void testBatchWithManyGets() {
 		List<String> ids = create20Patients();
 
 		
@@ -211,7 +211,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	}
 
 	@Test
-	public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testTransactionWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -220,7 +220,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 			.addEntry()
 			.getRequest()
 			.setMethod(HTTPVerb.GET)
-			.setUrl("Patient?_count=5");
+			.setUrl("Patient?_count=5&_sort=_id");
 		
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
 		
@@ -236,7 +236,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	}
 	
 	@Test
-	public void testTransactionWithGetNormalSearch() throws Exception {
+	public void testTransactionWithGetNormalSearch() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -268,7 +268,7 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
 	 * 30 searches in one Transaction! Whoa!
 	 */
 	@Test
-	public void testTransactionWithManyGets() throws Exception {
+	public void testTransactionWithManyGets() {
 		List<String> ids = create20Patients();
 
 		

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.jpa.config.TestR4Config;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.jpa.util.StopWatch;
@@ -54,6 +55,8 @@ import org.junit.*;
 import org.springframework.test.util.AopTestUtils;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -1642,31 +1645,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 	}
 
-	// private void delete(String theResourceType, String theParamName, String theParamValue) {
-	// Bundle resources;
-	// do {
-	// IQuery<Bundle> forResource = myClient.search().forResource(theResourceType);
-	// if (theParamName != null) {
-	// forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
-	// }
-	// resources = forResource.execute();
-	// for (IResource next : resources.toListOfResources()) {
-	// ourLog.info("Deleting resource: {}", next.getId());
-	// myClient.delete().resource(next).execute();
-	// }
-	// } while (resources.size() > 0);
-	// }
-	//
-	// private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue)
-	// {
-	// Bundle resources = myClient.search().forResource(theResourceType).where(new
-	// TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
-	// for (IResource next : resources.toListOfResources()) {
-	// ourLog.info("Deleting resource: {}", next.getId());
-	// myClient.delete().resource(next).execute();
-	// }
-	// }
-
 	@Test
 	public void testHasParameter() throws Exception {
 		IIdType pid0;
@@ -1704,6 +1682,31 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertThat(ids, contains(pid0.getValue()));
 	}
 
+	// private void delete(String theResourceType, String theParamName, String theParamValue) {
+	// Bundle resources;
+	// do {
+	// IQuery<Bundle> forResource = myClient.search().forResource(theResourceType);
+	// if (theParamName != null) {
+	// forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
+	// }
+	// resources = forResource.execute();
+	// for (IResource next : resources.toListOfResources()) {
+	// ourLog.info("Deleting resource: {}", next.getId());
+	// myClient.delete().resource(next).execute();
+	// }
+	// } while (resources.size() > 0);
+	// }
+	//
+	// private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue)
+	// {
+	// Bundle resources = myClient.search().forResource(theResourceType).where(new
+	// TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
+	// for (IResource next : resources.toListOfResources()) {
+	// ourLog.info("Deleting resource: {}", next.getId());
+	// myClient.delete().resource(next).execute();
+	// }
+	// }
+
 	@Test
 	public void testHasParameterNoResults() throws Exception {
 
@@ -2347,6 +2350,54 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 	}
 
+	@Test
+	public void testRetrieveMissingVersionsDoesntCrashSearch() {
+		Patient p1 = new Patient();
+		p1.setActive(true);
+		final IIdType id1 = myClient.create().resource(p1).execute().getId();
+
+		Patient p2 = new Patient();
+		p2.setActive(false);
+		IIdType id2 = myClient.create().resource(p2).execute().getId();
+
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus status) {
+				ResourceHistoryTable version = myResourceHistoryTableDao.findForIdAndVersion(id1.getIdPartAsLong(), 1);
+				myResourceHistoryTableDao.delete(version);
+			}
+		});
+
+		Bundle bundle = myClient.search().forResource("Patient").returnBundle(Bundle.class).execute();
+		assertEquals(2, bundle.getTotal());
+		assertEquals(1, bundle.getEntry().size());
+		assertEquals(id2.getIdPart(), bundle.getEntry().get(0).getResource().getIdElement().getIdPart());
+	}
+
+	@Test
+	public void testRetrieveMissingVersionsDoesntCrashHistory() {
+		Patient p1 = new Patient();
+		p1.setActive(true);
+		final IIdType id1 = myClient.create().resource(p1).execute().getId();
+
+		Patient p2 = new Patient();
+		p2.setActive(false);
+		IIdType id2 = myClient.create().resource(p2).execute().getId();
+
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus status) {
+				ResourceHistoryTable version = myResourceHistoryTableDao.findForIdAndVersion(id1.getIdPartAsLong(), 1);
+				myResourceHistoryTableDao.delete(version);
+			}
+		});
+
+		Bundle bundle = myClient.history().onServer().andReturnBundle(Bundle.class).execute();
+		assertEquals(1, bundle.getTotal());
+		assertEquals(1, bundle.getEntry().size());
+		assertEquals(id2.getIdPart(), bundle.getEntry().get(0).getResource().getIdElement().getIdPart());
+	}
+
 	@Test
 	public void testSaveAndRetrieveExistingNarrativeJson() {
 		Patient p1 = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderTransactionSearchR4Test.java

@@ -33,11 +33,11 @@ import ca.uhn.fhir.util.TestUtil;
 
 public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchR4Test.class);
 	private static RestfulServer myRestServer;
 	private static IGenericClient ourClient;
 	private static FhirContext ourCtx;
 	private static CloseableHttpClient ourHttpClient;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchR4Test.class);
 	private static Server ourServer;
 	private static String ourServerBase;
 	private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
@@ -116,17 +116,19 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 		List<String> ids = new ArrayList<String>();
 		for (int i = 0; i < 20; i++) {
 			Patient patient = new Patient();
+			char letter = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".charAt(i);
+			patient.setId("" + letter);
 			patient.setGender(AdministrativeGender.MALE);
 			patient.addIdentifier().setSystem("urn:foo").setValue("A");
 			patient.addName().setFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
-			String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
+			String id = myPatientDao.update(patient).getId().toUnqualifiedVersionless().getValue();
 			ids.add(id);
 		}
 		return ids;
 	}
 
 	@Test
-	public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testBatchWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -135,7 +137,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 			.addEntry()
 			.getRequest()
 			.setMethod(HTTPVerb.GET)
-			.setUrl("Patient?_count=5");
+			.setUrl("Patient?_count=5&_sort=_id");
 		
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
 		
@@ -151,7 +153,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	}
 	
 	@Test
-	public void testBatchWithGetNormalSearch() throws Exception {
+	public void testBatchWithGetNormalSearch() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -183,7 +185,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	 * 30 searches in one batch! Whoa!
 	 */
 	@Test
-	public void testBatchWithManyGets() throws Exception {
+	public void testBatchWithManyGets() {
 		List<String> ids = create20Patients();
 
 		
@@ -211,7 +213,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	}
 
 	@Test
-	public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
+	public void testTransactionWithGetHardLimitLargeSynchronous() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -220,7 +222,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 			.addEntry()
 			.getRequest()
 			.setMethod(HTTPVerb.GET)
-			.setUrl("Patient?_count=5");
+			.setUrl("Patient?_count=5&_sort=_id");
 		
 		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
 		
@@ -236,7 +238,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	}
 	
 	@Test
-	public void testTransactionWithGetNormalSearch() throws Exception {
+	public void testTransactionWithGetNormalSearch() {
 		List<String> ids = create20Patients();
 		
 		Bundle input = new Bundle();
@@ -268,7 +270,7 @@ public class SystemProviderTransactionSearchR4Test extends BaseJpaR4Test {
 	 * 30 searches in one Transaction! Whoa!
 	 */
 	@Test
-	public void testTransactionWithManyGets() throws Exception {
+	public void testTransactionWithManyGets() {
 		List<String> ids = create20Patients();
 
 		

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java

@@ -27,6 +27,7 @@ import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.*;
 
+import ca.uhn.fhir.util.CollectionUtil;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -308,6 +309,29 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 			}
 		}
 
+		/*
+		 * Remove any null entries in the list - This generally shouldn't happen but can if
+		 * data has been manually purged from the JPA database
+		 */
+		boolean hasNull = false;
+		for (IBaseResource next : resourceList) {
+			if (next == null) {
+				hasNull = true;
+				break;
+			}
+		}
+		if (hasNull) {
+			for (Iterator<IBaseResource> iter = resourceList.iterator(); iter.hasNext(); ) {
+				if (iter.next() == null) {
+					iter.remove();
+				}
+			}
+		}
+
+		/*
+		 * Make sure all returned resources have an ID (if not, this is a bug
+		 * in the user server code)
+		 */
 		for (IBaseResource next : resourceList) {
 			if (next.getIdElement() == null || next.getIdElement().isEmpty()) {
 				if (!(next instanceof BaseOperationOutcome)) {

hapi-fhir-validation/src/test/resources/logback-test.xml

@@ -1,9 +1,11 @@
 <configuration>
 
 	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+			<level>INFO</level>
+		</filter>
 		<encoder>
-			<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] - %msg%n
-			</pattern>
+			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
 		</encoder>
 	</appender>
 

pom.xml

@@ -1026,6 +1026,14 @@
 	<build>
 		<pluginManagement>
 			<plugins>
+				<plugin>
+					<groupId>com.gemnasium</groupId>
+					<artifactId>gemnasium-maven-plugin</artifactId>
+					<version>0.2.0</version>
+					<configuration>
+						<projectSlug>github.com/jamesagnew/hapi-fhir</projectSlug>
+					</configuration>
+				</plugin>
 				<plugin>
 					<groupId>org.basepom.maven</groupId>
 					<artifactId>duplicate-finder-maven-plugin</artifactId>

src/changes/changes.xml

@@ -86,6 +86,12 @@
 				DSTU3/R4 structure in the getMeta() version field instead of in the
 				getIdElement() ID. Thanks to GitHub user @Chrisjobling for reporting!
 			</action>
+			<action type="fix">
+				A bug was fixed in the JPA server when performing a validate operation with a mode
+				of DELETE on a server with referential integrity disabled, the validate operation would delete
+				resource reference indexes as though the delete was actually happening, which negatively
+				affected searching for the resource being validated.
+			</action>
 			<action type="add">
 				The HAPI FHIR Server framework now has initial support for
 				multitenancy. At this time the support is limited to the server

src/site/xdoc/download.xml.vm

@@ -19,6 +19,15 @@
 				and support for draft pre-release versions of FHIR are shown in 
 				<span style="background: #EEB; padding: 3px;">YELLOW</span>.
 			</p>
+			<p>
+				Note also that after the release of the FHIR DSTU2 specification, the FHIR
+				standard itself stopped using the DSTUx naming scheme, in favour or naming
+				new releases STUx or simply Rx. Because HAPI FHIR already had draft support
+				for what was then called DSTU3 at this time, we did not update our naming
+				conventions until R4 in order to avoid breaking existing users' code.
+				From the perspective of a user of HAPI FHIR, consider the terms
+				DSTU3 / STU3 / R3 to be interchangeable.
+			</p>
 			<table>
 				<thead>
 					<tr>