Merge branch 'rel_5_4'
This commit is contained in:
jamesagnew
commit
5c4fcac530
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@ -0,0 +1,8 @@
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---
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type: fix
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issue: 2643
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title: "When using Auto-Version references in the JPA server, if an auto-versioned reference
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within a FHIR transaction pointed to a resource that did not actually change during the
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transaction (e.g. an update/PUT where the resource body was unchanged from the existing
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version), the reference would point to an incremented version number even though none existed.
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This has been corrected."
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 2647
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title: "The new Match URL cache suffered from potential cache poisoning if multiple threads performed
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a condiitonal create operation at the same time."
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@ -0,0 +1,3 @@
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---
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release-date: "2021-05-20"
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codename: "Pangolin"
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@ -1142,6 +1142,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
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mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest);
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changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
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if (theForceUpdate) {
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changed.setChanged(true);
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}
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if (changed.isChanged()) {
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entity.setUpdated(theTransactionDetails.getTransactionDate());
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if (theResource instanceof IResource) {
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@ -179,6 +179,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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private IRequestPartitionHelperSvc myPartitionHelperSvc;
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@Autowired
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private MemoryCacheService myMemoryCacheService;
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private TransactionTemplate myTxTemplate;
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@Override
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public DaoMethodOutcome create(final T theResource) {
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@ -273,14 +274,22 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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};
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Supplier<IIdType> idSupplier = () -> {
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return myTxTemplate.execute(tx-> {
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IIdType retVal = myIdHelperService.translatePidIdToForcedId(myFhirContext, myResourceName, pid);
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if (!retVal.hasVersionIdPart()) {
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return myMemoryCacheService.get(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, retVal, t -> {
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long version = myResourceTableDao.findCurrentVersionByPid(pid.getIdAsLong());
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return myFhirContext.getVersion().newIdType().setParts(retVal.getBaseUrl(), retVal.getResourceType(), retVal.getIdPart(), Long.toString(version));
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});
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IIdType idWithVersion = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getIdAsLong());
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if (idWithVersion == null) {
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Long version = myResourceTableDao.findCurrentVersionByPid(pid.getIdAsLong());
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if (version != null) {
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retVal = myFhirContext.getVersion().newIdType().setParts(retVal.getBaseUrl(), retVal.getResourceType(), retVal.getIdPart(), Long.toString(version));
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myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getIdAsLong(), retVal);
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}
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} else {
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retVal = idWithVersion;
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}
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}
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return retVal;
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});
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};
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return toMethodOutcomeLazy(theRequest, pid, entitySupplier, idSupplier).setCreated(false).setNop(true);
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@ -1057,6 +1066,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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public void start() {
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ourLog.debug("Starting resource DAO for type: {}", getResourceName());
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myInstanceValidator = getApplicationContext().getBean(IInstanceValidatorModule.class);
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myTxTemplate = new TransactionTemplate(myPlatformTransactionManager);
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super.start();
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}
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@ -1537,7 +1547,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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String id = theResource.getIdElement().getValue();
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Runnable onRollback = () -> theResource.getIdElement().setValue(id);
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// Execute the update in a retriable transasction
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// Execute the update in a retriable transaction
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return myTransactionService.execute(theRequest, tx -> doUpdate(theResource, theMatchUrl, thePerformIndexing, theForceUpdateVersion, theRequest, theTransactionDetails), onRollback);
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}
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@ -922,118 +922,7 @@ public abstract class BaseTransactionProcessor {
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* Perform ID substitutions and then index each resource we have saved
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*/
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FhirTerser terser = myContext.newTerser();
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theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
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int i = 0;
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for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
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if (i++ % 250 == 0) {
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ourLog.debug("Have indexed {} entities out of {} in transaction", i, theIdToPersistedOutcome.values().size());
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}
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if (nextOutcome.isNop()) {
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continue;
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}
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IBaseResource nextResource = nextOutcome.getResource();
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if (nextResource == null) {
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continue;
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}
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// References
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Set<IBaseReference> referencesToVersion = BaseStorageDao.extractReferencesToAutoVersion(myContext, myModelConfig, nextResource);
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List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(nextResource);
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for (ResourceReferenceInfo nextRef : allRefs) {
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IBaseReference resourceReference = nextRef.getResourceReference();
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IIdType nextId = resourceReference.getReferenceElement();
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IIdType newId = null;
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if (!nextId.hasIdPart()) {
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if (resourceReference.getResource() != null) {
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IIdType targetId = resourceReference.getResource().getIdElement();
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if (targetId.getValue() == null) {
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// This means it's a contained resource
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continue;
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} else if (theIdSubstitutions.containsValue(targetId)) {
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newId = targetId;
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} else {
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throw new InternalErrorException("References by resource with no reference ID are not supported in DAO layer");
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}
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} else {
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continue;
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}
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}
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if (newId != null || theIdSubstitutions.containsKey(nextId)) {
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if (newId == null) {
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newId = theIdSubstitutions.get(nextId);
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}
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ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
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if (referencesToVersion.contains(resourceReference)) {
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resourceReference.setReference(newId.getValue());
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} else {
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resourceReference.setReference(newId.toVersionless().getValue());
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}
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} else if (nextId.getValue().startsWith("urn:")) {
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throw new InvalidRequestException("Unable to satisfy placeholder ID " + nextId.getValue() + " found in element named '" + nextRef.getName() + "' within resource of type: " + nextResource.getIdElement().getResourceType());
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} else {
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if (referencesToVersion.contains(resourceReference)) {
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DaoMethodOutcome outcome = theIdToPersistedOutcome.get(nextId);
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if (!outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
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resourceReference.setReference(nextId.getValue());
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}
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}
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}
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}
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// URIs
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Class<? extends IPrimitiveType<?>> uriType = (Class<? extends IPrimitiveType<?>>) myContext.getElementDefinition("uri").getImplementingClass();
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List<? extends IPrimitiveType<?>> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, uriType);
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for (IPrimitiveType<?> nextRef : allUris) {
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if (nextRef instanceof IIdType) {
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continue; // No substitution on the resource ID itself!
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}
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IIdType nextUriString = newIdType(nextRef.getValueAsString());
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if (theIdSubstitutions.containsKey(nextUriString)) {
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IIdType newId = theIdSubstitutions.get(nextUriString);
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ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
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nextRef.setValueAsString(newId.toVersionless().getValue());
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} else {
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ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
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}
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}
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IPrimitiveType<Date> deletedInstantOrNull;
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if (nextResource instanceof IAnyResource) {
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deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
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} else {
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deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) nextResource);
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}
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Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
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IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(nextResource.getClass());
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IJpaDao jpaDao = (IJpaDao) dao;
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IBasePersistedResource updateOutcome = null;
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if (updatedEntities.contains(nextOutcome.getEntity())) {
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updateOutcome = jpaDao.updateInternal(theRequest, nextResource, true, false, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource(), theTransactionDetails);
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} else if (!nonUpdatedEntities.contains(nextOutcome.getId())) {
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updateOutcome = jpaDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theTransactionDetails, false, true);
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}
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// Make sure we reflect the actual final version for the resource.
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if (updateOutcome != null) {
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IIdType newId = updateOutcome.getIdDt();
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for (IIdType nextEntry : entriesToProcess.values()) {
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if (nextEntry.getResourceType().equals(newId.getResourceType())) {
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if (nextEntry.getIdPart().equals(newId.getIdPart())) {
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if (!nextEntry.hasVersionIdPart() || !nextEntry.getVersionIdPart().equals(newId.getVersionIdPart())) {
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nextEntry.setParts(nextEntry.getBaseUrl(), nextEntry.getResourceType(), nextEntry.getIdPart(), newId.getVersionIdPart());
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}
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}
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}
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}
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}
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}
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resolveReferencesThenSaveAndIndexResources(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, theTransactionStopWatch, entriesToProcess, nonUpdatedEntities, updatedEntities);
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theTransactionStopWatch.endCurrentTask();
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theTransactionStopWatch.startTask("Flush writes to database");
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@ -1042,8 +931,6 @@ public abstract class BaseTransactionProcessor {
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theTransactionStopWatch.endCurrentTask();
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/*
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* Double check we didn't allow any duplicates we shouldn't have
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*/
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@ -1093,6 +980,183 @@ public abstract class BaseTransactionProcessor {
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}
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}
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/**
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* This method replaces any placeholder references in the
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* source transaction Bundle with their actual targets, then stores the resource contents and indexes
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* in the database. This is trickier than you'd think because of a couple of possibilities during the
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* save:
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* * There may be resources that have not changed (e.g. an update/PUT with a resource body identical
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* to what is already in the database)
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* * There may be resources with auto-versioned references, meaning we're replacing certain references
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* in the resource with a versioned references, referencing the current version at the time of the
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* transaction processing
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* * There may by auto-versioned references pointing to these unchanged targets
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*
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* If we're not doing any auto-versioned references, we'll just iterate through all resources in the
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* transaction and save them one at a time.
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*
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* However, if we have any auto-versioned references we do this in 2 passes: First the resources from the
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* transaction that don't have any auto-versioned references are stored. We do them first since there's
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* a chance they may be a NOP and we'll need to account for their version number not actually changing.
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* Then we do a second pass for any resources that have auto-versioned references. These happen in a separate
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* pass because it's too complex to try and insert the auto-versioned references and still
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* account for NOPs, so we block NOPs in that pass.
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*/
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private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
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FhirTerser terser = myContext.newTerser();
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theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
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IdentityHashMap<DaoMethodOutcome, Set<IBaseReference>> deferredIndexesForAutoVersioning = null;
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int i = 0;
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for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
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if (i++ % 250 == 0) {
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ourLog.debug("Have indexed {} entities out of {} in transaction", i, theIdToPersistedOutcome.values().size());
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}
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if (nextOutcome.isNop()) {
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continue;
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}
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IBaseResource nextResource = nextOutcome.getResource();
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if (nextResource == null) {
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continue;
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}
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Set<IBaseReference> referencesToAutoVersion = BaseStorageDao.extractReferencesToAutoVersion(myContext, myModelConfig, nextResource);
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if (referencesToAutoVersion.isEmpty()) {
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resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
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} else {
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if (deferredIndexesForAutoVersioning == null) {
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deferredIndexesForAutoVersioning = new IdentityHashMap<>();
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}
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deferredIndexesForAutoVersioning.put(nextOutcome, referencesToAutoVersion);
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}
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}
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// If we have any resources we'll be auto-versioning, index these next
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if (deferredIndexesForAutoVersioning != null) {
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for (Map.Entry<DaoMethodOutcome, Set<IBaseReference>> nextEntry : deferredIndexesForAutoVersioning.entrySet()) {
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DaoMethodOutcome nextOutcome = nextEntry.getKey();
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Set<IBaseReference> referencesToAutoVersion = nextEntry.getValue();
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IBaseResource nextResource = nextOutcome.getResource();
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resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
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}
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}
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}
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private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities, FhirTerser terser, DaoMethodOutcome nextOutcome, IBaseResource nextResource, Set<IBaseReference> theReferencesToAutoVersion) {
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// References
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List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(nextResource);
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for (ResourceReferenceInfo nextRef : allRefs) {
|
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IBaseReference resourceReference = nextRef.getResourceReference();
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IIdType nextId = resourceReference.getReferenceElement();
|
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IIdType newId = null;
|
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if (!nextId.hasIdPart()) {
|
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if (resourceReference.getResource() != null) {
|
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IIdType targetId = resourceReference.getResource().getIdElement();
|
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if (targetId.getValue() == null) {
|
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// This means it's a contained resource
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continue;
|
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} else if (theIdSubstitutions.containsValue(targetId)) {
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newId = targetId;
|
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} else {
|
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throw new InternalErrorException("References by resource with no reference ID are not supported in DAO layer");
|
||||
}
|
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} else {
|
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continue;
|
||||
}
|
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}
|
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if (newId != null || theIdSubstitutions.containsKey(nextId)) {
|
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if (newId == null) {
|
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newId = theIdSubstitutions.get(nextId);
|
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}
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ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
|
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if (theReferencesToAutoVersion.contains(resourceReference)) {
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resourceReference.setReference(newId.getValue());
|
||||
} else {
|
||||
resourceReference.setReference(newId.toVersionless().getValue());
|
||||
}
|
||||
} else if (nextId.getValue().startsWith("urn:")) {
|
||||
throw new InvalidRequestException("Unable to satisfy placeholder ID " + nextId.getValue() + " found in element named '" + nextRef.getName() + "' within resource of type: " + nextResource.getIdElement().getResourceType());
|
||||
} else {
|
||||
if (theReferencesToAutoVersion.contains(resourceReference)) {
|
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DaoMethodOutcome outcome = theIdToPersistedOutcome.get(nextId);
|
||||
if (!outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
|
||||
resourceReference.setReference(nextId.getValue());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// URIs
|
||||
Class<? extends IPrimitiveType<?>> uriType = (Class<? extends IPrimitiveType<?>>) myContext.getElementDefinition("uri").getImplementingClass();
|
||||
List<? extends IPrimitiveType<?>> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, uriType);
|
||||
for (IPrimitiveType<?> nextRef : allUris) {
|
||||
if (nextRef instanceof IIdType) {
|
||||
continue; // No substitution on the resource ID itself!
|
||||
}
|
||||
IIdType nextUriString = newIdType(nextRef.getValueAsString());
|
||||
if (theIdSubstitutions.containsKey(nextUriString)) {
|
||||
IIdType newId = theIdSubstitutions.get(nextUriString);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
|
||||
nextRef.setValueAsString(newId.toVersionless().getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
|
||||
}
|
||||
}
|
||||
|
||||
IPrimitiveType<Date> deletedInstantOrNull;
|
||||
if (nextResource instanceof IAnyResource) {
|
||||
deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
|
||||
} else {
|
||||
deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) nextResource);
|
||||
}
|
||||
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
|
||||
|
||||
IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(nextResource.getClass());
|
||||
IJpaDao jpaDao = (IJpaDao) dao;
|
||||
|
||||
IBasePersistedResource updateOutcome = null;
|
||||
if (updatedEntities.contains(nextOutcome.getEntity())) {
|
||||
boolean forceUpdateVersion = false;
|
||||
if (!theReferencesToAutoVersion.isEmpty()) {
|
||||
forceUpdateVersion = true;
|
||||
}
|
||||
|
||||
updateOutcome = jpaDao.updateInternal(theRequest, nextResource, true, forceUpdateVersion, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource(), theTransactionDetails);
|
||||
} else if (!nonUpdatedEntities.contains(nextOutcome.getId())) {
|
||||
updateOutcome = jpaDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theTransactionDetails, false, true);
|
||||
}
|
||||
|
||||
// Make sure we reflect the actual final version for the resource.
|
||||
if (updateOutcome != null) {
|
||||
IIdType newId = updateOutcome.getIdDt();
|
||||
for (IIdType nextEntry : entriesToProcess.values()) {
|
||||
if (nextEntry.getResourceType().equals(newId.getResourceType())) {
|
||||
if (nextEntry.getIdPart().equals(newId.getIdPart())) {
|
||||
if (!nextEntry.hasVersionIdPart() || !nextEntry.getVersionIdPart().equals(newId.getVersionIdPart())) {
|
||||
nextEntry.setParts(nextEntry.getBaseUrl(), nextEntry.getResourceType(), nextEntry.getIdPart(), newId.getVersionIdPart());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
nextOutcome.setId(newId);
|
||||
|
||||
for (IIdType next : theIdSubstitutions.values()) {
|
||||
if (next.getResourceType().equals(newId.getResourceType())) {
|
||||
if (next.getIdPart().equals(newId.getIdPart())) {
|
||||
if (!next.getValue().equals(newId.getValue())) {
|
||||
next.setValue(newId.getValue());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
private void validateNoDuplicates(RequestDetails theRequest, String theActionName, Map<String, Class<? extends IBaseResource>> conditionalRequestUrls) {
|
||||
for (Map.Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
|
||||
String matchUrl = nextEntry.getKey();
|
||||
|
|
|
|||
|
|
@ -43,6 +43,8 @@ import org.apache.commons.lang3.Validate;
|
|||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.stereotype.Service;
|
||||
import org.springframework.transaction.support.TransactionSynchronization;
|
||||
import org.springframework.transaction.support.TransactionSynchronizationManager;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.Set;
|
||||
|
|
@ -80,7 +82,8 @@ public class MatchResourceUrlService {
|
|||
Set<ResourcePersistentId> retVal = search(paramMap, theResourceType, theRequest);
|
||||
|
||||
if (myDaoConfig.getMatchUrlCache() && retVal.size() == 1) {
|
||||
myMemoryCacheService.put(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, retVal.iterator().next());
|
||||
ResourcePersistentId pid = retVal.iterator().next();
|
||||
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, pid);
|
||||
}
|
||||
|
||||
return retVal;
|
||||
|
|
@ -113,7 +116,7 @@ public class MatchResourceUrlService {
|
|||
Validate.notBlank(theMatchUrl);
|
||||
Validate.notNull(theResourcePersistentId);
|
||||
if (myDaoConfig.getMatchUrlCache()) {
|
||||
myMemoryCacheService.put(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, theResourcePersistentId);
|
||||
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, theResourcePersistentId);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -93,5 +93,5 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
|
|||
Collection<Object[]> findLookupFieldsByResourcePidInPartitionNull(@Param("pid") List<Long> thePids);
|
||||
|
||||
@Query("SELECT t.myVersion FROM ResourceTable t WHERE t.myId = :pid")
|
||||
long findCurrentVersionByPid(@Param("pid") Long thePid);
|
||||
Long findCurrentVersionByPid(@Param("pid") Long thePid);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,12 +23,15 @@ package ca.uhn.fhir.jpa.util;
|
|||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.api.model.TranslationQuery;
|
||||
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
|
||||
import com.github.benmanes.caffeine.cache.Cache;
|
||||
import com.github.benmanes.caffeine.cache.Caffeine;
|
||||
import org.apache.commons.lang3.builder.EqualsBuilder;
|
||||
import org.apache.commons.lang3.builder.HashCodeBuilder;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.transaction.support.TransactionSynchronization;
|
||||
import org.springframework.transaction.support.TransactionSynchronizationManager;
|
||||
|
||||
import javax.annotation.Nonnull;
|
||||
import javax.annotation.PostConstruct;
|
||||
|
|
@ -100,6 +103,19 @@ public class MemoryCacheService {
|
|||
getCache(theCache).put(theKey, theValue);
|
||||
}
|
||||
|
||||
public <K, V> void putAfterCommit(CacheEnum theCache, K theKey, V theValue) {
|
||||
if (TransactionSynchronizationManager.isSynchronizationActive()) {
|
||||
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronization() {
|
||||
@Override
|
||||
public void afterCommit() {
|
||||
put(theCache, theKey, theValue);
|
||||
}
|
||||
});
|
||||
} else {
|
||||
put(theCache, theKey, theValue);
|
||||
}
|
||||
}
|
||||
|
||||
public <K, V> Map<K, V> getAllPresent(CacheEnum theCache, Iterable<K> theKeys) {
|
||||
return (Map<K, V>) getCache(theCache).getAllPresent(theKeys);
|
||||
}
|
||||
|
|
@ -122,7 +138,7 @@ public class MemoryCacheService {
|
|||
CONCEPT_TRANSLATION(TranslationQuery.class),
|
||||
MATCH_URL(String.class),
|
||||
CONCEPT_TRANSLATION_REVERSE(TranslationQuery.class),
|
||||
RESOURCE_CONDITIONAL_CREATE_VERSION(IIdType.class),
|
||||
RESOURCE_CONDITIONAL_CREATE_VERSION(Long.class),
|
||||
HISTORY_COUNT(HistoryCountKey.class);
|
||||
|
||||
private final Class<?> myKeyType;
|
||||
|
|
|
|||
|
|
@ -11,15 +11,20 @@ import ca.uhn.fhir.rest.server.RestfulServer;
|
|||
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.BundleBuilder;
|
||||
import ca.uhn.fhir.util.HapiExtensions;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.Coverage;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.hl7.fhir.r4.model.Practitioner;
|
||||
import org.hl7.fhir.r4.model.SearchParameter;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
|
|
@ -35,6 +40,7 @@ import java.util.concurrent.ExecutionException;
|
|||
import java.util.concurrent.ExecutorService;
|
||||
import java.util.concurrent.Executors;
|
||||
import java.util.concurrent.Future;
|
||||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
|
|
@ -70,6 +76,83 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
|
|||
myInterceptorRegistry.unregisterInterceptor(myRetryInterceptor);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConcurrentTransactionCreates() throws ExecutionException, InterruptedException {
|
||||
myDaoConfig.setMatchUrlCache(true);
|
||||
|
||||
AtomicInteger counter = new AtomicInteger(0);
|
||||
Runnable creator = () -> {
|
||||
BundleBuilder bb = new BundleBuilder(myFhirCtx);
|
||||
String patientId = "Patient/PT" + counter.get();
|
||||
IdType practitionerId = IdType.newRandomUuid();
|
||||
IdType practitionerId2 = IdType.newRandomUuid();
|
||||
|
||||
ExplanationOfBenefit eob = new ExplanationOfBenefit();
|
||||
eob.addIdentifier().setSystem("foo").setValue("" + counter.get());
|
||||
eob.getPatient().setReference(patientId);
|
||||
eob.addCareTeam().getProvider().setReference(practitionerId.getValue());
|
||||
eob.addCareTeam().getProvider().setReference(practitionerId2.getValue());
|
||||
bb.addTransactionUpdateEntry(eob).conditional("ExplanationOfBenefit?identifier=foo|" + counter.get());
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setId(patientId);
|
||||
pt.setActive(true);
|
||||
bb.addTransactionUpdateEntry(pt);
|
||||
|
||||
Coverage coverage = new Coverage();
|
||||
coverage.addIdentifier().setSystem("foo").setValue("" + counter.get());
|
||||
coverage.getBeneficiary().setReference(patientId);
|
||||
bb.addTransactionUpdateEntry(coverage).conditional("Coverage?identifier=foo|" + counter.get());
|
||||
|
||||
Practitioner practitioner = new Practitioner();
|
||||
practitioner.setId(practitionerId);
|
||||
practitioner.addIdentifier().setSystem("foo").setValue("" + counter.get());
|
||||
bb.addTransactionCreateEntry(practitioner).conditional("Practitioner?identifier=foo|" + counter.get());
|
||||
|
||||
Practitioner practitioner2 = new Practitioner();
|
||||
practitioner2.setId(practitionerId2);
|
||||
practitioner2.addIdentifier().setSystem("foo2").setValue("" + counter.get());
|
||||
bb.addTransactionCreateEntry(practitioner2).conditional("Practitioner?identifier=foo2|" + counter.get());
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.setId("Observation/OBS" + counter);
|
||||
obs.getSubject().setReference(pt.getId());
|
||||
bb.addTransactionUpdateEntry(obs);
|
||||
|
||||
Bundle input = (Bundle) bb.getBundle();
|
||||
mySystemDao.transaction(new SystemRequestDetails(), input);
|
||||
};
|
||||
|
||||
for (int i = 0; i < 10; i++) {
|
||||
counter.set(i);
|
||||
ourLog.info("*********************************************************************************");
|
||||
ourLog.info("Starting pass {}", i);
|
||||
ourLog.info("*********************************************************************************");
|
||||
|
||||
List<Future<?>> futures = new ArrayList<>();
|
||||
for (int j = 0; j < 10; j++) {
|
||||
futures.add(myExecutor.submit(creator));
|
||||
}
|
||||
|
||||
for (Future<?> next : futures) {
|
||||
try {
|
||||
next.get();
|
||||
} catch (Exception e) {
|
||||
// ignore
|
||||
}
|
||||
}
|
||||
|
||||
creator.run();
|
||||
}
|
||||
|
||||
runInTransaction(()->{
|
||||
assertEquals(60, myResourceTableDao.count());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreateWithClientAssignedId() {
|
||||
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
|
||||
|
|
|
|||
|
|
@ -698,7 +698,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
|
|||
|
||||
myCaptureQueriesListener.clear();
|
||||
mySystemDao.transaction(mySrd, bundleCreator.get());
|
||||
assertEquals(1, myCaptureQueriesListener.countSelectQueries());
|
||||
assertEquals(2, myCaptureQueriesListener.countSelectQueries());
|
||||
assertEquals(5, myCaptureQueriesListener.countInsertQueries());
|
||||
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
|
|||
|
||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
|
||||
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
|
|
@ -11,8 +12,10 @@ import org.hl7.fhir.instance.model.api.IIdType;
|
|||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Condition;
|
||||
import org.hl7.fhir.r4.model.Encounter;
|
||||
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.hl7.fhir.r4.model.Organization;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.hl7.fhir.r4.model.Reference;
|
||||
import org.hl7.fhir.r4.model.Task;
|
||||
|
|
@ -23,8 +26,12 @@ import java.util.Arrays;
|
|||
import java.util.Date;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
import java.util.function.Supplier;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.matchesPattern;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
|
|
@ -40,6 +47,167 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
|
|||
myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateAndUpdateVersionedReferencesInTransaction_VersionedReferenceToUpsertWithNop() {
|
||||
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
|
||||
myModelConfig.setAutoVersionReferenceAtPaths("ExplanationOfBenefit.patient");
|
||||
|
||||
// We'll submit the same bundle twice. It has an UPSERT (with no changes
|
||||
// the second time) on a Patient, and a CREATE on an ExplanationOfBenefit
|
||||
// referencing that Patient.
|
||||
Supplier<Bundle> supplier = () -> {
|
||||
BundleBuilder bb = new BundleBuilder(myFhirCtx);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("Patient/A");
|
||||
patient.setActive(true);
|
||||
bb.addTransactionUpdateEntry(patient);
|
||||
|
||||
ExplanationOfBenefit eob = new ExplanationOfBenefit();
|
||||
eob.setId(IdType.newRandomUuid());
|
||||
eob.setPatient(new Reference("Patient/A"));
|
||||
bb.addTransactionCreateEntry(eob);
|
||||
|
||||
return (Bundle) bb.getBundle();
|
||||
};
|
||||
|
||||
// Send it the first time
|
||||
Bundle outcome1 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Patient/A/_history/1", outcome1.getEntry().get(0).getResponse().getLocation());
|
||||
String eobId1 = outcome1.getEntry().get(1).getResponse().getLocation();
|
||||
assertThat(eobId1, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
ExplanationOfBenefit eob1 = myExplanationOfBenefitDao.read(new IdType(eobId1), new SystemRequestDetails());
|
||||
assertEquals("Patient/A/_history/1", eob1.getPatient().getReference());
|
||||
|
||||
// Send it again
|
||||
Bundle outcome2 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Patient/A/_history/1", outcome2.getEntry().get(0).getResponse().getLocation());
|
||||
String eobId2 = outcome2.getEntry().get(1).getResponse().getLocation();
|
||||
assertThat(eobId2, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
ExplanationOfBenefit eob2 = myExplanationOfBenefitDao.read(new IdType(eobId2), new SystemRequestDetails());
|
||||
assertEquals("Patient/A/_history/1", eob2.getPatient().getReference());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreateAndUpdateVersionedReferencesInTransaction_VersionedReferenceToVersionedReferenceToUpsertWithNop() {
|
||||
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
|
||||
myModelConfig.setAutoVersionReferenceAtPaths(
|
||||
"Patient.managingOrganization",
|
||||
"ExplanationOfBenefit.patient"
|
||||
);
|
||||
|
||||
// We'll submit the same bundle twice. It has an UPSERT (with no changes
|
||||
// the second time) on a Patient, and a CREATE on an ExplanationOfBenefit
|
||||
// referencing that Patient.
|
||||
Supplier<Bundle> supplier = () -> {
|
||||
BundleBuilder bb = new BundleBuilder(myFhirCtx);
|
||||
|
||||
Organization organization = new Organization();
|
||||
organization.setId("Organization/O");
|
||||
organization.setActive(true);
|
||||
bb.addTransactionUpdateEntry(organization);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("Patient/A");
|
||||
patient.setManagingOrganization(new Reference("Organization/O"));
|
||||
patient.setActive(true);
|
||||
bb.addTransactionUpdateEntry(patient);
|
||||
|
||||
ExplanationOfBenefit eob = new ExplanationOfBenefit();
|
||||
eob.setId(IdType.newRandomUuid());
|
||||
eob.setPatient(new Reference("Patient/A"));
|
||||
bb.addTransactionCreateEntry(eob);
|
||||
|
||||
return (Bundle) bb.getBundle();
|
||||
};
|
||||
|
||||
// Send it the first time
|
||||
Bundle outcome1 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Organization/O/_history/1", outcome1.getEntry().get(0).getResponse().getLocation());
|
||||
assertEquals("Patient/A/_history/1", outcome1.getEntry().get(1).getResponse().getLocation());
|
||||
String eobId1 = outcome1.getEntry().get(2).getResponse().getLocation();
|
||||
assertThat(eobId1, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
ExplanationOfBenefit eob1 = myExplanationOfBenefitDao.read(new IdType(eobId1), new SystemRequestDetails());
|
||||
assertEquals("Patient/A/_history/1", eob1.getPatient().getReference());
|
||||
|
||||
// Send it again
|
||||
Bundle outcome2 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Organization/O/_history/1", outcome2.getEntry().get(0).getResponse().getLocation());
|
||||
// Technically the patient did not change - If this ever got optimized so that the version here
|
||||
// was 1 that would be even better
|
||||
String patientId = outcome2.getEntry().get(1).getResponse().getLocation();
|
||||
assertEquals("Patient/A/_history/2", patientId);
|
||||
String eobId2 = outcome2.getEntry().get(2).getResponse().getLocation();
|
||||
assertThat(eobId2, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
Patient patient = myPatientDao.read(new IdType("Patient/A"), new SystemRequestDetails());
|
||||
assertEquals(patientId, patient.getId());
|
||||
|
||||
ExplanationOfBenefit eob2 = myExplanationOfBenefitDao.read(new IdType(eobId2), new SystemRequestDetails());
|
||||
assertEquals(patientId, eob2.getPatient().getReference());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateAndUpdateVersionedReferencesInTransaction_VersionedReferenceToVersionedReferenceToUpsertWithChange() {
|
||||
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
|
||||
myModelConfig.setAutoVersionReferenceAtPaths(
|
||||
"Patient.managingOrganization",
|
||||
"ExplanationOfBenefit.patient"
|
||||
);
|
||||
|
||||
AtomicInteger counter = new AtomicInteger();
|
||||
Supplier<Bundle> supplier = () -> {
|
||||
BundleBuilder bb = new BundleBuilder(myFhirCtx);
|
||||
|
||||
Organization organization = new Organization();
|
||||
organization.setId("Organization/O");
|
||||
organization.setName("Org " + counter.incrementAndGet()); // change each time
|
||||
organization.setActive(true);
|
||||
bb.addTransactionUpdateEntry(organization);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("Patient/A");
|
||||
patient.setManagingOrganization(new Reference("Organization/O"));
|
||||
patient.setActive(true);
|
||||
bb.addTransactionUpdateEntry(patient);
|
||||
|
||||
ExplanationOfBenefit eob = new ExplanationOfBenefit();
|
||||
eob.setId(IdType.newRandomUuid());
|
||||
eob.setPatient(new Reference("Patient/A"));
|
||||
bb.addTransactionCreateEntry(eob);
|
||||
|
||||
return (Bundle) bb.getBundle();
|
||||
};
|
||||
|
||||
// Send it the first time
|
||||
Bundle outcome1 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Organization/O/_history/1", outcome1.getEntry().get(0).getResponse().getLocation());
|
||||
assertEquals("Patient/A/_history/1", outcome1.getEntry().get(1).getResponse().getLocation());
|
||||
String eobId1 = outcome1.getEntry().get(2).getResponse().getLocation();
|
||||
assertThat(eobId1, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
ExplanationOfBenefit eob1 = myExplanationOfBenefitDao.read(new IdType(eobId1), new SystemRequestDetails());
|
||||
assertEquals("Patient/A/_history/1", eob1.getPatient().getReference());
|
||||
|
||||
// Send it again
|
||||
Bundle outcome2 = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
|
||||
assertEquals("Organization/O/_history/2", outcome2.getEntry().get(0).getResponse().getLocation());
|
||||
String patientId = outcome2.getEntry().get(1).getResponse().getLocation();
|
||||
assertEquals("Patient/A/_history/2", patientId);
|
||||
String eobId2 = outcome2.getEntry().get(2).getResponse().getLocation();
|
||||
assertThat(eobId2, matchesPattern("ExplanationOfBenefit/[0-9]+/_history/1"));
|
||||
|
||||
Patient patient = myPatientDao.read(new IdType("Patient/A"), new SystemRequestDetails());
|
||||
assertEquals(patientId, patient.getId());
|
||||
|
||||
ExplanationOfBenefit eob2 = myExplanationOfBenefitDao.read(new IdType(eobId2), new SystemRequestDetails());
|
||||
assertEquals(patientId, eob2.getPatient().getReference());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreAndRetrieveVersionedReference() {
|
||||
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
|
||||
|
|
|
|||
|
|
@ -85,6 +85,7 @@ import java.util.List;
|
|||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.function.Supplier;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
|
|
|
|||
|
|
@ -122,11 +122,13 @@ public abstract class BaseTask {
|
|||
return changesCount;
|
||||
} catch (DataAccessException e) {
|
||||
if (myFailureAllowed) {
|
||||
ourLog.info("Task did not exit successfully, but task is allowed to fail");
|
||||
ourLog.info("Task {} did not exit successfully, but task is allowed to fail", getFlywayVersion());
|
||||
ourLog.debug("Error was: {}", e.getMessage(), e);
|
||||
return 0;
|
||||
} else {
|
||||
throw e;
|
||||
throw new DataAccessException("Failed during task " + getFlywayVersion() + ": " + e, e) {
|
||||
private static final long serialVersionUID = 8211678931579252166L;
|
||||
};
|
||||
}
|
||||
}
|
||||
});
|
||||
|
|
|
|||
Loading…
Reference in New Issue