Ongoing work on subscriptions

examples/src/main/java/example/ValidatorExamples.java

@@ -214,6 +214,12 @@ public class ValidatorExamples {
 				return null;
 			}
 
+			@Override
+			public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
+				// TODO: implement
+				return null;
+			}
+
 			@Override
 			public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
 				// TODO: implement

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

@@ -165,11 +165,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@Autowired
 	private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
 
-	private <T extends IBaseResource> void autoCreateResource(T theResource) {
-		IFhirResourceDao<T> dao = (IFhirResourceDao<T>) getDao(theResource.getClass());
-		dao.create(theResource);
-	}
-
 	protected void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
 		if (theRequestDetails != null) {
 			theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
@@ -423,11 +418,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					if (getConfig().isAutoCreatePlaceholderReferenceTargets()) {
 						IBaseResource newResource = missingResourceDef.newInstance();
 						newResource.setId(resName + "/" + id);
-						autoCreateResource(newResource);
+						IFhirResourceDao<IBaseResource> placeholderResourceDao = (IFhirResourceDao<IBaseResource>) getDao(newResource.getClass());
-					}
+						ourLog.info("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
-
+						valueOf = placeholderResourceDao.update(newResource).getEntity().getId();
+					} else {
 						throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
 					}
+				}
 				ResourceTable target = myEntityManager.find(ResourceTable.class, valueOf);
 				RuntimeResourceDefinition targetResourceDef = getContext().getResourceDefinition(type);
 				if (target == null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -662,6 +662,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				String nextReplacementIdPart = nextReplacementId.getValueAsString();
 				if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
 					matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
+					matchUrl = matchUrl.replace(UrlUtil.escape(nextTemporaryIdPart), nextReplacementIdPart);
 				}
 			}
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java

@@ -662,6 +662,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				String nextReplacementIdPart = nextReplacementId.getValueAsString();
 				if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
 					matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
+					matchUrl = matchUrl.replace(UrlUtil.escape(nextTemporaryIdPart), nextReplacementIdPart);
 				}
 			}
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionInterceptor.java

@@ -46,10 +46,7 @@ import org.springframework.transaction.support.TransactionSynchronizationManager
 
 import javax.annotation.PostConstruct;
 import javax.annotation.PreDestroy;
-import java.util.Enumeration;
+import java.util.*;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
 import java.util.concurrent.*;
 
 public abstract class BaseSubscriptionInterceptor extends ServerOperationInterceptorAdapter {
@@ -63,13 +60,15 @@ public abstract class BaseSubscriptionInterceptor extends ServerOperationInterce
 	private static final Integer MAX_SUBSCRIPTION_RESULTS = 1000;
 	private SubscribableChannel myProcessingChannel;
 	private SubscribableChannel myDeliveryChannel;
-	private ExecutorService myExecutor;
+	private ExecutorService myProcessingExecutor;
 	private int myExecutorThreadCount;
 	private SubscriptionActivatingSubscriber mySubscriptionActivatingSubscriber;
 	private MessageHandler mySubscriptionCheckingSubscriber;
 	private ConcurrentHashMap<String, IBaseResource> myIdToSubscription = new ConcurrentHashMap<>();
 	private Logger ourLog = LoggerFactory.getLogger(BaseSubscriptionInterceptor.class);
-	private BlockingQueue<Runnable> myExecutorQueue;
+	private ThreadPoolExecutor myDeliveryExecutor;
+	private LinkedBlockingQueue<Runnable> myProcessingExecutorQueue;
+	private LinkedBlockingQueue<Runnable> myDeliveryExecutorQueue;
 
 	/**
 	 * Constructor
@@ -89,8 +88,8 @@ public abstract class BaseSubscriptionInterceptor extends ServerOperationInterce
 		myDeliveryChannel = theDeliveryChannel;
 	}
 
-	public BlockingQueue<Runnable> getExecutorQueueForUnitTests() {
+	public int getExecutorQueueSizeForUnitTests() {
-		return myExecutorQueue;
+		return myProcessingExecutorQueue.size() + myDeliveryExecutorQueue.size();
 	}
 
 	public int getExecutorThreadCount() {
@@ -157,15 +156,16 @@ public abstract class BaseSubscriptionInterceptor extends ServerOperationInterce
 
 	@PostConstruct
 	public void postConstruct() {
-		myExecutorQueue = new LinkedBlockingQueue<>(1000);
+		{
+			myProcessingExecutorQueue = new LinkedBlockingQueue<>(1000);
 
 			RejectedExecutionHandler rejectedExecutionHandler = new RejectedExecutionHandler() {
 				@Override
 				public void rejectedExecution(Runnable theRunnable, ThreadPoolExecutor theExecutor) {
-				ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", myExecutorQueue.size());
+					ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", myProcessingExecutorQueue.size());
 					StopWatch sw = new StopWatch();
 					try {
-					myExecutorQueue.put(theRunnable);
+						myProcessingExecutorQueue.put(theRunnable);
 					} catch (InterruptedException theE) {
 						throw new RejectedExecutionException("Task " + theRunnable.toString() +
 							" rejected from " + theE.toString());
@@ -174,25 +174,55 @@ public abstract class BaseSubscriptionInterceptor extends ServerOperationInterce
 				}
 			};
 			ThreadFactory threadFactory = new BasicThreadFactory.Builder()
-			.namingPattern("subscription-%d")
+				.namingPattern("subscription-proc-%d")
 				.daemon(false)
 				.priority(Thread.NORM_PRIORITY)
 				.build();
-		myExecutor = new ThreadPoolExecutor(
+			myProcessingExecutor = new ThreadPoolExecutor(
 				1,
 				getExecutorThreadCount(),
 				0L,
 				TimeUnit.MILLISECONDS,
-			myExecutorQueue,
+				myProcessingExecutorQueue,
 				threadFactory,
 				rejectedExecutionHandler);
-
+		}
+		{
+			myDeliveryExecutorQueue = new LinkedBlockingQueue<>(1000);
+			BasicThreadFactory threadFactory = new BasicThreadFactory.Builder()
+				.namingPattern("subscription-delivery-%d")
+				.daemon(false)
+				.priority(Thread.NORM_PRIORITY)
+				.build();
+			RejectedExecutionHandler rejectedExecutionHandler2 = new RejectedExecutionHandler() {
+				@Override
+				public void rejectedExecution(Runnable theRunnable, ThreadPoolExecutor theExecutor) {
+					ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", myDeliveryExecutorQueue.size());
+					StopWatch sw = new StopWatch();
+					try {
+						myDeliveryExecutorQueue.put(theRunnable);
+					} catch (InterruptedException theE) {
+						throw new RejectedExecutionException("Task " + theRunnable.toString() +
+							" rejected from " + theE.toString());
+					}
+					ourLog.info("Slot become available after {}ms", sw.getMillis());
+				}
+			};
+			myDeliveryExecutor = new ThreadPoolExecutor(
+				1,
+				getExecutorThreadCount(),
+				0L,
+				TimeUnit.MILLISECONDS,
+				myDeliveryExecutorQueue,
+				threadFactory,
+				rejectedExecutionHandler2);
+		}
 
 		if (getProcessingChannel() == null) {
-			setProcessingChannel(new ExecutorSubscribableChannel(myExecutor));
+			setProcessingChannel(new ExecutorSubscribableChannel(myProcessingExecutor));
 		}
 		if (getDeliveryChannel() == null) {
-			setDeliveryChannel(new ExecutorSubscribableChannel(myExecutor));
+			setDeliveryChannel(new ExecutorSubscribableChannel(myDeliveryExecutor));
 		}
 
 		if (mySubscriptionActivatingSubscriber == null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionDeliveringRestHookSubscriber.java

@@ -21,12 +21,14 @@ package ca.uhn.fhir.jpa.subscription;
  */
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
 import ca.uhn.fhir.rest.gclient.IClientExecutable;
 import org.apache.commons.lang3.ObjectUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Subscription;
@@ -78,7 +80,7 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionSu
 		if (!(theMessage.getPayload() instanceof ResourceDeliveryMessage)) {
 			return;
 		}
-
+		try {
 			ResourceDeliveryMessage msg = (ResourceDeliveryMessage) theMessage.getPayload();
 
 			if (!subscriptionTypeApplies(getContext(), msg.getSubscription())) {
@@ -90,11 +92,12 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionSu
 
 			// Grab the endpoint from the subscription
 			IPrimitiveType<?> endpoint = getContext().newTerser().getSingleValueOrNull(subscription, BaseSubscriptionInterceptor.SUBSCRIPTION_ENDPOINT, IPrimitiveType.class);
-		String endpointUrl = endpoint.getValueAsString();
+			String endpointUrl = endpoint != null ? endpoint.getValueAsString() : null;
 
 			// Grab the payload type (encoding mimetype) from the subscription
 			IPrimitiveType<?> payload = getContext().newTerser().getSingleValueOrNull(subscription, BaseSubscriptionInterceptor.SUBSCRIPTION_PAYLOAD, IPrimitiveType.class);
-		String payloadString = payload.getValueAsString();
+			String payloadString = payload != null ? payload.getValueAsString() : null;
+			payloadString = StringUtils.defaultString(payloadString, Constants.CT_FHIR_XML_NEW);
 			if (payloadString.contains(";")) {
 				payloadString = payloadString.substring(0, payloadString.indexOf(';'));
 			}
@@ -104,7 +107,9 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionSu
 
 			// Create the client request
 			getContext().getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
-		IGenericClient client = getContext().newRestfulGenericClient(endpointUrl);
+			IGenericClient client = null;
+			if (isNotBlank(endpointUrl)) {
+				client = getContext().newRestfulGenericClient(endpointUrl);
 
 				// Additional headers specified in the subscription
 				List<IPrimitiveType> headers = getContext().newTerser().getValues(subscription, BaseSubscriptionInterceptor.SUBSCRIPTION_HEADER, IPrimitiveType.class);
@@ -113,9 +118,13 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionSu
 						client.registerInterceptor(new SimpleRequestHeaderInterceptor(next.getValueAsString()));
 					}
 				}
+			}
 
 			deliverPayload(msg, subscription, payloadType, client);
-
+		} catch (Exception e) {
+			ourLog.error("Failure handling subscription payload", e);
+			throw new MessagingException(theMessage, "Failure handling subscription payload", e);
+		}
 	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -57,6 +57,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	@Autowired
+	@Qualifier("myCoverageDaoDstu3")
+	protected IFhirResourceDao<Coverage> myCoverageDao;
 	@Autowired
 	protected IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java

@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.util.JpaConstants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
@@ -36,6 +37,185 @@ public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test
 		myDaoConfig.setDefaultSearchParamsCanBeOverridden(new DaoConfig().isDefaultSearchParamsCanBeOverridden());
 	}
 
+
+
+	@Test
+	public void testIndexTransactionWithMatchUrl() {
+		Patient pt2 = new Patient();
+		pt2.setGender(Enumerations.AdministrativeGender.MALE);
+		pt2.setBirthDateElement(new DateType("2011-01-02"));
+		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
+
+		Coverage cov = new Coverage();
+		cov.getBeneficiary().setReference(id2.getValue());
+		cov.addIdentifier().setSystem("urn:foo:bar").setValue("123");
+		IIdType id3 = myCoverageDao.create(cov).getId().toUnqualifiedVersionless();
+
+		createUniqueIndexCoverageBeneficiary();
+
+		mySystemDao.markAllResourcesForReindexing();
+		mySystemDao.performReindexingPass(1000);
+
+		List<ResourceIndexedCompositeStringUnique> uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(uniques.toString(), 1, uniques.size());
+		assertEquals("Coverage/" + id3.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Coverage?beneficiary=Patient%2F" + id2.getIdPart() + "&identifier=urn%3Afoo%3Abar%7C123", uniques.get(0).getIndexString());
+
+
+	}
+
+
+	@Test
+	public void testIndexTransactionWithMatchUrl2() {
+		createUniqueIndexCoverageBeneficiary();
+
+		String input = "{\n" +
+			"  \"resourceType\": \"Bundle\",\n" +
+			"  \"type\": \"transaction\",\n" +
+			"  \"entry\": [\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Patient\",\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"use\": \"official\",\n" +
+			"            \"type\": {\n" +
+			"              \"coding\": [\n" +
+			"                {\n" +
+			"                  \"system\": \"http://hl7.org/fhir/v2/0203\",\n" +
+			"                  \"code\": \"MR\"\n" +
+			"                }\n" +
+			"              ]\n" +
+			"            },\n" +
+			"            \"system\": \"FOOORG:FOOSITE:patientid:MR:R\",\n" +
+			"            \"value\": \"007811959\"\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Patient?identifier=FOOORG%3AFOOSITE%3Apatientid%3AMR%3AR%7C007811959%2CFOOORG%3AFOOSITE%3Apatientid%3AMR%3AB%7C000929990%2CFOOORG%3AFOOSITE%3Apatientid%3API%3APH%7C00589363%2Chttp%3A%2F%2Fhl7.org%2Ffhir%2Fsid%2Fus-ssn%7C657-01-8133\"\n" +
+			"      }\n" +
+			"    },\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:b58ff639-11d1-4dac-942f-abf4f9a625d7\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Coverage\",\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"system\": \"FOOORG:FOOSITE:coverage:planId\",\n" +
+			"            \"value\": \"0403-010101\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"beneficiary\": {\n" +
+			"          \"reference\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\"\n" +
+			"        }\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Coverage?beneficiary=urn%3Auuid%3Ad2a46176-8e15-405d-bbda-baea1a9dc7f3&identifier=FOOORG%3AFOOSITE%3Acoverage%3AplanId%7C0403-010101\"\n" +
+			"      }\n" +
+			"    },\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:13f5da1a-6601-4c1a-82c9-41527be23fa0\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Coverage\",\n" +
+			"        \"contained\": [\n" +
+			"          {\n" +
+			"            \"resourceType\": \"RelatedPerson\",\n" +
+			"            \"id\": \"1\",\n" +
+			"            \"name\": [\n" +
+			"              {\n" +
+			"                \"family\": \"SMITH\",\n" +
+			"                \"given\": [\n" +
+			"                  \"FAKER\"\n" +
+			"                ]\n" +
+			"              }\n" +
+			"            ]\n" +
+			"          },\n" +
+			"          {\n" +
+			"            \"resourceType\": \"Organization\",\n" +
+			"            \"id\": \"2\",\n" +
+			"            \"name\": \"MEDICAID\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"system\": \"FOOORG:FOOSITE:coverage:planId\",\n" +
+			"            \"value\": \"0404-010101\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"policyHolder\": {\n" +
+			"          \"reference\": \"#1\"\n" +
+			"        },\n" +
+			"        \"beneficiary\": {\n" +
+			"          \"reference\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\"\n" +
+			"        },\n" +
+			"        \"payor\": [\n" +
+			"          {\n" +
+			"            \"reference\": \"#2\"\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Coverage?beneficiary=urn%3Auuid%3Ad2a46176-8e15-405d-bbda-baea1a9dc7f3&identifier=FOOORG%3AFOOSITE%3Acoverage%3AplanId%7C0404-010101\"\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ]\n" +
+			"}";
+
+		Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
+		mySystemDao.transaction(mySrd, inputBundle);
+
+		inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		mySystemDao.transaction(mySrd, inputBundle);
+
+	}
+
+
+	private void createUniqueIndexCoverageBeneficiary() {
+		SearchParameter sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-beneficiary");
+		sp.setCode("beneficiary");
+		sp.setExpression("Coverage.beneficiary");
+		sp.setType(Enumerations.SearchParamType.REFERENCE);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		mySearchParameterDao.update(sp);
+
+		sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-identifier");
+		sp.setCode("identifier");
+		sp.setExpression("Coverage.identifier");
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		mySearchParameterDao.update(sp);
+
+		sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-beneficiary-identifier");
+		sp.setCode("coverage-beneficiary-identifier");
+		sp.setExpression("Coverage.beneficiary");
+		sp.setType(Enumerations.SearchParamType.COMPOSITE);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		sp.addComponent()
+			.setExpression("Coverage")
+			.setDefinition(new Reference("/SearchParameter/coverage-beneficiary"));
+		sp.addComponent()
+			.setExpression("Coverage")
+			.setDefinition(new Reference("/SearchParameter/coverage-identifier"));
+		sp.addExtension()
+			.setUrl(JpaConstants.EXT_SP_UNIQUE)
+			.setValue(new BooleanType(true));
+		mySearchParameterDao.update(sp);
+		mySearchParamRegsitry.forceRefresh();
+	}
+
+
 	@Before
 	public void before() {
 		myDaoConfig.setDefaultSearchParamsCanBeOverridden(true);
@@ -143,7 +323,7 @@ public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test
 		try {
 			myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
 			fail();
-		} catch (JpaSystemException e) {
+		} catch (PreconditionFailedException e) {
 			// good
 		}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -146,6 +146,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myPatientDaoR4")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired
+	@Qualifier("myCoverageDaoR4")
+	protected IFhirResourceDao<Coverage> myCoverageDao;
+	@Autowired
 	@Qualifier("myPractitionerDaoR4")
 	protected IFhirResourceDao<Practitioner> myPractitionerDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java

@@ -83,12 +83,32 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		Observation o = new Observation();
 		o.setStatus(ObservationStatus.FINAL);
 		o.getSubject().setReference("Patient/FOO");
-		try {
 		myObservationDao.create(o, mySrd);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Resource Patient/FOO not found, specified in path: Observation.subject", e.getMessage());
 	}
+
+	@Test
+	public void testCreateWithMultiplePlaceholders() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		Task task = new Task();
+		task.addNote().setText("A note");
+		task.addPartOf().setReference("Task/AAA");
+		task.addPartOf().setReference("Task/AAA");
+		task.addPartOf().setReference("Task/AAA");
+		IIdType id = myTaskDao.create(task).getId().toUnqualifiedVersionless();
+
+		task = myTaskDao.read(id);
+		assertEquals(3, task.getPartOf().size());
+		assertEquals("Task/AAA", task.getPartOf().get(0).getReference());
+		assertEquals("Task/AAA", task.getPartOf().get(1).getReference());
+		assertEquals("Task/AAA", task.getPartOf().get(2).getReference());
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add(Task.SP_PART_OF, new ReferenceParam("Task/AAA"));
+		List<String> found = toUnqualifiedVersionlessIdValues(myTaskDao.search(params));
+		assertThat(found, contains(id.getValue()));
+
+
 	}
 
 	@Test
@@ -123,12 +143,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		o.setId(id);
 		o.setStatus(ObservationStatus.FINAL);
 		o.getSubject().setReference("Patient/FOO");
-		try {
 		myObservationDao.update(o, mySrd);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals("Resource Patient/FOO not found, specified in path: Observation.subject", e.getMessage());
-		}
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java

@@ -22,6 +22,7 @@ import org.springframework.orm.jpa.JpaSystemException;
 
 import java.util.Collections;
 import java.util.List;
+import java.util.UUID;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
@@ -346,6 +347,182 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 
 	}
 
+
+	private void createUniqueIndexCoverageBeneficiary() {
+		SearchParameter sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-beneficiary");
+		sp.setCode("beneficiary");
+		sp.setExpression("Coverage.beneficiary");
+		sp.setType(Enumerations.SearchParamType.REFERENCE);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		mySearchParameterDao.update(sp);
+
+		sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-identifier");
+		sp.setCode("identifier");
+		sp.setExpression("Coverage.identifier");
+		sp.setType(Enumerations.SearchParamType.TOKEN);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		mySearchParameterDao.update(sp);
+
+		sp = new SearchParameter();
+		sp.setId("SearchParameter/coverage-beneficiary-identifier");
+		sp.setCode("coverage-beneficiary-identifier");
+		sp.setExpression("Coverage.beneficiary");
+		sp.setType(Enumerations.SearchParamType.COMPOSITE);
+		sp.setStatus(PublicationStatus.ACTIVE);
+		sp.addBase("Coverage");
+		sp.addComponent()
+			.setExpression("Coverage")
+			.setDefinition(new Reference("/SearchParameter/coverage-beneficiary"));
+		sp.addComponent()
+			.setExpression("Coverage")
+			.setDefinition(new Reference("/SearchParameter/coverage-identifier"));
+		sp.addExtension()
+			.setUrl(JpaConstants.EXT_SP_UNIQUE)
+			.setValue(new BooleanType(true));
+		mySearchParameterDao.update(sp);
+		mySearchParamRegsitry.forceRefresh();
+	}
+
+	@Test
+	public void testIndexTransactionWithMatchUrl() {
+		Patient pt2 = new Patient();
+		pt2.setGender(Enumerations.AdministrativeGender.MALE);
+		pt2.setBirthDateElement(new DateType("2011-01-02"));
+		IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
+
+		Coverage cov = new Coverage();
+		cov.getBeneficiary().setReference(id2.getValue());
+		cov.addIdentifier().setSystem("urn:foo:bar").setValue("123");
+		IIdType id3 = myCoverageDao.create(cov).getId().toUnqualifiedVersionless();
+
+		createUniqueIndexCoverageBeneficiary();
+
+		mySystemDao.markAllResourcesForReindexing();
+		mySystemDao.performReindexingPass(1000);
+
+		List<ResourceIndexedCompositeStringUnique> uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(uniques.toString(), 1, uniques.size());
+		assertEquals("Coverage/" + id3.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Coverage?beneficiary=Patient%2F" + id2.getIdPart() + "&identifier=urn%3Afoo%3Abar%7C123", uniques.get(0).getIndexString());
+
+
+	}
+
+	@Test
+	public void testIndexTransactionWithMatchUrl2() {
+		createUniqueIndexCoverageBeneficiary();
+
+		String input = "{\n" +
+			"  \"resourceType\": \"Bundle\",\n" +
+			"  \"type\": \"transaction\",\n" +
+			"  \"entry\": [\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Patient\",\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"use\": \"official\",\n" +
+			"            \"type\": {\n" +
+			"              \"coding\": [\n" +
+			"                {\n" +
+			"                  \"system\": \"http://hl7.org/fhir/v2/0203\",\n" +
+			"                  \"code\": \"MR\"\n" +
+			"                }\n" +
+			"              ]\n" +
+			"            },\n" +
+			"            \"system\": \"FOOORG:FOOSITE:patientid:MR:R\",\n" +
+			"            \"value\": \"007811959\"\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Patient?identifier=FOOORG%3AFOOSITE%3Apatientid%3AMR%3AR%7C007811959%2CFOOORG%3AFOOSITE%3Apatientid%3AMR%3AB%7C000929990%2CFOOORG%3AFOOSITE%3Apatientid%3API%3APH%7C00589363%2Chttp%3A%2F%2Fhl7.org%2Ffhir%2Fsid%2Fus-ssn%7C657-01-8133\"\n" +
+			"      }\n" +
+			"    },\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:b58ff639-11d1-4dac-942f-abf4f9a625d7\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Coverage\",\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"system\": \"FOOORG:FOOSITE:coverage:planId\",\n" +
+			"            \"value\": \"0403-010101\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"beneficiary\": {\n" +
+			"          \"reference\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\"\n" +
+			"        }\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Coverage?beneficiary=urn%3Auuid%3Ad2a46176-8e15-405d-bbda-baea1a9dc7f3&identifier=FOOORG%3AFOOSITE%3Acoverage%3AplanId%7C0403-010101\"\n" +
+			"      }\n" +
+			"    },\n" +
+			"    {\n" +
+			"      \"fullUrl\": \"urn:uuid:13f5da1a-6601-4c1a-82c9-41527be23fa0\",\n" +
+			"      \"resource\": {\n" +
+			"        \"resourceType\": \"Coverage\",\n" +
+			"        \"contained\": [\n" +
+			"          {\n" +
+			"            \"resourceType\": \"RelatedPerson\",\n" +
+			"            \"id\": \"1\",\n" +
+			"            \"name\": [\n" +
+			"              {\n" +
+			"                \"family\": \"SMITH\",\n" +
+			"                \"given\": [\n" +
+			"                  \"FAKER\"\n" +
+			"                ]\n" +
+			"              }\n" +
+			"            ]\n" +
+			"          },\n" +
+			"          {\n" +
+			"            \"resourceType\": \"Organization\",\n" +
+			"            \"id\": \"2\",\n" +
+			"            \"name\": \"MEDICAID\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"identifier\": [\n" +
+			"          {\n" +
+			"            \"system\": \"FOOORG:FOOSITE:coverage:planId\",\n" +
+			"            \"value\": \"0404-010101\"\n" +
+			"          }\n" +
+			"        ],\n" +
+			"        \"policyHolder\": {\n" +
+			"          \"reference\": \"#1\"\n" +
+			"        },\n" +
+			"        \"beneficiary\": {\n" +
+			"          \"reference\": \"urn:uuid:d2a46176-8e15-405d-bbda-baea1a9dc7f3\"\n" +
+			"        },\n" +
+			"        \"payor\": [\n" +
+			"          {\n" +
+			"            \"reference\": \"#2\"\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      },\n" +
+			"      \"request\": {\n" +
+			"        \"method\": \"PUT\",\n" +
+			"        \"url\": \"/Coverage?beneficiary=urn%3Auuid%3Ad2a46176-8e15-405d-bbda-baea1a9dc7f3&identifier=FOOORG%3AFOOSITE%3Acoverage%3AplanId%7C0404-010101\"\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ]\n" +
+			"}";
+
+		Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
+		mySystemDao.transaction(mySrd, inputBundle);
+
+		inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		mySystemDao.transaction(mySrd, inputBundle);
+
+	}
+
+
 	@Test
 	public void testUniqueValuesAreIndexed_DateAndToken() {
 		createUniqueBirthdateAndGenderSps();
@@ -423,6 +600,119 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
 		assertEquals("Patient?name=GIVEN2&organization=Organization%2FORG", uniques.get(2).getIndexString());
 	}
 
+	@Test
+	public void testUniqueValuesAreIndexed_StringAndReference_UsingConditional() {
+		createUniqueNameAndManagingOrganizationSps();
+		List<ResourceIndexedCompositeStringUnique> uniques;
+
+		Organization org = new Organization();
+		org.setId("Organization/ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pt1 = new Patient();
+		pt1.addName().setFamily("FAMILY1");
+		pt1.setManagingOrganization(new Reference("Organization/ORG"));
+		IIdType id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization.name=ORG").getId().toUnqualifiedVersionless();
+
+		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(1, uniques.size());
+		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Patient?name=FAMILY1&organization=Organization%2FORG", uniques.get(0).getIndexString());
+
+		// Again
+
+		pt1 = new Patient();
+		pt1.addName().setFamily("FAMILY1");
+		pt1.setManagingOrganization(new Reference("Organization/ORG"));
+		id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization.name=ORG").getId().toUnqualifiedVersionless();
+
+		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(1, uniques.size());
+		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Patient?name=FAMILY1&organization=Organization%2FORG", uniques.get(0).getIndexString());
+	}
+
+	@Test
+	public void testUniqueValuesAreIndexed_StringAndReference_UsingConditionalInTransaction() {
+		createUniqueNameAndManagingOrganizationSps();
+		List<ResourceIndexedCompositeStringUnique> uniques;
+
+		Organization org = new Organization();
+		org.setId("Organization/ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Bundle bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.TRANSACTION);
+
+		String orgId = "urn:uuid:" + UUID.randomUUID().toString();
+		org = new Organization();
+		org.setName("ORG");
+		bundle
+			.addEntry()
+			.setResource(org)
+			.setFullUrl(orgId)
+			.getRequest()
+			.setMethod(Bundle.HTTPVerb.PUT)
+			.setUrl("/Organization?name=ORG");
+
+		Patient pt1 = new Patient();
+		pt1.addName().setFamily("FAMILY1");
+		pt1.setManagingOrganization(new Reference(orgId));
+		bundle
+			.addEntry()
+			.setResource(pt1)
+			.getRequest()
+			.setMethod(Bundle.HTTPVerb.PUT)
+			.setUrl("/Patient?name=FAMILY1&organization=" + orgId.replace(":", "%3A"));
+
+		Bundle resp = mySystemDao.transaction(mySrd, bundle);
+
+		IIdType id1 = new IdType(resp.getEntry().get(1).getResponse().getLocation());
+
+		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(1, uniques.size());
+		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Patient?name=FAMILY1&organization=Organization%2FORG", uniques.get(0).getIndexString());
+
+		// Again
+
+		bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.TRANSACTION);
+
+		orgId = IdType.newRandomUuid().getValue();
+		org = new Organization();
+		org.setName("ORG");
+		bundle
+			.addEntry()
+			.setResource(org)
+			.setFullUrl(orgId)
+			.getRequest()
+			.setMethod(Bundle.HTTPVerb.PUT)
+			.setUrl("/Organization?name=ORG");
+
+		pt1 = new Patient();
+		pt1.addName().setFamily("FAMILY1");
+		pt1.setManagingOrganization(new Reference(orgId));
+		bundle
+			.addEntry()
+			.setResource(pt1)
+			.getRequest()
+			.setMethod(Bundle.HTTPVerb.PUT)
+			.setUrl("/Patient?name=FAMILY1&organization=" + orgId);
+
+		resp = mySystemDao.transaction(mySrd, bundle);
+
+		id1 = new IdType(resp.getEntry().get(1).getResponse().getLocation());
+
+		uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
+		assertEquals(1, uniques.size());
+		assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
+		assertEquals("Patient?name=FAMILY1&organization=Organization%2FORG", uniques.get(0).getIndexString());
+
+	}
+
 	@Test
 	public void testUniqueValuesAreNotIndexedIfNotAllParamsAreFound_DateAndToken() {
 		createUniqueBirthdateAndGenderSps();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestDstu2Test.java

@@ -281,11 +281,11 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
 	}
 
 	public static void waitForQueueToDrain(BaseSubscriptionInterceptor theRestHookSubscriptionInterceptor) throws InterruptedException {
-		ourLog.info("QUEUE HAS {} ITEMS", theRestHookSubscriptionInterceptor.getExecutorQueueForUnitTests().size());
+		ourLog.info("QUEUE HAS {} ITEMS", theRestHookSubscriptionInterceptor.getExecutorQueueSizeForUnitTests());
-		while (theRestHookSubscriptionInterceptor.getExecutorQueueForUnitTests().size() > 0) {
+		while (theRestHookSubscriptionInterceptor.getExecutorQueueSizeForUnitTests() > 0) {
 			Thread.sleep(50);
 		}
-		ourLog.info("QUEUE HAS {} ITEMS", theRestHookSubscriptionInterceptor.getExecutorQueueForUnitTests().size());
+		ourLog.info("QUEUE HAS {} ITEMS", theRestHookSubscriptionInterceptor.getExecutorQueueSizeForUnitTests());
 	}
 
 	private void waitForQueueToDrain() throws InterruptedException {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookTestWithInterceptorRegisteredToDaoConfigR4Test.java

@@ -84,11 +84,11 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigR4Test extends Base
 	}
 
 	private void waitForQueueToDrain() throws InterruptedException {
-		ourLog.info("QUEUE HAS {} ITEMS", getRestHookSubscriptionInterceptor().getExecutorQueueForUnitTests().size());
+		ourLog.info("QUEUE HAS {} ITEMS", getRestHookSubscriptionInterceptor().getExecutorQueueSizeForUnitTests());
-		while (getRestHookSubscriptionInterceptor().getExecutorQueueForUnitTests().size() > 0) {
+		while (getRestHookSubscriptionInterceptor().getExecutorQueueSizeForUnitTests() > 0) {
 			Thread.sleep(250);
 		}
-		ourLog.info("QUEUE HAS {} ITEMS", getRestHookSubscriptionInterceptor().getExecutorQueueForUnitTests().size());
+		ourLog.info("QUEUE HAS {} ITEMS", getRestHookSubscriptionInterceptor().getExecutorQueueSizeForUnitTests());
 	}
 
 	private Observation sendObservation(String code, String system) throws InterruptedException {