Merge branch 'master' into ja_20190928_rationalize_search_param_extractor

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -1,4 +1,5 @@
 
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionRefersToUnknownCs=Unknown CodeSystem URI "{0}" referenced from ValueSet
 
 # Core Library Messages
 ca.uhn.fhir.context.FhirContext.unknownResourceName=Unknown resource name "{0}" (this name is not known in FHIR version "{1}")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -132,6 +132,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
+		if (!retVal.isUnchangedInCurrentOperation()) {
 
 			CodeSystem csDstu3 = (CodeSystem) theResource;
 
@@ -140,6 +141,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
 
 			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
 
+		}
+
 		return retVal;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java

@@ -161,6 +161,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
+		if (!retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				try {
 					ConceptMap conceptMap = (ConceptMap) theResource;
@@ -172,6 +173,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
 			} else {
 				myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
 			}
+		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java

@@ -415,7 +415,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
-		if (myDaoConfig.isPreExpandValueSets()) {
+		if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				try {
 					ValueSet valueSet = (ValueSet) theResource;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -136,10 +136,12 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
+		if (!retVal.isUnchangedInCurrentOperation()) {
 			CodeSystem cs = (CodeSystem) theResource;
 			addPidToResource(theEntity, theResource);
 
 			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
+		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java

@@ -161,12 +161,14 @@ public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<Concept
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
+		if (!retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				ConceptMap conceptMap = (ConceptMap) theResource;
 				myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
 			} else {
 				myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
 			}
+		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java

@@ -396,7 +396,7 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
-		if (myDaoConfig.isPreExpandValueSets()) {
+		if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				ValueSet valueSet = (ValueSet) theResource;
 				myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java

@@ -135,11 +135,13 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
 	public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
+		if (!retVal.isUnchangedInCurrentOperation()) {
 
 			CodeSystem cs = (CodeSystem) theResource;
 			addPidToResource(theEntity, theResource);
 
 			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
+		}
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java

@@ -161,6 +161,7 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
 	public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 													 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
+		if (!retVal.isUnchangedInCurrentOperation()) {
 
 			if (retVal.getDeleted() == null) {
 				ConceptMap conceptMap = (ConceptMap) theResource;
@@ -168,6 +169,7 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
 			} else {
 				myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
 			}
+		}
 		
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java

@@ -408,7 +408,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
 												 boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
 		ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
 
-		if (myDaoConfig.isPreExpandValueSets()) {
+		if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
 			if (retVal.getDeleted() == null) {
 				ValueSet valueSet = (ValueSet) theResource;
 				myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/JpaConformanceProviderR4.java

@@ -19,24 +19,25 @@ package ca.uhn.fhir.jpa.provider.r4;
  * limitations under the License.
  * #L%
  */
-import java.util.*;
-
-import javax.servlet.http.HttpServletRequest;
-
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.CapabilityStatement.*;
-import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.ExtensionConstants;
+import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.CapabilityStatement.*;
+import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
+
+import javax.servlet.http.HttpServletRequest;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Map;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -141,6 +142,9 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
 						case URI:
 							confSp.setType(SearchParamType.URI);
 							break;
+						case SPECIAL:
+							confSp.setType(SearchParamType.SPECIAL);
+							break;
 						case HAS:
 							// Shouldn't happen
 							break;
@@ -171,6 +175,10 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
 		return myIncludeResourceCounts;
 	}
 
+	public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
+		myIncludeResourceCounts = theIncludeResourceCounts;
+	}
+
 	/**
 	 * Subclasses may override
 	 */
@@ -187,10 +195,6 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
 		myImplementationDescription = theImplDesc;
 	}
 
-	public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
-		myIncludeResourceCounts = theIncludeResourceCounts;
-	}
-
 	@Override
 	public void setRestfulServer(RestfulServer theRestfulServer) {
 		this.myRestfulServer = theRestfulServer;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaConformanceProviderR5.java

@@ -140,6 +140,9 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
 						case URI:
 							confSp.setType(SearchParamType.URI);
 							break;
+						case SPECIAL:
+							confSp.setType(SearchParamType.SPECIAL);
+							break;
 						case HAS:
 							// Shouldn't happen
 							break;
@@ -170,6 +173,10 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
 		return myIncludeResourceCounts;
 	}
 
+	public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
+		myIncludeResourceCounts = theIncludeResourceCounts;
+	}
+
 	/**
 	 * Subclasses may override
 	 */
@@ -186,10 +193,6 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
 		myImplementationDescription = theImplDesc;
 	}
 
-	public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
-		myIncludeResourceCounts = theIncludeResourceCounts;
-	}
-
 	@Override
 	public void setRestfulServer(RestfulServer theRestfulServer) {
 		this.myRestfulServer = theRestfulServer;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java

@@ -195,6 +195,11 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_SECOND, true, jobDetail);
 	}
 
+	@VisibleForTesting
+	ReentrantLock getIndexingLockForUnitTest() {
+		return myIndexingLock;
+	}
+
 	@Override
 	@Transactional(Transactional.TxType.NEVER)
 	public Integer runReindexingPass() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

@@ -675,7 +675,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
 
 				CodeSystem codeSystemFromContext = getCodeSystemFromContext(system);
 				if (codeSystemFromContext == null) {
-					throw new InvalidRequestException("Unknown code system: " + system);
+					String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionRefersToUnknownCs", system);
+					ourLog.warn(msg);
+					theValueSetCodeAccumulator.addMessage(msg);
+					return false;
 				}
 
 				if (!theIncludeOrExclude.getConcept().isEmpty()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IValueSetConceptAccumulator.java

@@ -27,6 +27,8 @@ import java.util.Collection;
 
 public interface IValueSetConceptAccumulator {
 
+	void addMessage(String theMessage);
+
 	void includeConcept(String theSystem, String theCode, String theDisplay);
 
 	void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java

@@ -57,6 +57,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 		myConceptsExcluded = 0;
 	}
 
+	@Override
+	public void addMessage(String theMessage) {
+		// ignore for now
+
+	}
+
 	@Override
 	public void includeConcept(String theSystem, String theCode, String theDisplay) {
 		saveConcept(theSystem, theCode, theDisplay);
@@ -82,7 +88,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 		if (optionalConcept.isPresent()) {
 			TermValueSetConcept concept = optionalConcept.get();
 
-			ourLog.info("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
+			ourLog.debug("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
 			for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
 				myValueSetConceptDesignationDao.deleteById(designation.getId());
 				myTermValueSet.decrementTotalConceptDesignations();
@@ -90,7 +96,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
 			myValueSetConceptDao.deleteById(concept.getId());
 			myTermValueSet.decrementTotalConcepts();
 			myValueSetDao.save(myTermValueSet);
-			ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
+			ourLog.debug("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
 
 			if (++myConceptsExcluded % 250 == 0) {
 				ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSet.getUrl());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java

@@ -22,9 +22,11 @@ package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
 import ca.uhn.fhir.model.api.annotation.Block;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
 
 import javax.annotation.Nullable;
@@ -54,6 +56,13 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
 		return myMaxCapacity - myConceptsCount;
 	}
 
+	@Override
+	public void addMessage(String theMessage) {
+		addExtension()
+			.setUrl(JpaConstants.EXT_VALUESET_EXPANSION_MESSAGE)
+			.setValue(new StringType(theMessage));
+	}
+
 	@Override
 	public void includeConcept(String theSystem, String theCode, String theDisplay) {
 		incrementConceptsCount();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5SearchNoFtTest.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.dao.r5;
 
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.TestUtil;
 import ca.uhn.fhir.rest.api.Constants;
@@ -9,11 +11,14 @@ import ca.uhn.fhir.rest.param.HasOrListParam;
 import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import org.hl7.fhir.r5.model.Organization;
+import org.hl7.fhir.r5.model.Patient;
 import org.hl7.fhir.r5.model.Practitioner;
 import org.hl7.fhir.r5.model.PractitionerRole;
 import org.junit.AfterClass;
 import org.junit.Test;
 
+import java.util.Date;
+
 import static org.junit.Assert.assertEquals;
 
 @SuppressWarnings({"unchecked", "Duplicates"})
@@ -98,6 +103,40 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
 		assertEquals(1, outcome.getResources(0, 1).size());
 	}
 
+	@Test
+	public void testSearchDoesntFailIfResourcesAreDeleted() {
+
+		Patient p = new Patient();
+		p.addIdentifier().setValue("1");
+		myPatientDao.create(p);
+
+		p = new Patient();
+		p.addIdentifier().setValue("2");
+		myPatientDao.create(p);
+
+		p = new Patient();
+		p.addIdentifier().setValue("3");
+		Long id = myPatientDao.create(p).getId().getIdPartAsLong();
+
+		IBundleProvider outcome = myPatientDao.search(new SearchParameterMap());
+		assertEquals(3, outcome.size().intValue());
+
+		runInTransaction(()->{
+			ResourceTable table = myResourceTableDao.findById(id).orElseThrow(() -> new IllegalArgumentException());
+			table.setDeleted(new Date());
+			myResourceTableDao.save(table);
+		});
+
+		assertEquals(2, outcome.getResources(0, 3).size());
+
+		runInTransaction(()->{
+			myResourceHistoryTableDao.deleteAll();
+		});
+
+		assertEquals(0, outcome.getResources(0, 3).size());
+	}
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -4080,22 +4080,16 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		Patient patient = new Patient();
 		patient.addName().addGiven("James");
 		patient.setBirthDateElement(new DateType("2011-02-02"));
-		patient.addContact().setGender(AdministrativeGender.MALE);
 
 		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
 		post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 
-		CloseableHttpResponse response = ourHttpClient.execute(post);
+		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
-		try {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(412, response.getStatusLine().getStatusCode());
+			assertEquals(200, response.getStatusLine().getStatusCode());
 			assertThat(resp, not(containsString("Resource has no id")));
-			assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
-		} finally {
-			IOUtils.closeQuietly(response.getEntity().getContent());
-			response.close();
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java

@@ -68,7 +68,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 	private static SubscriptionMatcherInterceptor ourSubscriptionMatcherInterceptor;
 	protected static Server ourServer;
 	protected IGenericClient ourClient;
-	ResourceCountCache ourResourceCountsCache;
+	ResourceCountCache myResourceCountsCache;
 	private TerminologyUploaderProvider myTerminologyUploaderProvider;
 	private boolean ourRestHookSubscriptionInterceptorRequested;
 
@@ -93,6 +93,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 		myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
 		myFhirCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
 		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+		myResourceCountsCache = (ResourceCountCache) myAppCtx.getBean("myResourceCountsCache");
 
 		if (ourServer == null) {
 			ourRestServer = new RestfulServer(myFhirCtx);
@@ -113,7 +114,6 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
 			ourRestServer.setServerConformanceProvider(confProvider);
 
 			ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
-			ourResourceCountsCache = (ResourceCountCache) myAppCtx.getBean("myResourceCountsCache");
 
 			Server server = new Server(0);
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -5308,7 +5308,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Patient patient = new Patient();
 		patient.addName().addGiven("James");
 		patient.setBirthDateElement(new DateType("2011-02-02"));
-		patient.addContact().setGender(AdministrativeGender.MALE);
 
 		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
@@ -5317,9 +5316,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(412, response.getStatusLine().getStatusCode());
+			assertEquals(200, response.getStatusLine().getStatusCode());
 			assertThat(resp, not(containsString("Resource has no id")));
-			assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
 		}
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ServerR4Test.java

@@ -1,6 +1,9 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.util.ExtensionConstants;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
@@ -13,6 +16,7 @@ import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.AfterClass;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
@@ -25,6 +29,29 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerR4Test.class);
 
+	@Autowired
+	private IFhirResourceDao<CapabilityStatement> myCapabilityStatementDao;
+
+	@Test
+	public void testCapabilityStatementValidates() throws IOException {
+		HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=json");
+		try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
+			assertEquals(200, resp.getStatusLine().getStatusCode());
+			String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
+
+			ourLog.info(respString);
+
+			CapabilityStatement cs = myFhirCtx.newJsonParser().parseResource(CapabilityStatement.class, respString);
+
+			try {
+				myCapabilityStatementDao.validate(cs, null, respString, EncodingEnum.JSON, null, null, null);
+			} catch (PreconditionFailedException e) {
+				ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+				fail();
+			}
+		}
+	}
+
 
 	/**
 	 * See #519
@@ -71,7 +98,7 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
 		 * Initial fetch after a clear should return
 		 * no results
 		 */
-		ourResourceCountsCache.clear();
+		myResourceCountsCache.clear();
 
 		CapabilityStatement capabilityStatement = ourClient
 			.capabilities()
@@ -93,7 +120,7 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
 		 * Now run a background pass (the update
 		 * method is called by the scheduler normally)
 		 */
-		ourResourceCountsCache.update();
+		myResourceCountsCache.update();
 
 		capabilityStatement = ourClient
 			.capabilities()

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ServerR5Test.java

@@ -0,0 +1,151 @@
+package ca.uhn.fhir.jpa.provider.r5;
+
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.util.ExtensionConstants;
+import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.r5.model.CapabilityStatement;
+import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
+import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.Patient;
+import org.junit.AfterClass;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.HashSet;
+import java.util.Set;
+
+import static org.junit.Assert.*;
+
+public class ServerR5Test extends BaseResourceProviderR5Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerR5Test.class);
+
+	@Autowired
+	private IFhirResourceDao<CapabilityStatement> myCapabilityStatementDao;
+
+	@Test
+	@Ignore
+	public void testCapabilityStatementValidates() throws IOException {
+		HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=json");
+		try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
+			assertEquals(200, resp.getStatusLine().getStatusCode());
+			String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
+
+			ourLog.info(respString);
+
+			CapabilityStatement cs = myFhirCtx.newJsonParser().parseResource(CapabilityStatement.class, respString);
+
+			try {
+				myCapabilityStatementDao.validate(cs, null, respString, EncodingEnum.JSON, null, null, null);
+			} catch (PreconditionFailedException e) {
+				ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+				fail();
+			}
+		}
+	}
+
+
+	/**
+	 * See #519
+	 */
+	@Test
+	public void saveIdParamOnlyAppearsOnce() throws IOException {
+		HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=xml");
+		CloseableHttpResponse resp = ourHttpClient.execute(get);
+		try {
+			ourLog.info(resp.toString());
+			assertEquals(200, resp.getStatusLine().getStatusCode());
+
+			String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(respString);
+
+			CapabilityStatement cs = myFhirCtx.newXmlParser().parseResource(CapabilityStatement.class, respString);
+
+			for (CapabilityStatementRestResourceComponent nextResource : cs.getRest().get(0).getResource()) {
+				ourLog.info("Testing resource: " + nextResource.getType());
+				Set<String> sps = new HashSet<String>();
+				for (CapabilityStatementRestResourceSearchParamComponent nextSp : nextResource.getSearchParam()) {
+					if (sps.add(nextSp.getName()) == false) {
+						fail("Duplicate search parameter " + nextSp.getName() + " for resource " + nextResource.getType());
+					}
+				}
+
+				if (!sps.contains("_id")) {
+					fail("No search parameter _id for resource " + nextResource.getType());
+				}
+			}
+		} finally {
+			IOUtils.closeQuietly(resp.getEntity().getContent());
+		}
+	}
+
+
+	@Test
+	public void testMetadataIncludesResourceCounts() {
+		Patient p = new Patient();
+		p.setActive(true);
+		ourClient.create().resource(p).execute();
+
+		/*
+		 * Initial fetch after a clear should return
+		 * no results
+		 */
+		myResourceCountsCache.clear();
+
+		CapabilityStatement capabilityStatement = ourClient
+			.capabilities()
+			.ofType(CapabilityStatement.class)
+			.execute();
+
+		Extension patientCountExt = capabilityStatement
+			.getRest()
+			.get(0)
+			.getResource()
+			.stream()
+			.filter(t -> t.getType().equals("Patient"))
+			.findFirst()
+			.orElseThrow(() -> new InternalErrorException("No patient"))
+			.getExtensionByUrl(ExtensionConstants.CONF_RESOURCE_COUNT);
+		assertNull(patientCountExt);
+
+		/*
+		 * Now run a background pass (the update
+		 * method is called by the scheduler normally)
+		 */
+		myResourceCountsCache.update();
+
+		capabilityStatement = ourClient
+			.capabilities()
+			.ofType(CapabilityStatement.class)
+			.execute();
+
+		patientCountExt = capabilityStatement
+			.getRest()
+			.get(0)
+			.getResource()
+			.stream()
+			.filter(t -> t.getType().equals("Patient"))
+			.findFirst()
+			.orElseThrow(() -> new InternalErrorException("No patient"))
+			.getExtensionByUrl(ExtensionConstants.CONF_RESOURCE_COUNT);
+		assertEquals("1", patientCountExt.getValueAsPrimitive().getValueAsString());
+
+	}
+
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java

@@ -26,6 +26,8 @@ import org.springframework.data.domain.SliceImpl;
 import org.springframework.transaction.PlatformTransactionManager;
 
 import java.util.*;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
 
 import static org.junit.Assert.assertEquals;
 import static org.mockito.ArgumentMatchers.any;
@@ -94,6 +96,17 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 		mySvc.start();
 	}
 
+	@Test
+	public void testNoParallelReindexing() throws InterruptedException {
+		CountDownLatch latch = new CountDownLatch(1);
+		new Thread(()->{
+			mySvc.getIndexingLockForUnitTest().lock();
+			latch.countDown();
+		}).start();
+		latch.await(10, TimeUnit.SECONDS);
+		mySvc.runReindexingPass();
+	}
+
 	@Test
 	public void testReindexPassOnlyReturnsValuesAtLowThreshold() {
 		mockNothingToExpunge();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulatorTest.java

@@ -0,0 +1,75 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
+import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.util.Optional;
+
+import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.*;
+
+@RunWith(MockitoJUnitRunner.class)
+public class ValueSetConceptAccumulatorTest {
+
+	private ValueSetConceptAccumulator myAccumulator;
+	private TermValueSet myValueSet;
+	@Mock
+	private ITermValueSetDao myValueSetDao;
+	@Mock
+	private ITermValueSetConceptDesignationDao myValueSetDesignationDao;
+	@Mock
+	private ITermValueSetConceptDao myValueSetConceptDao;
+
+	@Before
+	public void before() {
+		myValueSet = new TermValueSet();
+		myAccumulator = new ValueSetConceptAccumulator(myValueSet, myValueSetDao, myValueSetConceptDao, myValueSetDesignationDao);
+	}
+
+	@Test
+	public void testIncludeConcept() {
+		for (int i = 0; i < 1000; i++) {
+			myAccumulator.includeConcept("sys", "code", "display");
+		}
+		verify(myValueSetConceptDao, times(1000)).save(any());
+	}
+
+	@Test
+	public void testExcludeBlankConcept() {
+		myAccumulator.excludeConcept("", "");
+		verifyNoInteractions(myValueSetConceptDao);
+	}
+
+	@Test
+	public void testAddMessage() {
+		myAccumulator.addMessage("foo");
+		verifyNoInteractions(myValueSetConceptDao);
+	}
+
+	@Test
+	public void testExcludeConceptWithDesignations() {
+		for (int i = 0; i <1000; i++) {
+
+			TermValueSetConcept value = new TermValueSetConcept();
+			value.setCode("code");
+			value.getDesignations().add(new TermValueSetConceptDesignation().setValue("foo"));
+
+			when(myValueSetConceptDao.findByTermValueSetIdSystemAndCode(any(), eq("sys"), eq("code"+i))).thenReturn(Optional.of(value));
+
+			myAccumulator.excludeConcept("sys", "code"+i);
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

@@ -2,11 +2,13 @@ package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import com.google.common.collect.Lists;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.HttpVerb;
 import org.junit.Test;
@@ -688,6 +690,21 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 		assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
 	}
 
+	@Test
+	public void testExpandValueSetWithUnknownCodeSystem() {
+		ValueSet vs = new ValueSet();
+		ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
+		include.setSystem("http://unknown-system");
+		ValueSet outcome = myTermSvc.expandValueSetInMemory(vs, null);
+		assertEquals(0, outcome.getExpansion().getContains().size());
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
+		ourLog.info(encoded);
+
+		Extension extensionByUrl = outcome.getExpansion().getExtensionByUrl(JpaConstants.EXT_VALUESET_EXPANSION_MESSAGE);
+		assertEquals("Unknown CodeSystem URI \"http://unknown-system\" referenced from ValueSet", extensionByUrl.getValueAsPrimitive().getValueAsString());
+	}
+
+
 	@Test
 	public void testExpandTermValueSetAndChildrenWithOffsetAndCountWithClientAssignedId() throws Exception {
 		myDaoConfig.setPreExpandValueSets(true);

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -24,6 +24,13 @@ import ca.uhn.fhir.rest.api.Constants;
 
 public class JpaConstants {
 
+	/**
+	 * Non-instantiable
+	 */
+	private JpaConstants() {
+		// nothing
+	}
+
 	/**
 	 * Operation name for the $apply-codesystem-delta-add operation
 	 */
@@ -243,6 +250,12 @@ public class JpaConstants {
 	 */
 	public static final String EXTENSION_EXT_SYSTEMDEFINED = JpaConstants.class.getName() + "_EXTENSION_EXT_SYSTEMDEFINED";
 
+	/**
+	 * Message added to expansion valueset
+	 */
+	public static final String EXT_VALUESET_EXPANSION_MESSAGE = "http://hapifhir.io/fhir/StructureDefinition/valueset-expansion-message";
+
+
 	/**
 	 * Parameter for the $export operation
 	 */

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/cache/SubscriptionLoaderTest.java

@@ -11,6 +11,8 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.TimeUnit;
 
 import static org.junit.Assert.assertEquals;
 
@@ -50,7 +52,17 @@ public class SubscriptionLoaderTest extends BaseBlockingQueueSubscribableChannel
 	@Test
 	public void testMultipleThreadsDontBlock() throws InterruptedException {
 		SubscriptionLoader svc = new SubscriptionLoader();
+		CountDownLatch latch = new CountDownLatch(1);
+		new Thread(()->{
+			try {
 				svc.acquireSemaphoreForUnitTest();
+				latch.countDown();
+			} catch (InterruptedException theE) {
+				// ignore
+			}
+		}).start();
+
+		latch.await(10, TimeUnit.SECONDS);
 		svc.syncSubscriptions();
 	}
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ReadMethodBinding.java

@@ -140,8 +140,7 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding {
 		if (Constants.PARAM_HISTORY.equals(theRequest.getOperation())) {
 			if (mySupportsVersion == false) {
 				return false;
-			}
+			} else if (theRequest.getId().hasVersionIdPart() == false) {
-			if (theRequest.getId().hasVersionIdPart() == false) {
 				return false;
 			}
 		} else if (!StringUtils.isBlank(theRequest.getOperation())) {

hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/method/ReadMethodBindingTest.java

@@ -101,6 +101,31 @@ public class ReadMethodBindingTest {
 		when(myRequestDetails.getOperation()).thenReturn("$foo");
 		assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
 
+		// History operation
+		when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123"));
+		when(myRequestDetails.getOperation()).thenReturn("_history");
+		assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
+
+	}
+
+	@Test
+	public void testIncomingServerRequestNoMatch_HasCompartment() throws NoSuchMethodException {
+
+		class MyProvider {
+			@Read(version = false)
+			public IBaseResource read(@IdParam IIdType theIdType) {
+				return null;
+			}
+		}
+
+		when(myCtx.getResourceDefinition(any(Class.class))).thenReturn(definition);
+		when(definition.getName()).thenReturn("Patient");
+		when(myRequestDetails.getResourceName()).thenReturn("Patient");
+		when(myRequestDetails.getCompartmentName()).thenReturn("Patient");
+		when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123"));
+
+		ReadMethodBinding binding = createBinding(new MyProvider());
+		assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
 	}
 
 	public ReadMethodBinding createBinding(Object theProvider) throws NoSuchMethodException {

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java

@@ -9,7 +9,10 @@ import ca.uhn.fhir.rest.annotation.Metadata;
 import ca.uhn.fhir.rest.annotation.Read;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.*;
+import ca.uhn.fhir.rest.server.Bindings;
+import ca.uhn.fhir.rest.server.IServerConformanceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.RestfulServerConfiguration;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.method.*;
 import ca.uhn.fhir.rest.server.method.SearchParameter;
@@ -113,7 +116,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
   }
 
 
-
   private DateTimeType conformanceDate(RequestDetails theRequestDetails) {
     IPrimitiveType<Date> buildDate = getServerConfiguration(theRequestDetails).getConformanceDate();
     if (buildDate != null && buildDate.getValue() != null) {
@@ -127,7 +129,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
   }
 
 
-
   /**
    * Gets the value of the "publisher" that will be placed in the generated conformance statement. As this is a mandatory element, the value should not be null (although this is not enforced). The
    * value defaults to "Not provided" but may be set to null, which will cause this element to be omitted.
@@ -194,7 +195,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
         // Map<String, CapabilityStatement.RestResourceSearchParam> nameToSearchParam = new HashMap<String,
         // CapabilityStatement.RestResourceSearchParam>();
         for (BaseMethodBinding<?> nextMethodBinding : nextEntry.getValue()) {
-          if (nextMethodBinding.getRestOperationType() != null) {
+          nextMethodBinding.getRestOperationType();
           String resOpCode = nextMethodBinding.getRestOperationType().getCode();
           if (resOpCode != null) {
             TypeRestfulInteraction resOp;
@@ -238,7 +239,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
               }
             }
           }
-          }
 
           checkBindingForSystemOps(rest, systemOps, nextMethodBinding);
 
@@ -315,28 +315,18 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
     }
     sortSearchParameters(searchParameters);
     if (!searchParameters.isEmpty()) {
-      // boolean allOptional = searchParameters.get(0).isRequired() == false;
-      //
-      // OperationDefinition query = null;
-      // if (!allOptional) {
-      // RestOperation operation = rest.addOperation();
-      // query = new OperationDefinition();
-      // operation.setDefinition(new ResourceReferenceDt(query));
-      // query.getDescriptionElement().setValue(searchMethodBinding.getDescription());
-      // query.addUndeclaredExtension(false, ExtensionConstants.QUERY_RETURN_TYPE, new CodeDt(resourceName));
-      // for (String nextInclude : searchMethodBinding.getIncludes()) {
-      // query.addUndeclaredExtension(false, ExtensionConstants.QUERY_ALLOWED_INCLUDE, new StringDt(nextInclude));
-      // }
-      // }
 
       for (SearchParameter nextParameter : searchParameters) {
 
+        if (nextParameter.getParamType() == null) {
+          ourLog.warn("SearchParameter {}:{} does not declare a type - Not exporting in CapabilityStatement", def.getName(), nextParameter.getName());
+          continue;
+        }
+
         String nextParamName = nextParameter.getName();
 
-        String chain = null;
         String nextParamUnchainedName = nextParamName;
         if (nextParamName.contains(".")) {
-          chain = nextParamName.substring(nextParamName.indexOf('.') + 1);
           nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
         }
 
@@ -352,43 +342,16 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
           }
         }
 
+
         CapabilityStatementRestResourceSearchParamComponent param = resource.addSearchParam();
+        String typeCode = nextParameter.getParamType().getCode();
+        param.getTypeElement().setValueAsString(typeCode);
         param.setName(nextParamUnchainedName);
-
-//				if (StringUtils.isNotBlank(chain)) {
-//					param.addChain(chain);
-//				}
-//
-//				if (nextParameter.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
-//					for (String nextWhitelist : new TreeSet<String>(nextParameter.getQualifierWhitelist())) {
-//						if (nextWhitelist.startsWith(".")) {
-//							param.addChain(nextWhitelist.substring(1));
-//						}
-//					}
-//				}
-
         param.setDocumentation(nextParamDescription);
-        if (nextParameter.getParamType() != null) {
-          param.getTypeElement().setValueAsString(nextParameter.getParamType().getCode());
-        }
-        for (Class<? extends IBaseResource> nextTarget : nextParameter.getDeclaredTypes()) {
-          RuntimeResourceDefinition targetDef = getServerConfiguration(theRequestDetails).getFhirContext().getResourceDefinition(nextTarget);
-          if (targetDef != null) {
-            ResourceType code;
-            try {
-              code = ResourceType.fromCode(targetDef.getName());
-            } catch (FHIRException e) {
-              code = null;
-            }
-//						if (code != null) {
-//							param.addTarget(targetDef.getName());
-//						}
-          }
-        }
-      }
-    }
-  }
 
+      }
+    }
+  }
 
 
   @Read(type = OperationDefinition.class)

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java

@@ -111,7 +111,11 @@ public class ValidatorWrapper {
 				profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(nextProfile, true));
 			}
 
-			v.validate(null, messages, document, profileSet);
+			String resourceAsString = theValidationContext.getResourceAsString();
+			InputStream inputStream = new ReaderInputStream(new StringReader(resourceAsString), Charsets.UTF_8);
+
+			Manager.FhirFormat format = Manager.FhirFormat.XML;
+			v.validate(null, messages, inputStream, format, profileSet);
 
 		} else if (encoding == EncodingEnum.JSON) {
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -799,6 +799,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		ourLog.info(output.getMessages().get(0).getMessage());
 		assertEquals("/f:Patient", output.getMessages().get(0).getLocationString());
 		assertEquals("Undefined element 'foo'", output.getMessages().get(0).getMessage());
+		assertEquals(28, output.getMessages().get(0).getLocationCol().intValue());
+		assertEquals(4, output.getMessages().get(0).getLocationLine().intValue());
 	}
 
 	@Test

src/changes/changes.xml

@@ -476,6 +476,10 @@
 			<action type="fix">
 				Search parameters of type URI did not work in the hapi-fhir-testpage-overlay. This has been corrected.
 			</action>
+			<action type="fix" issue="1568">
+				JPA servers accidentally stripped the type attribute from the server-exported CapabilityStatement
+				when search parameters of type "special" were found. This has been corrected.
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">

src/site/xdoc/download.xml.vm

@@ -262,6 +262,16 @@
 						<td style="background: #CEC;">4.0.0</td>
 						<td style="background: #EEB;">4.1.0-e0e3caf9ba</td>
 					</tr>
+					<tr>
+						<td>HAPI FHIR 4.1.0</td>
+						<td>JDK8</td>
+						<td style="background: #DDD;"></td>
+						<td style="background: #CEC;">1.0.2</td>
+						<td style="background: #EEB;">1.4.0</td>
+						<td style="background: #CEC;">3.0.1</td>
+						<td style="background: #CEC;">4.0.0</td>
+						<td style="background: #EEB;">4.1.0-1a7623d866</td>
+					</tr>
 
 		</tbody>
 			</table>