private void writeOptionalTagWithTextNode(
XMLStreamWriter theEventWriter, String theTagName, InstantDt theInstantDt)
throws XMLStreamException {
if (theInstantDt.getValue() != null) {
theEventWriter.writeStartElement(theTagName);
theEventWriter.writeCharacters(theInstantDt.getValueAsString());
theEventWriter.writeEndElement();
}
}
private void encodeResourceToXmlStreamWriter(
IBaseResource theResource,
XMLStreamWriter theEventWriter,
boolean theContainedResource,
String theResourceId)
throws XMLStreamException {
if (!theContainedResource) {
super.containResourcesForEncoding(theResource);
}
RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
if (resDef == null) {
throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
}
theEventWriter.writeStartElement(resDef.getName());
theEventWriter.writeDefaultNamespace(FHIR_NS);
if (theResource instanceof IAnyResource) {
// HL7.org Structures
encodeCompositeElementToStreamWriter(
theResource, theResource, theEventWriter, resDef, theContainedResource);
} else {
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
// DSTU2+
IResource resource = (IResource) theResource;
writeOptionalTagWithValue(theEventWriter, "id", theResourceId);
InstantDt updated =
(InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt resourceId = resource.getId();
String versionIdPart = resourceId.getVersionIdPart();
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
List<BaseCodingDt> securityLabels =
extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
List<IdDt> profiles =
extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
theEventWriter.writeStartElement("meta");
writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
for (IdDt profile : profiles) {
theEventWriter.writeStartElement("profile");
theEventWriter.writeAttribute("value", profile.getValue());
theEventWriter.writeEndElement();
}
for (BaseCodingDt securityLabel : securityLabels) {
theEventWriter.writeStartElement("security");
BaseRuntimeElementCompositeDefinition<?> def =
(BaseRuntimeElementCompositeDefinition<?>)
myContext.getElementDefinition(securityLabel.getClass());
encodeCompositeElementChildrenToStreamWriter(
resource, securityLabel, theEventWriter, def.getChildren(), theContainedResource);
theEventWriter.writeEndElement();
}
if (tags != null) {
for (Tag tag : tags) {
theEventWriter.writeStartElement("tag");
writeOptionalTagWithValue(theEventWriter, "system", tag.getScheme());
writeOptionalTagWithValue(theEventWriter, "code", tag.getTerm());
writeOptionalTagWithValue(theEventWriter, "display", tag.getLabel());
theEventWriter.writeEndElement();
}
}
theEventWriter.writeEndElement();
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
} else {
encodeResourceToStreamWriterInDstu2Format(
resDef, theResource, theResource, theEventWriter, resDef, theContainedResource);
}
} else {
// DSTU1
if (theResourceId != null && theContainedResource) {
theEventWriter.writeAttribute("id", theResourceId);
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
if (bin.getContentType() != null) {
theEventWriter.writeAttribute("contentType", bin.getContentType());
}
theEventWriter.writeCharacters(bin.getContentAsBase64());
} else {
encodeCompositeElementToStreamWriter(
theResource, theResource, theEventWriter, resDef, theContainedResource);
}
}
}
theEventWriter.writeEndElement();
}
private void encodeBundleToWriterDstu2(Bundle theBundle, XMLStreamWriter theEventWriter)
throws XMLStreamException {
theEventWriter.writeStartElement("Bundle");
theEventWriter.writeDefaultNamespace(FHIR_NS);
writeOptionalTagWithValue(theEventWriter, "id", theBundle.getId().getIdPart());
InstantDt updated =
(InstantDt) theBundle.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt bundleId = theBundle.getId();
if (bundleId != null && isNotBlank(bundleId.getVersionIdPart())
|| (updated != null && !updated.isEmpty())) {
theEventWriter.writeStartElement("meta");
writeOptionalTagWithValue(theEventWriter, "versionId", bundleId.getVersionIdPart());
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
theEventWriter.writeEndElement();
}
String bundleBaseUrl = theBundle.getLinkBase().getValue();
writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
writeOptionalTagWithValue(theEventWriter, "base", bundleBaseUrl);
writeOptionalTagWithValue(
theEventWriter, "total", theBundle.getTotalResults().getValueAsString());
writeBundleResourceLink(theEventWriter, "first", theBundle.getLinkFirst());
writeBundleResourceLink(theEventWriter, "previous", theBundle.getLinkPrevious());
writeBundleResourceLink(theEventWriter, "next", theBundle.getLinkNext());
writeBundleResourceLink(theEventWriter, "last", theBundle.getLinkLast());
writeBundleResourceLink(theEventWriter, "self", theBundle.getLinkSelf());
for (BundleEntry nextEntry : theBundle.getEntries()) {
theEventWriter.writeStartElement("entry");
boolean deleted = false;
if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
deleted = true;
}
writeOptionalTagWithValue(
theEventWriter, "base", determineResourceBaseUrl(bundleBaseUrl, nextEntry));
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
theEventWriter.writeStartElement("resource");
encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
theEventWriter.writeEndElement(); // content
} else {
ourLog.debug("Bundle entry contains null resource");
}
if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
theEventWriter.writeStartElement("search");
writeOptionalTagWithValue(
theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
writeOptionalTagWithValue(theEventWriter, "score", nextEntry.getScore().getValueAsString());
theEventWriter.writeEndElement();
// IResource nextResource = nextEntry.getResource();
}
if (nextEntry.getTransactionMethod().isEmpty() == false
|| nextEntry.getLinkSearch().isEmpty() == false) {
theEventWriter.writeStartElement("transaction");
writeOptionalTagWithValue(
theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
theEventWriter.writeEndElement();
}
if (deleted) {
theEventWriter.writeStartElement("deleted");
writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
writeOptionalTagWithValue(
theEventWriter, "versionId", nextEntry.getId().getVersionIdPart());
writeOptionalTagWithValue(
theEventWriter, "instant", nextEntry.getDeletedAt().getValueAsString());
theEventWriter.writeEndElement();
}
theEventWriter.writeEndElement(); // entry
}
theEventWriter.writeEndElement();
theEventWriter.close();
}
@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;
}
