private void encodeResourceReferenceToStreamWriter( XMLStreamWriter theEventWriter, BaseResourceReferenceDt theRef) throws XMLStreamException { String reference = determineReferenceText(theRef); if (StringUtils.isNotBlank(reference)) { theEventWriter.writeStartElement(RESREF_REFERENCE); theEventWriter.writeAttribute("value", reference); theEventWriter.writeEndElement(); } if (!(theRef.getDisplayElement().isEmpty())) { theEventWriter.writeStartElement(RESREF_DISPLAY); theEventWriter.writeAttribute("value", theRef.getDisplayElement().getValue()); theEventWriter.writeEndElement(); } }
private void encodeChildElementToStreamWriter( IBaseResource theResource, XMLStreamWriter theEventWriter, IBase nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl, boolean theIncludedResource) throws XMLStreamException, DataFormatException { if (nextValue.isEmpty()) { if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && getContainedResources().isEmpty() == false && theIncludedResource == false) { // We still want to go in.. } else { return; } } switch (childDef.getChildType()) { case PRIMITIVE_DATATYPE: { IPrimitiveType<?> pd = (IPrimitiveType<?>) nextValue; String value = pd.getValueAsString(); if (value != null) { theEventWriter.writeStartElement(childName); theEventWriter.writeAttribute("value", value); encodeExtensionsIfPresent(theResource, theEventWriter, nextValue, theIncludedResource); theEventWriter.writeEndElement(); } break; } case RESOURCE_BLOCK: case COMPOSITE_DATATYPE: { theEventWriter.writeStartElement(childName); if (isNotBlank(theExtensionUrl)) { theEventWriter.writeAttribute("url", theExtensionUrl); } BaseRuntimeElementCompositeDefinition<?> childCompositeDef = (BaseRuntimeElementCompositeDefinition<?>) childDef; encodeCompositeElementToStreamWriter( theResource, nextValue, theEventWriter, childCompositeDef, theIncludedResource); theEventWriter.writeEndElement(); break; } case RESOURCE_REF: { BaseResourceReferenceDt ref = (BaseResourceReferenceDt) nextValue; if (!ref.isEmpty()) { theEventWriter.writeStartElement(childName); encodeResourceReferenceToStreamWriter(theEventWriter, ref); theEventWriter.writeEndElement(); } break; } case CONTAINED_RESOURCES: { BaseContainedDt value = (BaseContainedDt) nextValue; /* * Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; } * theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue())); * theEventWriter.writeEndElement(); } */ for (IBaseResource next : getContainedResources().getContainedResources()) { IdDt resourceId = getContainedResources().getResourceId(next); theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter( next, theEventWriter, true, fixContainedResourceId(resourceId.getValue())); theEventWriter.writeEndElement(); } break; } case RESOURCE: { theEventWriter.writeStartElement(childName); IBaseResource resource = (IBaseResource) nextValue; encodeResourceToXmlStreamWriter(resource, theEventWriter, false); theEventWriter.writeEndElement(); break; } case PRIMITIVE_XHTML: { XhtmlDt dt = (XhtmlDt) nextValue; if (dt.hasContent()) { encodeXhtml(dt, theEventWriter); } break; } case EXTENSION_DECLARED: case UNDECL_EXT: { throw new IllegalStateException("state should not happen: " + childDef.getName()); } } }
@Transactional(propagation = Propagation.REQUIRED) @Override public List<IResource> transaction( RequestDetails theRequestDetails, List<IResource> theResources) { ourLog.info("Beginning transaction with {} resources", theResources.size()); // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(null, null); notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails); long start = System.currentTimeMillis(); Set<IdDt> allIds = new HashSet<IdDt>(); for (int i = 0; i < theResources.size(); i++) { IResource res = theResources.get(i); if (res.getId().hasIdPart() && !res.getId().hasResourceType() && !isPlaceholder(res.getId())) { res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart())); } /* * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness */ if (isPlaceholder(res.getId())) { if (!allIds.add(res.getId())) { throw new InvalidRequestException( "Transaction bundle contains multiple resources with ID: " + res.getId()); } } else if (res.getId().hasResourceType() && res.getId().hasIdPart()) { IdDt nextId = res.getId().toUnqualifiedVersionless(); if (!allIds.add(nextId)) { throw new InvalidRequestException( "Transaction bundle contains multiple resources with ID: " + nextId); } } } FhirTerser terser = getContext().newTerser(); int creations = 0; int updates = 0; Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>(); List<ResourceTable> persistedResources = new ArrayList<ResourceTable>(); List<IResource> retVal = new ArrayList<IResource>(); OperationOutcome oo = new OperationOutcome(); retVal.add(oo); Date updateTime = new Date(); for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) { IResource nextResource = theResources.get(resourceIdx); IdDt nextId = nextResource.getId(); if (nextId == null) { nextId = new IdDt(); } String resourceName = toResourceName(nextResource); BundleEntryTransactionMethodEnum nextResouceOperationIn = ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(nextResource); if (nextResouceOperationIn == null && hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) { nextResouceOperationIn = BundleEntryTransactionMethodEnum.DELETE; } String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource); Set<Long> candidateMatches = null; if (StringUtils.isNotBlank(matchUrl)) { candidateMatches = processMatchUrl(matchUrl, nextResource.getClass()); } ResourceTable entity; if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) { entity = null; } else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT || nextResouceOperationIn == BundleEntryTransactionMethodEnum.DELETE) { if (candidateMatches == null || candidateMatches.size() == 0) { if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) { throw new InvalidRequestException( getContext() .getLocalizer() .getMessage( BaseHapiFhirSystemDao.class, "transactionOperationFailedNoId", nextResouceOperationIn.name())); } entity = tryToLoadEntity(nextId); if (entity == null) { if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT) { ourLog.debug( "Attempting to UPDATE resource with unknown ID '{}', will CREATE instead", nextId); } else if (candidateMatches == null) { throw new InvalidRequestException( getContext() .getLocalizer() .getMessage( BaseHapiFhirSystemDao.class, "transactionOperationFailedUnknownId", nextResouceOperationIn.name(), nextId)); } else { ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl); persistedResources.add(null); retVal.add(nextResource); continue; } } } else if (candidateMatches.size() == 1) { entity = loadFirstEntityFromCandidateMatches(candidateMatches); } else { throw new InvalidRequestException( getContext() .getLocalizer() .getMessage( BaseHapiFhirSystemDao.class, "transactionOperationWithMultipleMatchFailure", nextResouceOperationIn.name(), matchUrl, candidateMatches.size())); } } else if (nextId.isEmpty() || isPlaceholder(nextId)) { entity = null; } else { entity = tryToLoadEntity(nextId); } BundleEntryTransactionMethodEnum nextResouceOperationOut; if (entity == null) { nextResouceOperationOut = BundleEntryTransactionMethodEnum.POST; entity = toEntity(nextResource); entity.setUpdated(updateTime); entity.setPublished(updateTime); if (nextId.isEmpty() == false && "cid:".equals(nextId.getBaseUrl())) { ourLog.debug( "Resource in transaction has ID[{}], will replace with server assigned ID", nextId.getIdPart()); } else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) { if (nextId.isEmpty() == false) { ourLog.debug( "Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID", nextId.getIdPart()); } if (candidateMatches != null) { if (candidateMatches.size() == 1) { ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl); BaseHasResource existingEntity = loadFirstEntityFromCandidateMatches(candidateMatches); IResource existing = (IResource) toResource(existingEntity, false); persistedResources.add(null); retVal.add(existing); continue; } if (candidateMatches.size() > 1) { throw new InvalidRequestException( getContext() .getLocalizer() .getMessage( BaseHapiFhirSystemDao.class, "transactionOperationWithMultipleMatchFailure", BundleEntryTransactionMethodEnum.POST.name(), matchUrl, candidateMatches.size())); } } } else { createForcedIdIfNeeded(entity, nextId); } myEntityManager.persist(entity); if (entity.getForcedId() != null) { myEntityManager.persist(entity.getForcedId()); } creations++; ourLog.info( "Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId); } else { nextResouceOperationOut = nextResouceOperationIn; if (nextResouceOperationOut == null) { nextResouceOperationOut = BundleEntryTransactionMethodEnum.PUT; } updates++; ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId); } persistedResources.add(entity); retVal.add(nextResource); ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(nextResource, nextResouceOperationOut); } ourLog.info("Flushing transaction to database"); myEntityManager.flush(); for (int i = 0; i < persistedResources.size(); i++) { ResourceTable entity = persistedResources.get(i); String resourceName = toResourceName(theResources.get(i)); IdDt nextId = theResources.get(i).getId(); IdDt newId; if (entity == null) { newId = retVal.get(i + 1).getId().toUnqualifiedVersionless(); } else { newId = entity.getIdDt().toUnqualifiedVersionless(); } if (nextId == null || nextId.isEmpty()) { ourLog.info( "Transaction resource (with no preexisting ID) has been assigned new ID[{}]", nextId, newId); } else { if (nextId.toUnqualifiedVersionless().equals(newId)) { ourLog.info("Transaction resource ID[{}] is being updated", newId); } else { if (isPlaceholder(nextId)) { // nextId = new IdDt(resourceName, nextId.getIdPart()); ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId); idConversions.put(nextId, newId); idConversions.put(new IdDt(resourceName + "/" + nextId.getValue()), newId); } } } } for (IResource nextResource : theResources) { List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class); for (BaseResourceReferenceDt nextRef : allRefs) { IdDt nextId = nextRef.getReference(); if (idConversions.containsKey(nextId)) { IdDt newId = idConversions.get(nextId); ourLog.info(" * Replacing resource ref {} with {}", nextId, newId); nextRef.setReference(newId); } else { ourLog.debug(" * Reference [{}] does not exist in bundle", nextId); } } } ourLog.info("Re-flushing updated resource references and extracting search criteria"); for (int i = 0; i < theResources.size(); i++) { IResource resource = theResources.get(i); ResourceTable table = persistedResources.get(i); if (table == null) { continue; } InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource); Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null; if (deletedInstantOrNull == null && ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(resource) == BundleEntryTransactionMethodEnum.DELETE) { deletedTimestampOrNull = updateTime; ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull)); } updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull, updateTime); } long delay = System.currentTimeMillis() - start; ourLog.info( "Transaction completed in {}ms with {} creations and {} updates", new Object[] {delay, creations, updates}); oo.addIssue() .setSeverity(IssueSeverityEnum.INFORMATION) .setDetails( "Transaction completed in " + delay + "ms with " + creations + " creations and " + updates + " updates"); return retVal; }