Sync with upstream/master

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java

@@ -53,8 +53,8 @@ public class FhirTerser {
 		if (theChildDefinition == null)
 			return null;
 		if (theCurrentList == null || theCurrentList.isEmpty())
-			return new ArrayList<String>(Arrays.asList(theChildDefinition.getElementName()));
+			return new ArrayList<>(Arrays.asList(theChildDefinition.getElementName()));
-		List<String> newList = new ArrayList<String>(theCurrentList);
+		List<String> newList = new ArrayList<>(theCurrentList);
 		newList.add(theChildDefinition.getElementName());
 		return newList;
 	}

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

@@ -174,20 +174,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	@Autowired
 	private ISearchDao mySearchDao;
 	@Autowired
-	private ISearchParamExtractor mySearchParamExtractor;
-	@Autowired
 	private ISearchParamPresenceSvc mySearchParamPresenceSvc;
 	//@Autowired
 	//private ISearchResultDao mySearchResultDao;
 	@Autowired
-	private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
-	@Autowired
 	private BeanFactory beanFactory;
 	@Autowired
 	private DaoRegistry myDaoRegistry;
 	@Autowired
-	private SearchParamExtractorService mySearchParamExtractorService;
-	@Autowired
 	private SearchParamWithInlineReferencesExtractor mySearchParamWithInlineReferencesExtractor;
 	@Autowired
 	private DatabaseSearchParamSynchronizer myDatabaseSearchParamSynchronizer;

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

@@ -58,4 +58,6 @@ public interface IResourceReindexingSvc {
 	 * to be used by unit tests.
 	 */
 	void cancelAndPurgeAllJobs();
+
+	int countReindexJobs();
 }

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search.reindex;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -30,11 +30,11 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceReindexJobDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
-import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
+import ca.uhn.fhir.jpa.model.entity.ForcedId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;
@@ -98,6 +98,8 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	private FhirContext myContext;
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
 
 	@VisibleForTesting
 	void setReindexJobDaoForUnitTest(IResourceReindexJobDao theReindexJobDao) {
@@ -186,7 +188,6 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		runReindexingPass();
 	}
 
-
 	@Override
 	@Transactional(Transactional.TxType.NEVER)
 	public Integer runReindexingPass() {
@@ -203,7 +204,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		return null;
 	}
 
-	private Integer doReindexingPassInsideLock() {
+	private int doReindexingPassInsideLock() {
 		expungeJobsMarkedAsDeleted();
 		return runReindexJobs();
 	}
@@ -233,13 +234,13 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	}
 
 	private int runReindexJobs() {
-		Collection<ResourceReindexJobEntity> jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false));
+		Collection<ResourceReindexJobEntity> jobs = getResourceReindexJobEntities();
-		assert jobs != null;
 
 		if (jobs.size() > 0) {
 			ourLog.info("Running {} reindex jobs: {}", jobs.size(), jobs);
 		} else {
 			ourLog.debug("Running {} reindex jobs: {}", jobs.size(), jobs);
+			return 0;
 		}
 
 		int count = 0;
@@ -255,6 +256,17 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		return count;
 	}
 
+	@Override
+	public int countReindexJobs() {
+		return getResourceReindexJobEntities().size();
+	}
+
+	private Collection<ResourceReindexJobEntity> getResourceReindexJobEntities() {
+		Collection<ResourceReindexJobEntity> jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false));
+		assert jobs != null;
+		return jobs;
+	}
+
 	private void markJobAsDeleted(ResourceReindexJobEntity theJob) {
 		ourLog.info("Marking reindexing job ID[{}] as deleted", theJob.getId());
 		myTxTemplate.execute(t -> {
@@ -263,6 +275,11 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		});
 	}
 
+	@VisibleForTesting
+	public void setSearchParamRegistryForUnitTest(ISearchParamRegistry theSearchParamRegistry) {
+		mySearchParamRegistry = theSearchParamRegistry;
+	}
+
 	private int runReindexJob(ResourceReindexJobEntity theJob) {
 		if (theJob.getSuspendedUntil() != null) {
 			if (theJob.getSuspendedUntil().getTime() > System.currentTimeMillis()) {
@@ -274,6 +291,15 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		StopWatch sw = new StopWatch();
 		AtomicInteger counter = new AtomicInteger();
 
+		/*
+		 * On the first time we run a particular reindex job, let's make sure we
+		 * have the latest search parameters loaded. This is good since a common reason to
+		 * be reindexing is that the search parameters have changed in some way.
+		 */
+		if (theJob.getThresholdLow() == null) {
+			mySearchParamRegistry.forceRefresh();
+		}
+
 		// Calculate range
 		Date low = theJob.getThresholdLow() != null ? theJob.getThresholdLow() : BEGINNING_OF_TIME;
 		Date high = theJob.getThresholdHigh();
@@ -461,7 +487,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 
 						IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceTable.getResourceType());
 						long expectedVersion = resourceTable.getVersion();
-						IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null,true);
+						IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null, true);
 						if (resource == null) {
 							throw new InternalErrorException("Could not find resource version " + resourceTable.getIdDt().toUnqualified().getValue() + " in database");
 						}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java

@@ -10,6 +10,8 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
+import ca.uhn.fhir.rest.server.interceptor.ServerOperationInterceptorAdapter;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -17,15 +19,13 @@ import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.hamcrest.Matchers;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
-import org.hl7.fhir.r4.model.Organization;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Reference;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Test;
@@ -38,6 +38,7 @@ import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.stream.Collectors;
 
+import static org.hamcrest.Matchers.in;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.Assert.*;
 import static org.mockito.ArgumentMatchers.any;
@@ -236,6 +237,32 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 	}
 
 	@Test
+	public void testCreateReflexResourceTheHardWay() throws IOException, ServletException {
+		ServerOperationInterceptorAdapter interceptor = new ReflexInterceptor();
+
+		ourRestServer.registerInterceptor(interceptor);
+		try {
+
+			Patient p = new Patient();
+			p.setActive(true);
+			IIdType pid = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+
+			Bundle observations = ourClient
+				.search()
+				.forResource("Observation")
+				.where(Observation.SUBJECT.hasId(pid))
+				.returnBundle(Bundle.class)
+				.execute();
+			assertEquals(1, observations.getEntry().size());
+			ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(observations));
+
+		} finally {
+			ourRestServer.unregisterInterceptor(interceptor);
+		}
+	}
+
+
+		@Test
 	public void testCreateResourceWithVersionedReference() throws IOException, ServletException {
 		String methodName = "testCreateResourceWithVersionedReference";
 
@@ -353,6 +380,26 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		}
 	}
 
+	public class ReflexInterceptor extends ServerOperationInterceptorAdapter {
+		@Override
+		public void resourceCreated(RequestDetails theRequest, IBaseResource theResource) {
+			if (theResource instanceof Patient) {
+				((ServletRequestDetails) theRequest).getServletRequest().setAttribute("CREATED_PATIENT", theResource);
+			}
+		}
+
+		@Override
+		public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
+			Patient createdPatient = (Patient) theRequestDetails.getServletRequest().getAttribute("CREATED_PATIENT");
+			if (createdPatient != null) {
+				Observation observation = new Observation();
+				observation.setSubject(new Reference(createdPatient.getId()));
+
+				ourClient.create().resource(observation).execute();
+			}
+		}
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

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

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceReindexJobDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -63,6 +64,8 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 	@Captor
 	private ArgumentCaptor<Date> myHighCaptor;
 	private ResourceReindexJobEntity mySingleJob;
+	@Mock
+	private ISearchParamRegistry mySearchParamRegistry;
 
 	@Override
 	protected FhirContext getContext() {
@@ -87,6 +90,7 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 		mySvc.setReindexJobDaoForUnitTest(myReindexJobDao);
 		mySvc.setResourceTableDaoForUnitTest(myResourceTableDao);
 		mySvc.setTxManagerForUnitTest(myTxManager);
+		mySvc.setSearchParamRegistryForUnitTest(mySearchParamRegistry);
 		mySvc.start();
 	}
 
@@ -175,6 +179,8 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
 		verify(myReindexJobDao, times(1)).getReindexCount(any());
 		verify(myReindexJobDao, times(1)).setReindexCount(any(), anyInt());
 		verifyNoMoreInteractions(myReindexJobDao);
+
+		verify(mySearchParamRegistry, times(1)).forceRefresh();
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.collect.Lists;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
@@ -23,6 +24,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
@@ -583,6 +585,50 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	/**
+	 * Check that a custom ValueSet against a custom CodeSystem expands correctly
+	 */
+	@Test
+	public void testCustomValueSetExpansion() {
+
+		CodeSystem cs=  new CodeSystem();
+		cs.setUrl("http://codesystems-r-us");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		IIdType csId = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
+
+		TermCodeSystemVersion version = new TermCodeSystemVersion();
+		version.getConcepts().add(new TermConcept(version, "A"));
+		version.getConcepts().add(new TermConcept(version, "B"));
+		version.getConcepts().add(new TermConcept(version, "C"));
+		version.getConcepts().add(new TermConcept(version, "D"));
+		runInTransaction(()->{
+			ResourceTable resTable = myEntityManager.find(ResourceTable.class, csId.getIdPartAsLong());
+			version.setResource(resTable);
+			myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", version);
+		});
+
+		org.hl7.fhir.dstu3.model.ValueSet vs = new org.hl7.fhir.dstu3.model.ValueSet();
+		vs.setUrl("http://valuesets-r-us");
+		vs.getCompose()
+			.addInclude()
+			.setSystem(cs.getUrl())
+			.addConcept(new org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent().setCode("A"))
+			.addConcept(new org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent().setCode("C"));
+		myValueSetDao.create(vs);
+
+		org.hl7.fhir.dstu3.model.ValueSet expansion = myValueSetDao.expandByIdentifier(vs.getUrl(), null);
+		List<String> expansionCodes = expansion
+			.getExpansion()
+			.getContains()
+			.stream()
+			.map(t -> t.getCode())
+			.sorted()
+			.collect(Collectors.toList());
+		assertEquals(Lists.newArrayList("A","C"), expansionCodes);
+
+	}
+
+
 	public static List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
 		List<String> retVal = new ArrayList<>();
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -53,7 +53,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, true);
+					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), false, true);
 
 					Set<String> indexNames = new HashSet<>();
 					while (indexes.next()) {
@@ -81,7 +81,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, false);
+					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), false, false);
 
 					while (indexes.next()) {
 						String indexName = indexes.getString("INDEX_NAME");
@@ -112,7 +112,7 @@ public class JdbcUtils {
 					metadata = connection.getMetaData();
 					String catalog = connection.getCatalog();
 					String schema = connection.getSchema();
-					ResultSet indexes = metadata.getColumns(catalog, schema, theTableName, null);
+					ResultSet indexes = metadata.getColumns(catalog, schema, massageIdentifier(metadata, theTableName), null);
 
 					while (indexes.next()) {
 
@@ -165,7 +165,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), theTableName, connection.getCatalog(), connection.getSchema(), theForeignTable);
+					ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theForeignTable));
 
 					Set<String> columnNames = new HashSet<>();
 					while (indexes.next()) {
@@ -201,7 +201,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, null);
+					ResultSet indexes = metadata.getColumns(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), null);
 
 					Set<String> columnNames = new HashSet<>();
 					while (indexes.next()) {
@@ -253,7 +253,7 @@ public class JdbcUtils {
 						}
 					}
 					return sequenceNames;
-				} catch (SQLException e ) {
+				} catch (SQLException e) {
 					throw new InternalErrorException(e);
 				}
 			});
@@ -298,7 +298,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet tables = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, theColumnName);
+					ResultSet tables = metadata.getColumns(connection.getCatalog(), connection.getSchema(), massageIdentifier(metadata, theTableName), null);
 
 					while (tables.next()) {
 						String tableName = toUpperCase(tables.getString("TABLE_NAME"), Locale.US);
@@ -325,4 +325,14 @@ public class JdbcUtils {
 			});
 		}
 	}
+
+	private static String massageIdentifier(DatabaseMetaData theMetadata, String theCatalog) throws SQLException {
+		String retVal = theCatalog;
+		if (theMetadata.storesLowerCaseIdentifiers()) {
+			retVal = retVal.toLowerCase();
+		} else {
+			retVal = retVal.toUpperCase();
+		}
+		return retVal;
+	}
 }

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/BaseSearchParamRegistry.java

@@ -57,10 +57,9 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 	@Autowired
 	private ModelConfig myModelConfig;
 	private volatile long myLastRefresh;
-	private ApplicationContext myApplicationContext;
 	private ISearchParamProvider mySearchParamProvider;
 
-	public BaseSearchParamRegistry(ISearchParamProvider theSearchParamProvider) {
+	BaseSearchParamRegistry(ISearchParamProvider theSearchParamProvider) {
 		super();
 		mySearchParamProvider = theSearchParamProvider;
 	}
@@ -128,7 +127,7 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 		return Collections.unmodifiableList(retVal);
 	}
 
-	public Map<String, Map<String, RuntimeSearchParam>> getBuiltInSearchParams() {
+	private Map<String, Map<String, RuntimeSearchParam>> getBuiltInSearchParams() {
 		return myBuiltInSearchParams;
 	}
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java

@@ -66,6 +66,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 	private Function<IWorkerContext, IEnableWhenEvaluator> enableWhenEvaluatorSupplier = ctx -> new DefaultEnableWhenEvaluator();
 
 	private boolean errorForUnknownProfiles;
+	private List<String> extensionDomains = Collections.emptyList();
 
 	/**
 	 * Constructor
@@ -87,18 +88,52 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		myValidationSupport = theValidationSupport;
 	}
 
-	private String determineResourceName(Document theDocument) {
+	/**
-		Element root = null;
+	 * Every element in a resource or data type includes an optional <it>extension</it> child element
+	 * which is identified by it's {@code url attribute}. There exists a number of predefined
+	 * extension urls or extension domains:<ul>
+	 *  <li>any url which contains {@code example.org}, {@code nema.org}, or {@code acme.com}.</li>
+	 *  <li>any url which starts with {@code http://hl7.org/fhir/StructureDefinition/}.</li>
+	 * </ul>
+	 * It is possible to extend this list of known extension by defining custom extensions:
+	 * Any url which starts which one of the elements in the list of custom extension domains is
+	 * considered as known.
+	 * <p>
+	 * Any unknown extension domain will result in an information message when validating a resource.
+	 * </p>
+	 */
+	public FhirInstanceValidator setCustomExtensionDomains(List<String> extensionDomains) {
+		this.extensionDomains = extensionDomains;
+		return this;
+	}
 
+	/**
+	 * Every element in a resource or data type includes an optional <it>extension</it> child element
+	 * which is identified by it's {@code url attribute}. There exists a number of predefined
+	 * extension urls or extension domains:<ul>
+	 *  <li>any url which contains {@code example.org}, {@code nema.org}, or {@code acme.com}.</li>
+	 *  <li>any url which starts with {@code http://hl7.org/fhir/StructureDefinition/}.</li>
+	 * </ul>
+	 * It is possible to extend this list of known extension by defining custom extensions:
+	 * Any url which starts which one of the elements in the list of custom extension domains is
+	 * considered as known.
+	 * <p>
+	 * Any unknown extension domain will result in an information message when validating a resource.
+	 * </p>
+	 */
+	public FhirInstanceValidator setCustomExtensionDomains(String... extensionDomains) {
+		this.extensionDomains = Arrays.asList(extensionDomains);
+		return this;
+	}
+
+	private String determineResourceName(Document theDocument) {
 		NodeList list = theDocument.getChildNodes();
 		for (int i = 0; i < list.getLength(); i++) {
 			if (list.item(i) instanceof Element) {
-				root = (Element) list.item(i);
+				return list.item(i).getLocalName();
-				break;
 			}
 		}
-		root = theDocument.getDocumentElement();
+		return theDocument.getDocumentElement().getLocalName();
-		return root.getLocalName();
 	}
 
 	private ArrayList<String> determineIfProfilesSpecified(Document theDocument) {
@@ -144,7 +179,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 	 * guielines will be ignored.
 	 * </p>
 	 *
-	 * @see {@link #setBestPracticeWarningLevel(BestPracticeWarningLevel)}
+	 * @see #setBestPracticeWarningLevel(BestPracticeWarningLevel)
 	 */
 	public BestPracticeWarningLevel getBestPracticeWarningLevel() {
 		return myBestPracticeWarningLevel;
@@ -260,6 +295,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		v.setNoTerminologyChecks(isNoTerminologyChecks());
 		v.setMyEnableWhenEvaluator(enableWhenEvaluatorSupplier.apply(wrappedWorkerContext));
 		v.setErrorForUnknownProfiles(isErrorForUnknownProfiles());
+		v.addExtensionDomains(extensionDomains);
 
 		List<ValidationMessage> messages = new ArrayList<>();
 
@@ -368,7 +404,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		private LoadingCache<ResourceKey, org.hl7.fhir.r4.model.Resource> myFetchResourceCache;
 		private org.hl7.fhir.r4.model.Parameters myExpansionProfile;
 
-		public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
+		WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
 			myWrap = theWorkerContext;
 			myConverter = new VersionConvertor_30_40();
 
@@ -449,7 +485,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		}
 
 		@Override
-		public void cacheResource(org.hl7.fhir.r4.model.Resource res) throws FHIRException {
+		public void cacheResource(org.hl7.fhir.r4.model.Resource res) {
 			throw new UnsupportedOperationException();
 		}
 
@@ -471,7 +507,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 
 		@Override
 		public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r4.model.ValueSet source, boolean cacheOk, boolean heiarchical) {
-			ValueSet convertedSource = null;
+			ValueSet convertedSource;
 			try {
 				convertedSource = VersionConvertor_30_40.convertValueSet(source);
 			} catch (FHIRException e) {
@@ -495,7 +531,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		}
 
 		@Override
-		public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent binding, boolean cacheOk, boolean heiarchical) throws FHIRException {
+		public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent binding, boolean cacheOk, boolean heiarchical) {
 			throw new UnsupportedOperationException();
 		}
 
@@ -662,7 +698,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		}
 
 		@Override
-		public IResourceValidator newValidator() throws FHIRException {
+		public IResourceValidator newValidator() {
 			throw new UnsupportedOperationException();
 		}
 
@@ -687,7 +723,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		}
 
 		@Override
-		public boolean supportsSystem(String system) throws TerminologyServiceException {
+		public boolean supportsSystem(String system) {
 			return myWrap.supportsSystem(system);
 		}
 
@@ -704,6 +740,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		@Override
 		public ValidationResult validateCode(String system, String code, String display) {
 			org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display);
+			// TODO: converted code might be null -> NPE
 			return convertValidationResult(result);
 		}
 
@@ -754,6 +791,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 				throw new InternalErrorException(e);
 			}
 
+			// TODO: converted code might be null -> NPE
 			org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult result = myWrap.validateCode(convertedCode, convertedVs);
 			return convertValidationResult(result);
 		}
@@ -774,6 +812,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 				throw new InternalErrorException(e);
 			}
 
+			// TODO: converted code might be null -> NPE
 			org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult result = myWrap.validateCode(convertedCode, convertedVs);
 			return convertValidationResult(result);
 		}

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java

@@ -32,6 +32,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
 import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.util.Arrays;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -45,6 +46,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 	private DocumentBuilderFactory myDocBuilderFactory;
 	private boolean myNoTerminologyChecks;
 	private StructureDefinition myStructureDefintion;
+	private List<String> extensionDomains = Collections.emptyList();
 
 	private IValidationSupport myValidationSupport;
 
@@ -68,18 +70,52 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		myValidationSupport = theValidationSupport;
 	}
 
-	private String determineResourceName(Document theDocument) {
+	/**
-		Element root = null;
+	 * Every element in a resource or data type includes an optional <it>extension</it> child element
+	 * which is identified by it's {@code url attribute}. There exists a number of predefined
+	 * extension urls or extension domains:<ul>
+	 *  <li>any url which contains {@code example.org}, {@code nema.org}, or {@code acme.com}.</li>
+	 *  <li>any url which starts with {@code http://hl7.org/fhir/StructureDefinition/}.</li>
+	 * </ul>
+	 * It is possible to extend this list of known extension by defining custom extensions:
+	 * Any url which starts which one of the elements in the list of custom extension domains is
+	 * considered as known.
+	 * <p>
+	 * Any unknown extension domain will result in an information message when validating a resource.
+	 * </p>
+	 */
+	public FhirInstanceValidator setCustomExtensionDomains(List<String> extensionDomains) {
+		this.extensionDomains = extensionDomains;
+		return this;
+	}
 
+	/**
+	 * Every element in a resource or data type includes an optional <it>extension</it> child element
+	 * which is identified by it's {@code url attribute}. There exists a number of predefined
+	 * extension urls or extension domains:<ul>
+	 *  <li>any url which contains {@code example.org}, {@code nema.org}, or {@code acme.com}.</li>
+	 *  <li>any url which starts with {@code http://hl7.org/fhir/StructureDefinition/}.</li>
+	 * </ul>
+	 * It is possible to extend this list of known extension by defining custom extensions:
+	 * Any url which starts which one of the elements in the list of custom extension domains is
+	 * considered as known.
+	 * <p>
+	 * Any unknown extension domain will result in an information message when validating a resource.
+	 * </p>
+	 */
+	public FhirInstanceValidator setCustomExtensionDomains(String... extensionDomains) {
+		this.extensionDomains = Arrays.asList(extensionDomains);
+		return this;
+	}
+
+	private String determineResourceName(Document theDocument) {
 		NodeList list = theDocument.getChildNodes();
 		for (int i = 0; i < list.getLength(); i++) {
 			if (list.item(i) instanceof Element) {
-				root = (Element) list.item(i);
+				return list.item(i).getLocalName();
-				break;
 			}
 		}
-		root = theDocument.getDocumentElement();
+		return theDocument.getDocumentElement().getLocalName();
-		return root.getLocalName();
 	}
 
 	private ArrayList<String> determineIfProfilesSpecified(Document theDocument) {
@@ -120,8 +156,8 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 	 * reported at the ERROR level. If this setting is set to {@link BestPracticeWarningLevel#Ignore}, best practice
 	 * guielines will be ignored.
 	 * </p>
-	 *
+	 * 
-	 * @see {@link #setBestPracticeWarningLevel(BestPracticeWarningLevel)}
+	 * @see #setBestPracticeWarningLevel(BestPracticeWarningLevel)
 	 */
 	public BestPracticeWarningLevel getBestPracticeWarningLevel() {
 		return myBestPracticeWarningLevel;
@@ -211,8 +247,9 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		v.setAnyExtensionsAllowed(isAnyExtensionsAllowed());
 		v.setResourceIdRule(IdStatus.OPTIONAL);
 		v.setNoTerminologyChecks(isNoTerminologyChecks());
+		v.addExtensionDomains(extensionDomains);
 
-		List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
+		List<ValidationMessage> messages = new ArrayList<>();
 
 		if (theEncoding == EncodingEnum.XML) {
 			Document document;
@@ -312,7 +349,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 	public static class NullEvaluationContext implements IEvaluationContext {
 
 		@Override
-		public TypeDetails checkFunction(Object theAppContext, String theFunctionName, List<TypeDetails> theParameters) throws PathEngineException {
+		public TypeDetails checkFunction(Object theAppContext, String theFunctionName, List<TypeDetails> theParameters) {
 			return null;
 		}
 
@@ -327,12 +364,12 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 		}
 
 		@Override
-		public Base resolveConstant(Object theAppContext, String theName) throws PathEngineException {
+		public Base resolveConstant(Object theAppContext, String theName) {
 			return null;
 		}
 
 		@Override
-		public TypeDetails resolveConstantType(Object theAppContext, String theName) throws PathEngineException {
+		public TypeDetails resolveConstantType(Object theAppContext, String theName) {
 			return null;
 		}
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java

@@ -420,8 +420,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private boolean allowUnknownExtension(String url) {
-    if (url.contains("example.org") || url.contains("acme.com") || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression"))
+    if (isPredefinedExtension(url))
-      // Added structuredefinition-expression explicitly because it wasn't defined in the version of the spec it needs to be used with
       return true;
     for (String s : extensionDomains)
       if (url.startsWith(s))
@@ -430,8 +429,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private boolean isKnownExtension(String url) {
-    // Added structuredefinition-expression and following extensions explicitly because they weren't defined in the version of the spec they need to be used with
+    if (isPredefinedExtension(url))
-    if (url.contains("example.org") || url.contains("acme.com") || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression") || url.equals(VersionConvertorConstants.IG_DEPENDSON_PACKAGE_EXTENSION))
       return true;
     for (String s : extensionDomains)
       if (url.startsWith(s))
@@ -439,6 +437,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return false;
   }
 
+  private boolean isPredefinedExtension(String url) {
+    return url.contains("example.org")
+        || url.contains("acme.com")
+        || url.contains("nema.org")
+        || url.startsWith("http://hl7.org/fhir/StructureDefinition/")
+        || url.equals(VersionConvertorConstants.IG_DEPENDSON_PACKAGE_EXTENSION);
+  }
+
   private void bpCheck(List<ValidationMessage> errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message) {
     if (bpWarnings != null) {
       switch (bpWarnings) {
@@ -1954,6 +1960,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return extensionDomains;
   }
 
+  public InstanceValidator addExtensionDomains(List<String> extensionDomains) {
+    this.extensionDomains.addAll(extensionDomains);
+    return this;
+  }
+
   private Element getFromBundle(Element bundle, String ref, String fullUrl, List<ValidationMessage> errors, String path) {
     String targetUrl = null;
     String version = "";

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireValidatorDstu3Test.java

@@ -0,0 +1,134 @@
+package org.hl7.fhir.dstu3.hapi.validation;
+
+import java.util.Collections;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.ValidationResult;
+
+import org.hamcrest.Matchers;
+import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.dstu3.model.Questionnaire;
+import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.mockito.Mockito.mock;
+
+public class QuestionnaireValidatorDstu3Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(QuestionnaireValidatorDstu3Test.class);
+	private static DefaultProfileValidationSupport myDefaultValidationSupport = new DefaultProfileValidationSupport();
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private FhirInstanceValidator myInstanceVal;
+	private FhirValidator myVal;
+
+	@Before
+	public void before() {
+		IValidationSupport myValSupport = mock(IValidationSupport.class);
+
+		myVal = ourCtx.newValidator();
+		myVal.setValidateAgainstStandardSchema(false);
+		myVal.setValidateAgainstStandardSchematron(false);
+
+		ValidationSupportChain validationSupport = new ValidationSupportChain(myValSupport, myDefaultValidationSupport);
+		myInstanceVal = new FhirInstanceValidator(validationSupport);
+
+		myVal.registerValidatorModule(myInstanceVal);
+	}
+
+	@Test
+	public void testQuestionnaireWithPredefinedExtensionDomainsForCoding() {
+		String[] extensionDomainsToTest = new String[] {
+			"http://example.org/questionnaire-color-control-1",
+			"https://example.org/questionnaire-color-control-2",
+			"http://acme.com/questionnaire-color-control-3",
+			"https://acme.com/questionnaire-color-control-4",
+			"http://nema.org/questionnaire-color-control-5",
+			"https://nema.org/questionnaire-color-control-6",
+			"http://hl7.org/fhir/StructureDefinition/questionnaire-scoreItem",
+			"http://hl7.org/fhir/StructureDefinition/structuredefinition-expression",
+		};
+		for (String extensionDomainToTest : extensionDomainsToTest) {
+			Questionnaire q = new Questionnaire();
+			q.setStatus(PublicationStatus.ACTIVE)
+				.addItem()
+				.setLinkId("link0")
+				.setType(QuestionnaireItemType.STRING)
+				.addExtension()
+				.setUrl(extensionDomainToTest)
+				.setValue(new Coding(null, "text-box", null));
+
+			ValidationResult errors = myVal.validateWithResult(q);
+			ourLog.info(errors.toString());
+			assertThat(errors.isSuccessful(), Matchers.is(true));
+			assertThat(errors.getMessages(), Matchers.empty());
+		}
+	}
+
+	@Test
+	public void testQuestionnaireWithPredefinedExtensionDomainsForCodeableConcept() {
+		String[] extensionDomainsToTest = new String[] {
+			"http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
+		};
+		for (String extensionDomainToTest : extensionDomainsToTest) {
+			Questionnaire q = new Questionnaire();
+			q.setStatus(PublicationStatus.ACTIVE)
+				.addItem()
+				.setLinkId("link0")
+				.setType(QuestionnaireItemType.STRING)
+				.addExtension()
+				.setUrl(extensionDomainToTest)
+				.setValue(new CodeableConcept().addCoding(new Coding(null, "text-box", null)));
+
+			ValidationResult errors = myVal.validateWithResult(q);
+			ourLog.info(errors.toString());
+			assertThat(errors.isSuccessful(), Matchers.is(true));
+			assertThat(errors.getMessages(), Matchers.empty());
+		}
+	}
+
+	@Test
+	public void testQuestionnaireWithCustomExtensionDomain() {
+		Questionnaire q = new Questionnaire();
+		String extensionUrl = "http://my.own.domain/StructureDefinition/";
+		q.setStatus(PublicationStatus.ACTIVE)
+			.addItem()
+				.setLinkId("link0")
+				.setType(QuestionnaireItemType.STRING)
+				.addExtension()
+					.setUrl(extensionUrl + "questionnaire-itemControl")
+					.setValue(new Coding(null, "text-box", null));
+
+		ValidationResult errors = myVal.validateWithResult(q);
+
+		ourLog.info(errors.toString());
+		assertThat(errors.isSuccessful(), Matchers.is(true));
+		assertThat(errors.getMessages(), Matchers.hasSize(1));
+		assertEquals(errors.getMessages().get(0).getSeverity(), ResultSeverityEnum.INFORMATION);
+		assertThat(errors.getMessages().get(0).getMessage(), Matchers.startsWith("Unknown extension " + extensionUrl));
+
+		myInstanceVal.setCustomExtensionDomains(Collections.singletonList(extensionUrl));
+		errors = myVal.validateWithResult(q);
+
+		ourLog.info(errors.toString());
+		assertThat(errors.isSuccessful(), Matchers.is(true));
+		assertThat(errors.getMessages(), Matchers.empty());
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		myDefaultValidationSupport.flush();
+		myDefaultValidationSupport = null;
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+}

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/QuestionnaireValidatorR4Test.java

@@ -0,0 +1,145 @@
+package org.hl7.fhir.r4.validation;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.ValidationResult;
+
+import org.hamcrest.Matchers;
+import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
+import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
+import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.r4.hapi.validation.ValidationSupportChain;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r4.model.Narrative;
+import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
+import org.hl7.fhir.r4.model.Questionnaire;
+import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.mockito.Mockito.mock;
+
+public class QuestionnaireValidatorR4Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(QuestionnaireValidatorR4Test.class);
+	private static DefaultProfileValidationSupport myDefaultValidationSupport = new DefaultProfileValidationSupport();
+	private static FhirContext ourCtx = FhirContext.forR4();
+	private FhirInstanceValidator myInstanceVal;
+	private FhirValidator myVal;
+
+	@Before
+	public void before() {
+		IValidationSupport myValSupport = mock(IValidationSupport.class);
+
+		myVal = ourCtx.newValidator();
+		myVal.setValidateAgainstStandardSchema(false);
+		myVal.setValidateAgainstStandardSchematron(false);
+
+		ValidationSupportChain validationSupport = new ValidationSupportChain(myValSupport, myDefaultValidationSupport);
+		myInstanceVal = new FhirInstanceValidator(validationSupport);
+
+		myVal.registerValidatorModule(myInstanceVal);
+	}
+
+	@Test
+	public void testQuestionnaireWithPredefinedExtensionDomains() {
+		String[] extensionDomainsToTest = new String[] {
+			"http://example.org/questionnaire-color-control-1",
+			"https://example.org/questionnaire-color-control-2",
+			"http://acme.com/questionnaire-color-control-3",
+			"https://acme.com/questionnaire-color-control-4",
+			"http://nema.org/questionnaire-color-control-5",
+			"https://nema.org/questionnaire-color-control-6",
+			"http://hl7.org/fhir/StructureDefinition/questionnaire-scoreItem",
+			"http://hl7.org/fhir/StructureDefinition/structuredefinition-expression",
+
+		};
+		for (String extensionDomainToTest : extensionDomainsToTest) {
+			Questionnaire q = minimalValidQuestionnaire();
+			q.addItem()
+				.setLinkId("link0")
+				.setType(QuestionnaireItemType.STRING)
+				.addExtension()
+				.setUrl(extensionDomainToTest)
+				.setValue(new Coding(null, "text-box", null));
+
+			ValidationResult errors = myVal.validateWithResult(q);
+			ourLog.info(errors.toString());
+			assertThat(errors.isSuccessful(), Matchers.is(true));
+			assertThat(errors.getMessages(), Matchers.empty());
+		}
+	}
+
+	@Test
+	public void testQuestionnaireWithPredefinedExtensionDomainsForCodeableConcept() {
+		String[] extensionDomainsToTest = new String[] {
+			"http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
+		};
+		for (String extensionDomainToTest : extensionDomainsToTest) {
+			Questionnaire q = minimalValidQuestionnaire();
+			q.addItem()
+				.setLinkId("link0")
+				.setType(QuestionnaireItemType.STRING)
+				.addExtension()
+				.setUrl(extensionDomainToTest)
+				.setValue(new CodeableConcept().addCoding(new Coding(null, "text-box", null)));
+
+			ValidationResult errors = myVal.validateWithResult(q);
+			ourLog.info(errors.toString());
+			assertThat(errors.isSuccessful(), Matchers.is(true));
+			assertThat(errors.getMessages(), Matchers.empty());
+		}
+	}
+
+	@Test
+	public void testQuestionnaireWithCustomExtensionDomain() {
+		String extensionUrl = "http://my.own.domain/StructureDefinition/";
+		Questionnaire q = minimalValidQuestionnaire();
+		q.addItem()
+			.setLinkId("link0")
+			.setType(QuestionnaireItemType.STRING)
+			.addExtension()
+			.setUrl(extensionUrl + "questionnaire-itemControl")
+			.setValue(new Coding(null, "text-box", null));
+
+		ValidationResult errors = myVal.validateWithResult(q);
+
+		ourLog.info(errors.toString());
+		assertThat(errors.isSuccessful(), Matchers.is(true));
+		assertThat(errors.getMessages(), Matchers.hasSize(1));
+		assertEquals(errors.getMessages().get(0).getSeverity(), ResultSeverityEnum.INFORMATION);
+		assertThat(errors.getMessages().get(0).getMessage(), Matchers.startsWith("Unknown extension " + extensionUrl));
+
+		myInstanceVal.setCustomExtensionDomains(extensionUrl);
+		errors = myVal.validateWithResult(q);
+
+		ourLog.info(errors.toString());
+		assertThat(errors.isSuccessful(), Matchers.is(true));
+		assertThat(errors.getMessages(), Matchers.empty());
+	}
+
+	private Questionnaire minimalValidQuestionnaire() {
+		Narrative n = new Narrative().setStatus(NarrativeStatus.GENERATED);
+		n.setDivAsString("simple example");
+		Questionnaire q = new Questionnaire();
+		q.setText(n);
+		q.setName("SomeName");
+		q.setStatus(PublicationStatus.ACTIVE);
+		return q;
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		myDefaultValidationSupport.flush();
+		myDefaultValidationSupport = null;
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/AbstractGeneratorMojo.java

@@ -0,0 +1,50 @@
+package ca.uhn.fhir.tinder;
+
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.project.MavenProject;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * Base class for mojo generatorss.
+ */
+public abstract class AbstractGeneratorMojo extends AbstractMojo {
+
+	protected final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(getClass());
+
+	@Parameter(required = true, defaultValue = "${project.build.directory}/..")
+	protected String baseDir;
+
+	@Parameter
+	protected String packageBase = "";
+
+	@Parameter
+	protected List<String> baseResourceNames;
+
+	@Parameter
+	protected List<String> excludeResourceNames;
+
+	@Parameter
+	protected String templateName;
+
+	@Parameter(required = true)
+	protected String version;
+
+	@Component
+	protected MavenProject myProject;
+
+	@Override
+	public final void execute() throws MojoExecutionException, MojoFailureException {
+		doExecute(new Configuration(this.version, baseDir, getTargetDirectory(), this.packageBase, this.baseResourceNames, this.excludeResourceNames));
+	}
+
+	protected abstract void doExecute(Configuration mavenGeneratorConfiguration) throws MojoExecutionException, MojoFailureException;
+
+	protected abstract File getTargetDirectory();
+
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/Configuration.java

@@ -0,0 +1,134 @@
+package ca.uhn.fhir.tinder;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.tinder.parser.BaseStructureSpreadsheetParser;
+import org.apache.commons.lang.WordUtils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.TreeSet;
+
+public class Configuration {
+
+	private final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Configuration.class);
+
+	private String version;
+	private File targetDirectory;
+	private String packageSuffix;
+
+	private String packageBase;
+	private FhirContext fhirContext;
+	private File packageDirectoryBase;
+
+	private final List<String> resourceNames = new ArrayList<>();
+	private String baseDir;
+
+	public Configuration(String version, String baseDir, File targetDirectory, String packageBase, List<String> baseResourceNames, List<String> excludeResourceNames) {
+		this.targetDirectory = targetDirectory;
+		this.packageBase = packageBase;
+		this.packageDirectoryBase = new File(targetDirectory, packageBase.replace(".", File.separatorChar + ""));
+
+		switch (version) {
+			case "dstu2":
+				fhirContext = FhirContext.forDstu2();
+				break;
+			case "dstu3":
+				fhirContext = FhirContext.forDstu3();
+				packageSuffix = ".dstu3";
+				break;
+			case "r4":
+				fhirContext = FhirContext.forR4();
+				packageSuffix = ".r4";
+				break;
+			default:
+				throw new IllegalArgumentException("Unknown version configured: " + version);
+		}
+
+		this.version = version;
+		if (baseResourceNames == null || baseResourceNames.isEmpty()) {
+			ourLog.info("No resource names supplied, going to use all resources from version: {}", fhirContext.getVersion().getVersion());
+
+			Properties p = new Properties();
+			try {
+				p.load(fhirContext.getVersion().getFhirVersionPropertiesFile());
+			} catch (IOException e) {
+				throw new IllegalArgumentException("Failed to load version property file", e);
+			}
+
+			ourLog.debug("Property file contains: {}", p);
+
+			TreeSet<String> keys = new TreeSet<String>();
+			for (Object next : p.keySet()) {
+				keys.add((String) next);
+			}
+			for (String next : keys) {
+				if (next.startsWith("resource.")) {
+					resourceNames.add(next.substring("resource.".length()).toLowerCase());
+				}
+			}
+
+			if (fhirContext.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
+				resourceNames.remove("conformance");
+			}
+		} else {
+			for (String resourceName : baseResourceNames) {
+				resourceNames.add(resourceName.toLowerCase());
+			}
+		}
+
+		if (excludeResourceNames != null) {
+			for (String resourceName : excludeResourceNames) {
+				resourceNames.remove(resourceName.toLowerCase());
+			}
+		}
+
+		ourLog.info("Including the following resources: {}", resourceNames);
+	}
+
+	public File getPackageDirectoryBase() {
+		return packageDirectoryBase;
+	}
+
+	public String getPackageSuffix() {
+		return packageSuffix;
+	}
+
+	public List<String> getResourceNames() {
+		return resourceNames;
+	}
+
+	public String getPackageBase() {
+		return packageBase;
+	}
+
+	public String getVersion() {
+		return version;
+	}
+
+	public String getResourcePackage() {
+		if (BaseStructureSpreadsheetParser.determineVersionEnum(version).isRi()) {
+			return "org.hl7.fhir." + version + ".model";
+		}
+		return "ca.uhn.fhir.model." + version + ".resource";
+	}
+
+	public String getVersionCapitalized() {
+		String capitalize = WordUtils.capitalize(version);
+		if ("Dstu".equals(capitalize)) {
+			return "Dstu1";
+		}
+		return capitalize;
+	}
+
+	public File getTargetDirectory() {
+		return targetDirectory;
+	}
+
+	public String getBaseDir() {
+		return baseDir;
+	}
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderResourceGeneratorMojo.java

@@ -0,0 +1,75 @@
+package ca.uhn.fhir.tinder;
+
+import ca.uhn.fhir.tinder.parser.ResourceGeneratorUsingModel;
+import ca.uhn.fhir.tinder.parser.ResourceGeneratorUsingSpreadsheet;
+import org.apache.maven.model.Resource;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.velocity.VelocityContext;
+import org.apache.velocity.app.VelocityEngine;
+import org.apache.velocity.tools.generic.EscapeTool;
+
+import java.io.*;
+
+@Mojo(name = "generate-resource", defaultPhase = LifecyclePhase.GENERATE_RESOURCES)
+public class TinderResourceGeneratorMojo extends AbstractGeneratorMojo {
+
+	@Parameter(required = true, defaultValue = "${project.build.directory}/generated-resources/tinder")
+	protected File targetDirectory;
+
+	@Parameter(required = true)
+	protected String fileName = "";
+
+	@Override
+	protected void doExecute(Configuration configuration) throws MojoExecutionException, MojoFailureException {
+		File packageDirectoryBase = configuration.getPackageDirectoryBase();
+		packageDirectoryBase.mkdirs();
+
+		ResourceGeneratorUsingModel gen = new ResourceGeneratorUsingModel(configuration.getVersion(), configuration.getBaseDir());
+		gen.setBaseResourceNames(configuration.getResourceNames());
+
+		try {
+			gen.parse();
+
+			VelocityContext ctx = new VelocityContext();
+			ctx.put("resources", gen.getResources());
+			ctx.put("packageBase", configuration.getPackageBase());
+			ctx.put("version", configuration.getVersion());
+			ctx.put("package_suffix", configuration.getPackageSuffix());
+			ctx.put("esc", new EscapeTool());
+
+			ctx.put("resourcePackage", configuration.getResourcePackage());
+			ctx.put("versionCapitalized", configuration.getVersionCapitalized());
+
+			VelocityEngine v = new VelocityEngine();
+			v.setProperty("resource.loader", "cp");
+			v.setProperty("cp.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
+			v.setProperty("runtime.references.strict", Boolean.TRUE);
+
+			InputStream templateIs = ResourceGeneratorUsingSpreadsheet.class.getResourceAsStream(templateName);
+			InputStreamReader templateReader = new InputStreamReader(templateIs);
+
+			File file = new File(packageDirectoryBase, fileName);
+			OutputStreamWriter w = new OutputStreamWriter(new FileOutputStream(file, false), "UTF-8");
+			v.evaluate(ctx, w, "", templateReader);
+			w.close();
+
+			Resource resource = new Resource();
+			resource.setDirectory(packageDirectoryBase.getAbsolutePath());
+			//resource.setDirectory(targetDirectory.getAbsolutePath());
+			//resource.addInclude(packageBase);
+			myProject.addResource(resource);
+
+		} catch (Exception e) {
+			throw new MojoFailureException("Failed to generate resources", e);
+		}
+	}
+
+	@Override
+	public File getTargetDirectory() {
+		return targetDirectory;
+	}
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderSourcesGeneratorMojo.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.tinder;
+
+import java.io.*;
+import java.util.*;
+
+import org.apache.maven.plugin.*;
+import org.apache.maven.plugins.annotations.*;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.project.MavenProject;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.tinder.parser.*;
+
+@Mojo(name = "generate-sources", defaultPhase = LifecyclePhase.GENERATE_SOURCES)
+public class TinderSourcesGeneratorMojo extends AbstractGeneratorMojo {
+
+	@Parameter(required = true, defaultValue = "${project.build.directory}/generated-sources/tinder")
+	protected File targetDirectory;
+
+	@Parameter
+	private String filenameSuffix = "ResourceProvider";
+
+	@Parameter
+	private String filenamePrefix = "";
+
+	@Override
+	public void doExecute(Configuration configuration) throws MojoExecutionException, MojoFailureException {
+		File packageDirectoryBase = configuration.getPackageDirectoryBase();
+		packageDirectoryBase.mkdirs();
+
+		ResourceGeneratorUsingModel gen = new ResourceGeneratorUsingModel(configuration.getVersion(), configuration.getBaseDir());
+		gen.setBaseResourceNames(configuration.getResourceNames());
+
+		try {
+			gen.parse();
+
+			gen.setFilenameSuffix(filenameSuffix);
+			gen.setFilenamePrefix(filenamePrefix);
+			gen.setTemplate(templateName);
+			gen.writeAll(packageDirectoryBase, null, configuration.getPackageBase());
+		} catch (Exception e) {
+			throw new MojoFailureException("Failed to generate server", e);
+		}
+
+		myProject.addCompileSourceRoot(configuration.getTargetDirectory().getAbsolutePath());
+	}
+
+	@Override
+	protected File getTargetDirectory() {
+		return targetDirectory;
+	}
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/BaseStructureParser.java

@@ -711,7 +711,7 @@ public abstract class BaseStructureParser {
 		return null;
 	}
 
-	public static FhirVersionEnum determineVersionEnum(String version) throws MojoFailureException {
+	public static FhirVersionEnum determineVersionEnum(String version) {
 		FhirVersionEnum versionEnum;
 		if ("dstu2".equals(version)) {
 			versionEnum = FhirVersionEnum.DSTU2;
@@ -720,7 +720,7 @@ public abstract class BaseStructureParser {
 		} else if ("r4".equals(version)) {
 			versionEnum = FhirVersionEnum.R4;
 		} else {
-			throw new MojoFailureException("Unknown version: " + version);
+			throw new IllegalArgumentException("Unknown version: " + version);
 		}
 		return versionEnum;
 	}

pom.xml

@@ -518,7 +518,7 @@
 		<jaxb_api_version>2.3.0</jaxb_api_version>
 		<jaxb_core_version>2.3.0</jaxb_core_version>
 		<jersey_version>2.25.1</jersey_version>
-		<jetty_version>9.4.12.v20180830</jetty_version>
+		<jetty_version>9.4.14.v20181114</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
 		<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
 		<hibernate_version>5.3.6.Final</hibernate_version>

src/changes/changes.xml

@@ -98,9 +98,11 @@
 				or authorizing the contents of the response.
 			</action>
 			<action type="add">
+				JPA Migrator tool enhancements:
 				An invalid SQL syntax issue has been fixed when running the CLI JPA Migrator tool against 
 				Oracle or SQL Server. In addition, when using the "Dry Run" option, all generated SQL
-				statements will be logged at the end of the run.
+				statements will be logged at the end of the run. Also, a case sensitivity issue when running against
+				some Postgres databases has been corrected.
 			</action>
 			<action type="add">
 				In the JPA server, when performing a chained reference search on a search parameter with
@@ -142,6 +144,18 @@
 				causes Media resources to be served as raw content if the client explicitly requests
 				the correct content type cia the Accept header.
 			</action>
+			<action type="add" issue="917">
+				A new configuration item has been added to the FhirInstanceValidator that 
+				allows you to specify additional "known extension domains", meaning
+				domains in which the validator will not complain about when it
+				encounters new extensions. Thanks to Heinz-Dieter Conradi for the
+				pull request!
+			</action>
+			<action type="fix">
+				Under some circumstances, when a custom search parameter was added to the JPA server 
+				resources could start reindexing before the new search parameter had been saved, meaning that
+				it was not applied to all resources. This has been corrected.
+			</action>
 		</release>
 		<release version="3.6.0" date="2018-11-12" description="Food">
 			<action type="add">