protected List<String> toNameList(Bundle resp) {
List<String> names = new ArrayList<String>();
for (BundleEntryComponent next : resp.getEntry()) {
Patient nextPt = (Patient) next.getResource();
String nextStr =
nextPt.getName().size() > 0
? nextPt.getName().get(0).getGivenAsSingleString()
+ " "
+ nextPt.getName().get(0).getFamily()
: "";
if (isNotBlank(nextStr)) {
names.add(nextStr);
}
}
return names;
}
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
if (codeSystems.containsKey(system)) return true;
else if (nonSupportedCodeSystems.contains(system)) return false;
else if (system.startsWith("http://example.org")
|| system.startsWith("http://acme.com")
|| system.startsWith("http://hl7.org/fhir/valueset-")
|| system.startsWith("urn:oid:")) return false;
else {
if (noTerminologyServer) return false;
if (bndCodeSystems == null) {
try {
log("Terminology server: Check for supported code systems for " + system);
bndCodeSystems =
txServer.fetchFeed(
txServer.getAddress()
+ "/CodeSystem?content=not-present&_summary=true&_count=1000");
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
log("==============!! Running without terminology server !!==============");
return false;
} else throw new TerminologyServiceException(e);
}
}
if (bndCodeSystems != null) {
for (BundleEntryComponent be : bndCodeSystems.getEntry()) {
CodeSystem cs = (CodeSystem) be.getResource();
if (!codeSystems.containsKey(cs.getUrl())) {
codeSystems.put(cs.getUrl(), null);
}
}
}
if (codeSystems.containsKey(system)) return true;
}
nonSupportedCodeSystems.add(system);
return false;
}
@SuppressWarnings("unchecked")
private Bundle transaction(
ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
BundleType transactionType = theRequest.getTypeElement().getValue();
if (transactionType == BundleType.BATCH) {
return batch(theRequestDetails, theRequest);
}
if (transactionType == null) {
String message =
"Transactiion Bundle did not specify valid Bundle.type, assuming "
+ BundleType.TRANSACTION.toCode();
ourLog.warn(message);
transactionType = BundleType.TRANSACTION;
}
if (transactionType != BundleType.TRANSACTION) {
throw new InvalidRequestException(
"Unable to process transaction where incoming Bundle.type = " + transactionType.toCode());
}
ourLog.info("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
long start = System.currentTimeMillis();
Date updateTime = new Date();
Set<IdType> allIds = new LinkedHashSet<IdType>();
Map<IdType, IdType> idSubstitutions = new HashMap<IdType, IdType>();
Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdType, DaoMethodOutcome>();
// Do all entries have a verb?
for (int i = 0; i < theRequest.getEntry().size(); i++) {
BundleEntryComponent nextReqEntry = theRequest.getEntry().get(i);
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
if (verb == null) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionEntryHasInvalidVerb",
nextReqEntry.getRequest().getMethod(),
i));
}
}
/*
* 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<BundleEntryComponent> getEntries = new ArrayList<BundleEntryComponent>();
IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder =
new IdentityHashMap<Bundle.BundleEntryComponent, 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().getValue() == HTTPVerb.GET) {
getEntries.add(theRequest.getEntry().get(i));
}
}
Collections.sort(theRequest.getEntry(), new TransactionSorter());
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 {} non-GET entries out of {}", i, theRequest.getEntry().size());
}
BundleEntryComponent nextReqEntry = theRequest.getEntry().get(i);
Resource res = nextReqEntry.getResource();
IdType nextResourceId = null;
if (res != null) {
nextResourceId = res.getIdElement();
if (nextResourceId.hasIdPart() == false) {
if (isNotBlank(nextReqEntry.getFullUrl())) {
nextResourceId = new IdType(nextReqEntry.getFullUrl());
}
}
if (nextResourceId.hasIdPart()
&& nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*")
&& !isPlaceholder(nextResourceId)) {
throw new InvalidRequestException(
"Invalid placeholder ID found: "
+ nextResourceId.getIdPart()
+ " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
}
if (nextResourceId.hasIdPart()
&& !nextResourceId.hasResourceType()
&& !isPlaceholder(nextResourceId)) {
nextResourceId = new IdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
res.setId(nextResourceId);
}
/*
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
*/
if (isPlaceholder(nextResourceId)) {
if (!allIds.add(nextResourceId)) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionContainsMultipleWithDuplicateId",
nextResourceId));
}
} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
IdType nextId = nextResourceId.toUnqualifiedVersionless();
if (!allIds.add(nextId)) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionContainsMultipleWithDuplicateId",
nextId));
}
}
}
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
BundleEntryComponent nextRespEntry =
response.getEntry().get(originalRequestOrder.get(nextReqEntry));
switch (verb) {
case POST:
{
// CREATE
@SuppressWarnings("rawtypes")
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
res.setId((String) null);
DaoMethodOutcome outcome;
outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false);
handleTransactionCreateOrUpdateOutcome(
idSubstitutions,
idToPersistedOutcome,
nextResourceId,
outcome,
nextRespEntry,
resourceType,
res);
break;
}
case DELETE:
{
// DELETE
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
UrlParts parts = UrlUtil.parseUrl(url);
ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao =
toDao(parts, verb.toCode(), url);
int status = Constants.STATUS_HTTP_204_NO_CONTENT;
if (parts.getResourceId() != null) {
ResourceTable deleted =
dao.delete(
new IdType(parts.getResourceType(), parts.getResourceId()), deleteConflicts);
if (deleted != null) {
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless());
}
} else {
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;
}
}
nextRespEntry.getResponse().setStatus(toStatusString(status));
break;
}
case PUT:
{
// UPDATE
@SuppressWarnings("rawtypes")
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
DaoMethodOutcome outcome;
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
UrlParts parts = UrlUtil.parseUrl(url);
if (isNotBlank(parts.getResourceId())) {
res.setId(new IdType(parts.getResourceType(), parts.getResourceId()));
outcome = resourceDao.update(res, null, false);
} else {
res.setId((String) null);
outcome =
resourceDao.update(res, parts.getResourceType() + '?' + parts.getParams(), false);
}
handleTransactionCreateOrUpdateOutcome(
idSubstitutions,
idToPersistedOutcome,
nextResourceId,
outcome,
nextRespEntry,
resourceType,
res);
break;
}
}
}
/*
* 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()) {
IBaseResource nextResource = (IBaseResource) nextOutcome.getResource();
if (nextResource == null) {
continue;
}
List<IBaseReference> allRefs =
terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
for (IBaseReference nextRef : allRefs) {
IIdType nextId = nextRef.getReferenceElement();
if (idSubstitutions.containsKey(nextId)) {
IdType newId = idSubstitutions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId.getValue());
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
}
}
IPrimitiveType<Date> deletedInstantOrNull =
ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
Date deletedTimestampOrNull =
deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
updateEntity(
nextResource,
nextOutcome.getEntity(),
false,
deletedTimestampOrNull,
true,
false,
updateTime);
}
myEntityManager.flush();
/*
* Double check we didn't allow any duplicates we shouldn't have
*/
for (BundleEntryComponent nextEntry : theRequest.getEntry()) {
if (nextEntry.getRequest().getMethodElement().getValue() == HTTPVerb.POST) {
String matchUrl = nextEntry.getRequest().getIfNoneExist();
if (isNotBlank(matchUrl)) {
IFhirResourceDao<?> resourceDao = getDao(nextEntry.getResource().getClass());
Set<Long> val = resourceDao.processMatchUrl(matchUrl);
if (val.size() > 1) {
throw new InvalidRequestException(
"Unable to process "
+ theActionName
+ " - Request would cause multiple resources to match URL: \""
+ matchUrl
+ "\". Does transaction request contain duplicates?");
}
}
}
}
for (IdType next : allIds) {
IdType replacement = idSubstitutions.get(next);
if (replacement == null) {
continue;
}
if (replacement.equals(next)) {
continue;
}
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++) {
BundleEntryComponent nextReqEntry = getEntries.get(i);
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
requestDetails.setRequestType(RequestTypeEnum.GET);
requestDetails.setServer(theRequestDetails.getServer());
String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerb.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((Resource) 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});
response.setType(BundleType.TRANSACTIONRESPONSE);
return response;
}
private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
long start = System.currentTimeMillis();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
Bundle resp = new Bundle();
resp.setType(BundleType.BATCHRESPONSE);
OperationOutcome ooResp = new OperationOutcome();
resp.addEntry().setResource(ooResp);
/*
* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
*/
for (final BundleEntryComponent nextRequestEntry : theRequest.getEntry()) {
TransactionCallback<Bundle> callback =
new TransactionCallback<Bundle>() {
@Override
public Bundle doInTransaction(TransactionStatus theStatus) {
Bundle subRequestBundle = new Bundle();
subRequestBundle.setType(BundleType.TRANSACTION);
subRequestBundle.addEntry(nextRequestEntry);
Bundle subResponseBundle =
transaction(
(ServletRequestDetails) theRequestDetails,
subRequestBundle,
"Batch sub-request");
return subResponseBundle;
}
};
BaseServerResponseException caughtEx;
try {
Bundle nextResponseBundle = txTemplate.execute(callback);
caughtEx = null;
BundleEntryComponent subResponseEntry = nextResponseBundle.getEntry().get(0);
resp.addEntry(subResponseEntry);
/*
* If the individual entry didn't have a resource in its response, bring the sub-transaction's OperationOutcome across so the client can see it
*/
if (subResponseEntry.getResource() == null) {
subResponseEntry.setResource(nextResponseBundle.getEntry().get(0).getResource());
}
} catch (BaseServerResponseException e) {
caughtEx = e;
} catch (Throwable t) {
ourLog.error("Failure during BATCH sub transaction processing", t);
caughtEx = new InternalErrorException(t);
}
if (caughtEx != null) {
BundleEntryComponent nextEntry = resp.addEntry();
OperationOutcome oo = new OperationOutcome();
oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
nextEntry.setResource(oo);
BundleEntryResponseComponent nextEntryResp = nextEntry.getResponse();
nextEntryResp.setStatus(toStatusString(caughtEx.getStatusCode()));
}
}
long delay = System.currentTimeMillis() - start;
ourLog.info("Batch completed in {}ms", new Object[] {delay});
ooResp
.addIssue()
.setSeverity(IssueSeverity.INFORMATION)
.setDiagnostics("Batch completed in " + delay + "ms");
return resp;
}