Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -53,6 +53,7 @@ import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.utils.URLEncodedUtils;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -93,6 +94,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.ResourceTag;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -126,14 +128,20 @@ import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
 import net.sourceforge.cobertura.CoverageIgnore;
 
 public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
+	static final String OO_SEVERITY_ERROR = "error";
+	static final String OO_SEVERITY_INFO = "information";
+	static final String OO_SEVERITY_WARN = "warning";
+
 	/**
 	 * These are parameters which are supported by {@link BaseHapiFhirResourceDao#searchForIds(Map)}
 	 */
@@ -160,6 +168,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		RESOURCE_META_AND_PARAMS = Collections.unmodifiableMap(resourceMetaAndParams);
 	}
 
+	
 	public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
 	public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
 	public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
@@ -1562,6 +1571,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return retVal.toString();
 	}
 
+	protected void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
+		if (theDeleteConflicts.isEmpty()) {
+			return;
+		}
+
+		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+		for (DeleteConflict next : theDeleteConflicts) {
+			String msg = "Unable to delete " + next.getTargetId().toUnqualifiedVersionless().getValue() + " because at least one resource has a reference to this resource. First reference found was resource " + next.getTargetId().toUnqualifiedVersionless().getValue() + " in path " + next.getSourcePath();
+			OperationOutcomeUtil.addIssue(getContext(), oo, OO_SEVERITY_ERROR, msg, null, "processing");
+		}
+		
+		throw new ResourceVersionConflictException("Delete failed because of constraint failure", oo);
+	}
+
 	public BaseHasResource readEntity(IIdType theValueId) {
 		throw new NotImplementedException("");
 	}

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

@@ -62,6 +62,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
@@ -81,7 +82,6 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
@@ -91,31 +91,27 @@ import ca.uhn.fhir.util.ObjectUtil;
 @Transactional(propagation = Propagation.REQUIRED)
 public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
 
-	static final String OO_SEVERITY_ERROR = "error";
-	static final String OO_SEVERITY_INFO = "information";
-	static final String OO_SEVERITY_WARN = "warning";
-
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
 
+	@Autowired
+	private DaoConfig myDaoConfig;
+
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
 
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 
-	@Autowired
+	private String myResourceName;
-	private DaoConfig myDaoConfig;
 
+	private Class<T> myResourceType;
 	@Autowired(required = false)
 	protected ISearchDao mySearchDao;
-
-	private String myResourceName;
-	private Class<T> myResourceType;
-	private String mySecondaryPrimaryKeyParamName;
-
 	@Autowired()
 	protected ISearchResultDao mySearchResultDao;
 
+	private String mySecondaryPrimaryKeyParamName;
+
 	@Override
 	public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
 		StopWatch w = new StopWatch();
@@ -184,16 +180,28 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 	@Override
 	public DaoMethodOutcome delete(IIdType theId) {
+		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
+		StopWatch w = new StopWatch();
+		
+		ResourceTable savedEntity = delete(theId, deleteConflicts);
+
+		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+		
+		ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
+		return toMethodOutcome(savedEntity, null);
+	}
+
+	@Override
+	public ResourceTable delete(IIdType theId, List<DeleteConflict> deleteConflicts) {
 		if (theId == null || !theId.hasIdPart()) {
 			throw new InvalidRequestException("Can not perform delete, no ID provided");
 		}
-		StopWatch w = new StopWatch();
 		final ResourceTable entity = readEntityLatestVersion(theId);
 		if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
 			throw new InvalidRequestException("Trying to delete " + theId + " but this is not the current version");
 		}
 
-		validateOkToDeleteOrThrowResourceVersionConflictException(entity);
+		validateOkToDelete(deleteConflicts, entity);
 
 		// Notify interceptors
 		ActionRequestDetails requestDetails = new ActionRequestDetails(theId, theId.getResourceType());
@@ -208,37 +216,41 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 				((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
 			}
 		}
-
+		return savedEntity;
-		ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
-		return toMethodOutcome(savedEntity, null);
 	}
 
 	@Override
 	public DaoMethodOutcome deleteByUrl(String theUrl) {
-		return deleteByUrl(theUrl, false);
+		StopWatch w = new StopWatch();
+		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
+
+		List<ResourceTable> deletedResources = deleteByUrl(theUrl, deleteConflicts);
+		
+		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+		
+		if (deletedResources.isEmpty()) {
+			throw new ResourceNotFoundException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "unableToDeleteNotFound", theUrl));
+		}
+
+		ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[] { theUrl, deletedResources.size(), w.getMillisAndRestart() });
+		return new DaoMethodOutcome();
 	}
 
 	@Override
-	public DaoMethodOutcome deleteByUrl(String theUrl, boolean theInTransaction) {
+	public List<ResourceTable> deleteByUrl(String theUrl, List<DeleteConflict> deleteConflicts) {
-		StopWatch w = new StopWatch();
-
 		Set<Long> resource = processMatchUrl(theUrl, myResourceType);
-		if (resource.isEmpty()) {
+		if (resource.size() > 1) {
-			if (!theInTransaction) {
-				throw new ResourceNotFoundException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "unableToDeleteNotFound", theUrl));
-			} else {
-				return new DaoMethodOutcome();
-			}
-		} else if (resource.size() > 1) {
 			if (myDaoConfig.isAllowMultipleDelete() == false) {
 				throw new PreconditionFailedException(getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resource.size()));
 			}
 		}
 
+		List<ResourceTable> retVal = new ArrayList<ResourceTable>();
 		for (Long pid : resource) {
 			ResourceTable entity = myEntityManager.find(ResourceTable.class, pid);
+			retVal.add(entity);
 			
-			validateOkToDeleteOrThrowResourceVersionConflictException(entity);
+			validateOkToDelete(deleteConflicts, entity);
 
 			// Notify interceptors
 			IdDt idToDelete = entity.getIdDt();
@@ -258,9 +270,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 		}
 		
-		ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[] { theUrl, resource.size(), w.getMillisAndRestart() });
+		return retVal;
-
-		return new DaoMethodOutcome();
 	}
 
 	private DaoMethodOutcome doCreate(T theResource, String theIfNoneExist, boolean thePerformIndexing, Date theUpdateTime) {
@@ -491,6 +501,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return retVal;
 	}
 
+	@Override
+	public MetaDt metaAddOperation(IIdType theResourceId, MetaDt theMetaAdd) {
+		// Notify interceptors
+		ActionRequestDetails requestDetails = new ActionRequestDetails(theResourceId, getResourceName());
+		notifyInterceptors(RestOperationTypeEnum.META_ADD, requestDetails);
+
+		StopWatch w = new StopWatch();
+		BaseHasResource entity = readEntity(theResourceId);
+		if (entity == null) {
+			throw new ResourceNotFoundException(theResourceId);
+		}
+
+		List<TagDefinition> tags = toTagList(theMetaAdd);
+
+		//@formatter:off
+		for (TagDefinition nextDef : tags) {
+			
+			boolean hasTag = false;
+			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
+				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
+						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
+						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
+					hasTag = true;
+					break;
+				}
+			}
+
+			if (!hasTag) {
+				entity.setHasTags(true);
+				
+				TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
+				BaseTag newEntity = entity.addTag(def);
+				myEntityManager.persist(newEntity);
+			}
+		}
+		//@formatter:on
+
+		myEntityManager.merge(entity);
+		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
+
+		return metaGetOperation(theResourceId);
+	}
+
 	// @Override
 	// public IBundleProvider everything(IIdType theId) {
 	// Search search = new Search();
@@ -573,49 +626,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	// };
 	// }
 
-	@Override
-	public MetaDt metaAddOperation(IIdType theResourceId, MetaDt theMetaAdd) {
-		// Notify interceptors
-		ActionRequestDetails requestDetails = new ActionRequestDetails(theResourceId, getResourceName());
-		notifyInterceptors(RestOperationTypeEnum.META_ADD, requestDetails);
-
-		StopWatch w = new StopWatch();
-		BaseHasResource entity = readEntity(theResourceId);
-		if (entity == null) {
-			throw new ResourceNotFoundException(theResourceId);
-		}
-
-		List<TagDefinition> tags = toTagList(theMetaAdd);
-
-		//@formatter:off
-		for (TagDefinition nextDef : tags) {
-			
-			boolean hasTag = false;
-			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
-				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
-						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
-						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
-					hasTag = true;
-					break;
-				}
-			}
-
-			if (!hasTag) {
-				entity.setHasTags(true);
-				
-				TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
-				BaseTag newEntity = entity.addTag(def);
-				myEntityManager.persist(newEntity);
-			}
-		}
-		//@formatter:on
-
-		myEntityManager.merge(entity);
-		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
-
-		return metaGetOperation(theResourceId);
-	}
-
 	@Override
 	public MetaDt metaDeleteOperation(IIdType theResourceId, MetaDt theMetaDel) {
 		// Notify interceptors
@@ -810,6 +820,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return entity;
 	}
 
+	@Override
+	public void reindex(T theResource, ResourceTable theEntity) {
+		updateEntity(theResource, theEntity, false, null, true, false, theEntity.getUpdatedDate());
+	}
+
 	@Override
 	public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
 		// Notify interceptors
@@ -842,11 +857,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		ourLog.info("Processed remove tag {}/{} on {} in {}ms", new Object[] { theScheme, theTerm, theId.getValue(), w.getMillisAndRestart() });
 	}
 
-	@Override
-	public void reindex(T theResource, ResourceTable theEntity) {
-		updateEntity(theResource, theEntity, false, null, true, false, theEntity.getUpdatedDate());
-	}
-	
 	@Override
 	public IBundleProvider search(Map<String, IQueryParameterType> theParams) {
 		SearchParameterMap map = new SearchParameterMap();
@@ -924,9 +934,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return retVal;
 	}
 
-
-
-
 	private ArrayList<TagDefinition> toTagList(MetaDt theMeta) {
 		ArrayList<TagDefinition> retVal = new ArrayList<TagDefinition>();
 
@@ -943,6 +950,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return retVal;
 	}
 
+
+
+
 	@Override
 	public DaoMethodOutcome update(T theResource) {
 		return update(theResource, null);
@@ -1032,7 +1042,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		}
 	}
 
-	protected void validateOkToDeleteOrThrowResourceVersionConflictException(ResourceTable theEntity) {
+	protected void validateOkToDelete(List<DeleteConflict> theDeleteConflicts, ResourceTable theEntity) {
 		TypedQuery<ResourceLink> query = myEntityManager.createQuery("SELECT l FROM ResourceLink l WHERE l.myTargetResourcePid = :target_pid", ResourceLink.class);
 		query.setParameter("target_pid", theEntity.getId());
 		query.setMaxResults(1);
@@ -1042,13 +1052,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		}
 
 		ResourceLink link = resultList.get(0);
-		String targetId = theEntity.getIdDt().toUnqualifiedVersionless().getValue();
+		IdDt targetId = theEntity.getIdDt();
-		String sourceId = link.getSourceResource().getIdDt().toUnqualifiedVersionless().getValue();
+		IdDt sourceId = link.getSourceResource().getIdDt();
 		String sourcePath = link.getSourcePath();
 
-		throw new ResourceVersionConflictException("Unable to delete " + targetId + " because at least one resource has a reference to this resource. First reference found was resource " + sourceId + " in path " + sourcePath);
+		theDeleteConflicts.add(new DeleteConflict(sourceId, sourcePath, targetId));
 	}
 
+	
+	
 	private void validateResourceType(BaseHasResource entity) {
 		validateResourceType(entity, myResourceName);
 	}

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

@@ -37,6 +37,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
@@ -108,14 +109,15 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
 				throw new InvalidRequestException("No ID supplied. ID is required when validating with mode=DELETE");
 			}
 			final ResourceTable entity = readEntityLatestVersion(theId);
+
+			// Validate that there are no resources pointing to the candidate that
+			// would prevent deletion
+			List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
+			validateOkToDelete(deleteConflicts, entity);
+			validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
+				
 			OperationOutcome oo = new OperationOutcome();
-			try {
-				validateOkToDeleteOrThrowResourceVersionConflictException(entity);
 			oo.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDiagnostics("Ok to delete");
-			} catch (ResourceVersionConflictException e) {
-				oo.addIssue().setSeverity(IssueSeverityEnum.ERROR).setDiagnostics(e.getMessage());
-				throw new ResourceVersionConflictException(e.getMessage(), oo);
-			}
 			return new MethodOutcome(new IdDt(theId.getValue()), oo);
 		}
 

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

@@ -23,9 +23,14 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
@@ -35,6 +40,7 @@ import javax.persistence.TypedQuery;
 
 import org.apache.http.NameValuePair;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
@@ -47,7 +53,9 @@ import org.springframework.transaction.support.TransactionTemplate;
 import com.google.common.collect.ArrayListMultimap;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagDefinition;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
@@ -86,14 +94,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 	@Autowired
 	private PlatformTransactionManager myTxManager;
 
-	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
-		String url = nextEntry.getRequest().getUrl();
-		if (isBlank(url)) {
-			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
-		}
-		return url;
-	}
-
 	private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
 		ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
 		long start = System.currentTimeMillis();
@@ -165,6 +165,36 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 		return resp;
 	}
 
+	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
+		String url = nextEntry.getRequest().getUrl();
+		if (isBlank(url)) {
+			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
+		}
+		return url;
+	}
+
+	/**
+	 * This method is called for nested bundles (e.g. if we received a transaction with an entry that 
+	 * was a GET search, this method is called on the bundle for the search result, that will be placed in the
+	 * outer bundle). This method applies the _summary and _content parameters to the output of
+	 * that bundle.
+	 * 
+	 * TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
+	 */
+	private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
+		IParser p = getContext().newJsonParser();
+		RestfulServerUtils.configureResponseParser(theRequestDetails, p);
+		return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
+	}
+
+	private IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IResource> theClass) {
+		IFhirResourceDao<? extends IResource> retVal = getDao(theClass);
+		if (retVal == null) {
+			throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName());
+		}
+		return retVal;
+	}
+
 	@Override
 	public MetaDt metaGetOperation() {
 		// Notify interceptors
@@ -180,6 +210,31 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 		return retVal;
 	}
 
+	private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
+		RuntimeResourceDefinition resType;
+		try {
+			resType = getContext().getResourceDefinition(theParts.getResourceType());
+		} catch (DataFormatException e) {
+			String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
+			throw new InvalidRequestException(msg);
+		}
+		IFhirResourceDao<? extends IBaseResource> dao = null;
+		if (resType != null) {
+			dao = getDao(resType.getImplementingClass());
+		}
+		if (dao == null) {
+			String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
+			throw new InvalidRequestException(msg);
+		}
+
+		// if (theParts.getResourceId() == null && theParts.getParams() == null) {
+		// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
+		// throw new InvalidRequestException(msg);
+		// }
+
+		return dao;
+	}
+
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
@@ -215,26 +270,51 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 		Map<IdDt, IdDt> idSubstitutions = new HashMap<IdDt, IdDt>();
 		Map<IdDt, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdDt, DaoMethodOutcome>();
 
+		/*
+		 * We want to execute the transaction request bundle elements in the order
+		 * specified by the FHIR specification (see TransactionSorter) so we save the 
+		 * original order in the request, then sort it.
+		 * 
+		 * Entries with a type of GET are removed from the bundle so that they 
+		 * can be processed at the very end. We do this because the incoming resources
+		 * are saved in a two-phase way in order to deal with interdependencies, and
+		 * we want the GET processing to use the final indexing state
+		 */
 		Bundle response = new Bundle();
+		List<Entry> getEntries = new ArrayList<Entry>();
+		IdentityHashMap<Entry, Integer> originalRequestOrder = new IdentityHashMap<Bundle.Entry, Integer>();
+		for (int i = 0; i < theRequest.getEntry().size(); i++) {
+			originalRequestOrder.put(theRequest.getEntry().get(i), i);
+			response.addEntry();
+			if (theRequest.getEntry().get(i).getRequest().getMethodElement().getValueAsEnum() == HTTPVerbEnum.GET) {
+				getEntries.add(theRequest.getEntry().get(i));
+			}
+		}
+		Collections.sort(theRequest.getEntry(), new TransactionSorter());
 		
-		// TODO: process verbs in the correct order
+		List<IIdType> deletedResources = new ArrayList<IIdType>();
+		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
 		
+		/*
+		 * Loop through the request and process any entries of type
+		 * PUT, POST or DELETE
+		 */
 		for (int i = 0; i < theRequest.getEntry().size(); i++) {
 
 			if (i % 100 == 0) {
-				ourLog.info("Processed {} entries out of {}", i, theRequest.getEntry().size());
+				ourLog.info("Processed {} non-GET entries out of {}", i, theRequest.getEntry().size());
 			}
 
-			Entry nextEntry = theRequest.getEntry().get(i);
+			Entry nextReqEntry = theRequest.getEntry().get(i);
-			IResource res = nextEntry.getResource();
+			IResource res = nextReqEntry.getResource();
 			IdDt nextResourceId = null;
 			if (res != null) {
 
 				nextResourceId = res.getId();
 
 				if (nextResourceId.hasIdPart() == false) {
-					if (isNotBlank(nextEntry.getFullUrl())) {
+					if (isNotBlank(nextReqEntry.getFullUrl())) {
-						nextResourceId = new IdDt(nextEntry.getFullUrl());
+						nextResourceId = new IdDt(nextReqEntry.getFullUrl());
 					}
 				}
 
@@ -263,12 +343,13 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 
 			}
 
-			HTTPVerbEnum verb = nextEntry.getRequest().getMethodElement().getValueAsEnum();
+			HTTPVerbEnum verb = nextReqEntry.getRequest().getMethodElement().getValueAsEnum();
 			if (verb == null) {
-				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextEntry.getRequest().getMethod()));
+				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextReqEntry.getRequest().getMethod()));
 			}
 
 			String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
+			Entry nextRespEntry = response.getEntry().get(originalRequestOrder.get(nextReqEntry));
 
 			switch (verb) {
 			case POST: {
@@ -277,24 +358,32 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 				IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
 				res.setId((String) null);
 				DaoMethodOutcome outcome;
-				Entry newEntry = response.addEntry();
+				outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false);
-				outcome = resourceDao.create(res, nextEntry.getRequest().getIfNoneExist(), false);
+				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
-				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, newEntry, resourceType, res);
 				break;
 			}
 			case DELETE: {
 				// DELETE
-				Entry newEntry = response.addEntry();
+				String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
-				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
 				UrlParts parts = UrlUtil.parseUrl(url);
 				ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb.getCode(), url);
+				int status = Constants.STATUS_HTTP_204_NO_CONTENT;
 				if (parts.getResourceId() != null) {
-					dao.delete(new IdDt(parts.getResourceType(), parts.getResourceId()));
+					ResourceTable deleted = dao.delete(new IdDt(parts.getResourceType(), parts.getResourceId()), deleteConflicts);
+					if (deleted != null) {
+						deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless());
+					}
 				} else {
-					dao.deleteByUrl(parts.getResourceType() + '?' + parts.getParams(), true);
+					List<ResourceTable> allDeleted = dao.deleteByUrl(parts.getResourceType() + '?' + parts.getParams(), deleteConflicts);
+					for (ResourceTable deleted : allDeleted) {
+						deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless());						
+					}
+					if (allDeleted.isEmpty()) {
+						status = Constants.STATUS_HTTP_404_NOT_FOUND;
+					}
 				}
 
-				newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_204_NO_CONTENT));
+				nextRespEntry.getResponse().setStatus(toStatusString(status));
 				break;
 			}
 			case PUT: {
@@ -303,9 +392,8 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 				IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
 
 				DaoMethodOutcome outcome;
-				Entry newEntry = response.addEntry();
 
-				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
+				String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
 
 				UrlParts parts = UrlUtil.parseUrl(url);
 				if (isNotBlank(parts.getResourceId())) {
@@ -316,80 +404,32 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 					outcome = resourceDao.update(res, parts.getResourceType() + '?' + parts.getParams(), false);
 				}
 
-				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, newEntry, resourceType, res);
+				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
 				break;
 			}
-			case GET: {
-				// SEARCH/READ/VREAD
-				RequestDetails requestDetails = new RequestDetails();
-				requestDetails.setServletRequest(theRequestDetails.getServletRequest());
-				requestDetails.setRequestType(RequestTypeEnum.GET);
-				requestDetails.setServer(theRequestDetails.getServer());
-				
-				String url = extractTransactionUrlOrThrowException(nextEntry, verb);
-				
-				int qIndex = url.indexOf('?');
-				ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
-				requestDetails.setParameters(new HashMap<String, String[]>());
-				if (qIndex != -1) {
-					String params = url.substring(qIndex);
-					List<NameValuePair> parameters = translateMatchUrl(params);
-					for (NameValuePair next : parameters) {
-						paramValues.put(next.getName(), next.getValue());
-					}
-					for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
-						String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
-						requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
-					}
-					url = url.substring(0, qIndex);
-				}
-
-				requestDetails.setRequestPath(url);
-				requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
-
-				theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
-				BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
-				if (method == null) {
-					throw new IllegalArgumentException("Unable to handle GET " + url);
-				}
-				
-				if (isNotBlank(nextEntry.getRequest().getIfMatch())) {
-					requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextEntry.getRequest().getIfMatch());
-				}
-				if (isNotBlank(nextEntry.getRequest().getIfNoneExist())) {
-					requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextEntry.getRequest().getIfNoneExist());
-				}
-				if (isNotBlank(nextEntry.getRequest().getIfNoneMatch())) {
-					requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextEntry.getRequest().getIfNoneMatch());
-				}
-				
-				if (method instanceof BaseResourceReturningMethodBinding) {
-					try {
-						ResourceOrDstu1Bundle responseData = ((BaseResourceReturningMethodBinding) method).invokeServer(theRequestDetails.getServer(), requestDetails, new byte[0]);
-						Entry newEntry = response.addEntry();
-						IBaseResource resource = responseData.getResource();
-						if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
-							resource = filterNestedBundle(requestDetails, resource);
-						}
-						newEntry.setResource((IResource) resource);
-						newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
-					} catch (NotModifiedException e) {
-						Entry newEntry = response.addEntry();
-						newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
-					}
-				} else {
-					throw new IllegalArgumentException("Unable to handle GET " + url);
-				}
-			}
 			}
 		}
 
-		FhirTerser terser = getContext().newTerser();
+		/*
+		 * Make sure that there are no conflicts from deletions. E.g. we can't delete something
+		 * if something else has a reference to it.. Unless the thing that has a reference to it
+		 * was also deleted as a part of this transaction, which is why we check this now at the 
+		 * end.
+		 */
+		
+		for (Iterator<DeleteConflict> iter = deleteConflicts.iterator(); iter.hasNext(); ) {
+			DeleteConflict next = iter.next();
+			if (deletedResources.contains(next.getTargetId().toVersionless())) {
+				iter.remove();
+			}
+		}
+		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
 
 		/*
 		 * Perform ID substitutions and then index each resource we have saved
 		 */
 
+		FhirTerser terser = getContext().newTerser();
 		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
 			IResource nextResource = (IResource) nextOutcome.getResource();
 			if (nextResource == null) {
@@ -443,6 +483,74 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 			ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
 		}
 
+		/*
+		 * Loop through the request and process any entries of type GET
+		 */
+		for (int i = 0; i < getEntries.size(); i++) {
+			Entry nextReqEntry = getEntries.get(i);
+			Integer originalOrder = originalRequestOrder.get(nextReqEntry);
+			Entry nextRespEntry = response.getEntry().get(originalOrder);
+
+			RequestDetails requestDetails = new RequestDetails();
+			requestDetails.setServletRequest(theRequestDetails.getServletRequest());
+			requestDetails.setRequestType(RequestTypeEnum.GET);
+			requestDetails.setServer(theRequestDetails.getServer());
+			
+			String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerbEnum.GET);
+			
+			int qIndex = url.indexOf('?');
+			ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
+			requestDetails.setParameters(new HashMap<String, String[]>());
+			if (qIndex != -1) {
+				String params = url.substring(qIndex);
+				List<NameValuePair> parameters = translateMatchUrl(params);
+				for (NameValuePair next : parameters) {
+					paramValues.put(next.getName(), next.getValue());
+				}
+				for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
+					String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
+					requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
+				}
+				url = url.substring(0, qIndex);
+			}
+
+			requestDetails.setRequestPath(url);
+			requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
+
+			theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
+			BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
+			if (method == null) {
+				throw new IllegalArgumentException("Unable to handle GET " + url);
+			}
+			
+			if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
+				requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextReqEntry.getRequest().getIfMatch());
+			}
+			if (isNotBlank(nextReqEntry.getRequest().getIfNoneExist())) {
+				requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextReqEntry.getRequest().getIfNoneExist());
+			}
+			if (isNotBlank(nextReqEntry.getRequest().getIfNoneMatch())) {
+				requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
+			}
+			
+			if (method instanceof BaseResourceReturningMethodBinding) {
+				try {
+					ResourceOrDstu1Bundle responseData = ((BaseResourceReturningMethodBinding) method).invokeServer(theRequestDetails.getServer(), requestDetails, new byte[0]);
+					IBaseResource resource = responseData.getResource();
+					if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
+						resource = filterNestedBundle(requestDetails, resource);
+					}
+					nextRespEntry.setResource((IResource) resource);
+					nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
+				} catch (NotModifiedException e) {
+					nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
+				}
+			} else {
+				throw new IllegalArgumentException("Unable to handle GET " + url);
+			}
+
+		}
+		
 		long delay = System.currentTimeMillis() - start;
 		ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
 
@@ -450,53 +558,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 		return response;
 	}
 
-	/**
-	 * This method is called for nested bundles (e.g. if we received a transaction with an entry that 
-	 * was a GET search, this method is called on the bundle for the search result, that will be placed in the
-	 * outer bundle). This method applies the _summary and _content parameters to the output of
-	 * that bundle.
-	 * 
-	 * TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
-	 */
-	private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
-		IParser p = getContext().newJsonParser();
-		RestfulServerUtils.configureResponseParser(theRequestDetails, p);
-		return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
-	}
-
-	private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
-		RuntimeResourceDefinition resType;
-		try {
-			resType = getContext().getResourceDefinition(theParts.getResourceType());
-		} catch (DataFormatException e) {
-			String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
-			throw new InvalidRequestException(msg);
-		}
-		IFhirResourceDao<? extends IBaseResource> dao = null;
-		if (resType != null) {
-			dao = getDao(resType.getImplementingClass());
-		}
-		if (dao == null) {
-			String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
-			throw new InvalidRequestException(msg);
-		}
-
-		// if (theParts.getResourceId() == null && theParts.getParams() == null) {
-		// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
-		// throw new InvalidRequestException(msg);
-		// }
-
-		return dao;
-	}
-
-	private IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IResource> theClass) {
-		IFhirResourceDao<? extends IResource> retVal = getDao(theClass);
-		if (retVal == null) {
-			throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName());
-		}
-		return retVal;
-	}
-
 	private static void handleTransactionCreateOrUpdateOutcome(Map<IdDt, IdDt> idSubstitutions, Map<IdDt, DaoMethodOutcome> idToPersistedOutcome, IdDt nextResourceId, DaoMethodOutcome outcome,
 			Entry newEntry, String theResourceType, IResource theRes) {
 		IdDt newId = (IdDt) outcome.getId().toUnqualifiedVersionless();
@@ -532,4 +593,47 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle> {
 		return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
 	}
 
+	//@formatter:off
+	/**
+	 * Transaction Order, per the spec:
+	 * 
+	 * Process any DELETE interactions
+	 * Process any POST interactions
+	 * Process any PUT interactions
+	 * Process any GET interactions
+	 */
+	//@formatter:off
+	public class TransactionSorter implements Comparator<Entry> {
+
+		@Override
+		public int compare(Entry theO1, Entry theO2) {			
+			int o1 = toOrder(theO1);
+			int o2 = toOrder(theO2);
+
+			return o1 - o2;
+		}
+
+		private int toOrder(Entry theO1) {
+			int o1 = 0;
+			if (theO1.getRequest().getMethodElement().getValueAsEnum() != null) {
+			switch (theO1.getRequest().getMethodElement().getValueAsEnum()) {
+			case DELETE:
+				o1 = 1;
+				break;
+			case POST:
+				o1 = 2;
+				break;
+			case PUT:
+				o1 = 3;
+				break;
+			case GET:
+				o1 = 4;
+				break;
+			}
+			}
+			return o1;
+		}
+
+	}
+
 }

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

@@ -23,6 +23,7 @@ import java.util.Collection;
  */
 
 import java.util.Date;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
@@ -32,6 +33,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@@ -57,14 +59,28 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing);
 
+	/**
+	 * This method throws an exception if there are delete conflicts
+	 */
 	DaoMethodOutcome delete(IIdType theResource);
 
+	/**
+	 * This method does not throw an exception if there are delete conflicts, but populates them
+	 * in the provided list
+	 */
+	ResourceTable delete(IIdType theResource, List<DeleteConflict> theDeleteConflictsListToPopulate);
+
+	/**
+	 * This method throws an exception if there are delete conflicts
+	 */
 	DaoMethodOutcome deleteByUrl(String theString);
 
 	/**
-	 * @param theTransaction Is this being called in a bundle? If so, don't throw an exception if no matches
+	 * This method does not throw an exception if there are delete conflicts, but populates them
+	 * in the provided list
+	 * @return 
 	 */
-	DaoMethodOutcome deleteByUrl(String theUrl, boolean theTransaction);
+	List<ResourceTable> deleteByUrl(String theUrl, List<DeleteConflict> theDeleteConflictsListToPopulate);
 
 	TagList getAllResourceTags();
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/DeleteConflict.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.util;
+
+import ca.uhn.fhir.model.primitive.IdDt;
+
+public class DeleteConflict {
+
+	private final IdDt mySourceId;
+	private final String mySourcePath;
+	private final IdDt myTargetId;
+
+	public DeleteConflict(IdDt theSourceId, String theSourcePath, IdDt theTargetId) {
+		mySourceId = theSourceId;
+		mySourcePath = theSourcePath;
+		myTargetId = theTargetId;
+	}
+
+	public IdDt getSourceId() {
+		return mySourceId;
+	}
+
+	public String getSourcePath() {
+		return mySourcePath;
+	}
+
+	public IdDt getTargetId() {
+		return myTargetId;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaDstu2SystemTest.java

@@ -36,6 +36,7 @@ public abstract class BaseJpaDstu2SystemTest extends BaseJpaDstu2Test {
 		when(myRequestDetails.getServer()).thenReturn(myServer);
 		HttpServletRequest servletRequest = mock(HttpServletRequest.class);
 		when(myRequestDetails.getServletRequest()).thenReturn(servletRequest);
+		when(myRequestDetails.getFhirServerBase()).thenReturn("http://example.com/base");
 		when(servletRequest.getHeaderNames()).thenReturn(mock(Enumeration.class));
 		when(servletRequest.getRequestURL()).thenReturn(new StringBuffer("/Patient"));
 	}

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

@@ -685,8 +685,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			myOrganizationDao.delete(orgId);
 			fail();
 		} catch (ResourceVersionConflictException e) {
-			assertThat(e.getMessage(), containsString("Unable to delete Organization/" + orgId.getIdPart()
+			assertThat(e.getMessage(), containsString("Delete failed because of constraint"));
-					+ " because at least one resource has a reference to this resource. First reference found was resource Patient/" + patId.getIdPart() + " in path Patient.managingOrganization"));
 		}
 
 		myPatientDao.delete(patId);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2ValidateTest.java

@@ -215,7 +215,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 
 		String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
 		ourLog.info(ooString);
-		assertThat(ooString, containsString("Unable to delete "+orgId.getValue()+" because at least one resource has a reference to this resource. First reference found was resource " + patId.getValue() + " in path Patient.managingOrganization"));
+		assertThat(ooString, containsString("Unable to delete Organization"));
 
 		pat.setId(patId);
 		pat.getManagingOrganization().setReference("");

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

@@ -589,6 +589,124 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	}
 
+	/**
+	 * See #253 Test that the order of deletes is version independent
+	 */
+	@Test
+	public void testTransactionDeleteIsOrderIndependantTargetFirst() {
+		String methodName = "testTransactionDeleteIsOrderIndependantTargetFirst";
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IIdType pid = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
+		ourLog.info("Created patient, got it: {}", pid);
+
+		Observation o1 = new Observation();
+		o1.getSubject().setReference(pid);
+		IIdType oid1 = myObservationDao.create(o1).getId().toUnqualifiedVersionless();
+
+		Observation o2 = new Observation();
+		o2.addIdentifier().setValue(methodName);
+		o2.getSubject().setReference(pid);
+		IIdType oid2 = myObservationDao.create(o2).getId().toUnqualifiedVersionless();
+
+		myPatientDao.read(pid);
+		myObservationDao.read(oid1);
+
+		// The target is Patient, so try with it first in the bundle
+		Bundle request = new Bundle();
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl(pid.getValue());
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl(oid1.getValue());
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Observation?identifier=" + methodName);
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+
+		assertEquals(3, resp.getEntry().size());
+		assertEquals("204 No Content", resp.getEntry().get(0).getResponse().getStatus());
+		assertEquals("204 No Content", resp.getEntry().get(1).getResponse().getStatus());
+		assertEquals("204 No Content", resp.getEntry().get(2).getResponse().getStatus());
+
+		try {
+			myPatientDao.read(pid);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myObservationDao.read(oid1);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myObservationDao.read(oid2);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+	}
+
+	/**
+	 * See #253 Test that the order of deletes is version independent
+	 */
+	@Test
+	public void testTransactionDeleteIsOrderIndependantTargetLast() {
+		String methodName = "testTransactionDeleteIsOrderIndependantTargetFirst";
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue(methodName);
+		IIdType pid = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
+		ourLog.info("Created patient, got it: {}", pid);
+
+		Observation o1 = new Observation();
+		o1.getSubject().setReference(pid);
+		IIdType oid1 = myObservationDao.create(o1).getId().toUnqualifiedVersionless();
+
+		Observation o2 = new Observation();
+		o2.addIdentifier().setValue(methodName);
+		o2.getSubject().setReference(pid);
+		IIdType oid2 = myObservationDao.create(o2).getId().toUnqualifiedVersionless();
+
+		myPatientDao.read(pid);
+		myObservationDao.read(oid1);
+
+		// The target is Patient, so try with it last in the bundle
+		Bundle request = new Bundle();
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl(oid1.getValue());
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Observation?identifier=" + methodName);
+		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl(pid.getValue());
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+
+		assertEquals(3, resp.getEntry().size());
+		assertEquals("204 No Content", resp.getEntry().get(0).getResponse().getStatus());
+		assertEquals("204 No Content", resp.getEntry().get(1).getResponse().getStatus());
+		assertEquals("204 No Content", resp.getEntry().get(2).getResponse().getStatus());
+
+		try {
+			myPatientDao.read(pid);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myObservationDao.read(oid1);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myObservationDao.read(oid2);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+	}
+
 	@Test
 	public void testTransactionDeleteMatchUrlWithOneMatch() {
 		String methodName = "testTransactionDeleteMatchUrlWithOneMatch";
@@ -670,7 +788,10 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		request.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
 
 		// try {
-		mySystemDao.transaction(myRequestDetails, request);
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+		assertEquals(1, resp.getEntry().size());
+		assertEquals("404 Not Found", resp.getEntry().get(0).getResponse().getStatus());
+		
 		// fail();
 		// } catch (ResourceNotFoundException e) {
 		// assertThat(e.getMessage(), containsString("resource matching URL \"Patient?"));
@@ -762,6 +883,88 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
 	}
 
+	@Test
+	public void testTransactionOrdering() {
+		String methodName = "testTransactionOrdering";
+		
+		//@formatter:off
+		/*
+		 * Transaction Order, per the spec:
+		 * 
+		 * Process any DELETE interactions
+		 * Process any POST interactions
+		 * Process any PUT interactions
+		 * Process any GET interactions
+		 * 
+		 * This test creates a transaction bundle that includes 
+		 * these four operations in the reverse order and verifies
+		 * that they are invoked correctly.
+		 */
+		//@formatter:off
+		
+		int pass = 0;
+		IdDt patientPlaceholderId = IdDt.newRandomUuid();
+		
+		Bundle req = testTransactionOrderingCreateBundle(methodName, pass, patientPlaceholderId);
+		Bundle resp = mySystemDao.transaction(myRequestDetails, req);
+		testTransactionOrderingValidateResponse(pass, resp);
+		
+		pass = 1;
+		patientPlaceholderId = IdDt.newRandomUuid();
+		
+		req = testTransactionOrderingCreateBundle(methodName, pass, patientPlaceholderId);
+		resp = mySystemDao.transaction(myRequestDetails, req);
+		testTransactionOrderingValidateResponse(pass, resp);
+
+	}
+
+	private void testTransactionOrderingValidateResponse(int pass, Bundle resp) {
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		assertEquals(4, resp.getEntry().size());
+		assertEquals("200 OK", resp.getEntry().get(0).getResponse().getStatus());
+		if (pass == 0) {
+			assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
+			assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Observation/"));
+			assertThat(resp.getEntry().get(1).getResponse().getLocation(), endsWith("_history/1"));
+		} else {
+			assertEquals("200 OK", resp.getEntry().get(1).getResponse().getStatus());
+			assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Observation/"));
+			assertThat(resp.getEntry().get(1).getResponse().getLocation(), endsWith("_history/2"));
+		}
+		assertEquals("201 Created", resp.getEntry().get(2).getResponse().getStatus());
+		assertThat(resp.getEntry().get(2).getResponse().getLocation(), startsWith("Patient/"));
+		if (pass == 0) {
+			assertEquals("404 Not Found", resp.getEntry().get(3).getResponse().getStatus());
+		} else {
+			assertEquals("204 No Content", resp.getEntry().get(3).getResponse().getStatus());
+		}
+		
+		
+		Bundle respGetBundle = (Bundle) resp.getEntry().get(0).getResource();
+		assertEquals(1, respGetBundle.getEntry().size());
+		assertEquals("testTransactionOrdering" + pass, ((Patient)respGetBundle.getEntry().get(0).getResource()).getNameFirstRep().getFamilyFirstRep().getValue());
+		assertThat(respGetBundle.getLink("self").getUrl(), endsWith("/Patient?identifier=testTransactionOrdering"));
+	}
+
+	private Bundle testTransactionOrderingCreateBundle(String methodName, int pass, IdDt patientPlaceholderId) {
+		Bundle req = new Bundle();
+		req.addEntry().getRequest().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=" + methodName);
+		
+		Observation obs = new Observation();
+		obs.getSubject().setReference(patientPlaceholderId);
+		obs.addIdentifier().setValue(methodName);
+		obs.getCode().setText(methodName + pass);
+		req.addEntry().setResource(obs).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl("Observation?identifier=" + methodName);
+		
+		Patient pat = new Patient();
+		pat.addIdentifier().setValue(methodName);
+		pat.addName().addFamily(methodName + pass);
+		req.addEntry().setResource(pat).setFullUrl(patientPlaceholderId.getValue()).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
+		
+		req.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=" + methodName);
+		return req;
+	}
+
 	@Test
 	public void testTransactionReadAndSearch() {
 		String methodName = "testTransactionReadAndSearch";
@@ -829,6 +1032,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		details = detailsCapt.getValue();
 		assertEquals("Patient", details.getResourceType());
 
+		
 	}
 
 	@Test

src/changes/changes.xml

@@ -245,6 +245,12 @@
 				codes (specifically, ValueSets which defined concepts containing
 				child concepts did not result in Enum values for the child concepts)
 			</action>
+			<action type="fix" fix="253">
+				In the JPA server, order of transaction processing should be 
+				DELETE, POST, PUT, GET, and the order should not matter
+				within entries with the same verb. Thanks to Bill de Beaubien
+				for reporting!
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">