Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir

hapi-fhir-base/src/main/java/ca/uhn/fhir/fluentpath/IFluentPath.java

@@ -48,4 +48,8 @@ public interface IFluentPath {
 	<T extends IBase> Optional<T> evaluateFirst(IBase theInput, String thePath, Class<T> theReturnType);
 
 
+	/**
+	 * Parses the expression and throws an exception if it can not parse correctly
+	 */
+	void parse(String theExpression) throws Exception;
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java

@@ -1599,6 +1599,33 @@ public enum Pointcut {
 	),
 
 
+	/**
+	 * THIS IS AN EXPERIMENTAL HOOK AND MAY BE REMOVED OR CHANGED WITHOUT WARNING.
+	 *
+	 * Note that this is a performance tracing hook. Use with caution in production
+	 * systems, since calling it may (or may not) carry a cost.
+	 * <p>
+	 * This hook is invoked when a search has found an individual ID.
+	 * </p>
+	 * Hooks may accept the following parameters:
+	 * <ul>
+	 * <li>
+	 * java.lang.Integer - The query ID
+	 * </li>
+	 * <li>
+	 * java.lang.Object - The ID
+	 * </li>
+	 * </ul>
+	 * <p>
+	 * Hooks should return <code>void</code>.
+	 * </p>
+	 */
+	JPA_PERFTRACE_SEARCH_FOUND_ID(void.class,
+		"java.lang.Integer",
+		"java.lang.Object"
+	),
+
+
 	/**
 	 * Note that this is a performance tracing hook. Use with caution in production
 	 * systems, since calling it may (or may not) carry a cost.

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

@@ -109,6 +109,8 @@ ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.failedToExtractPa
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
 ca.uhn.fhir.jpa.dao.SearchBuilder.sourceParamDisabled=The _source parameter is disabled on this server
+ca.uhn.fhir.jpa.dao.SearchBuilder.invalidCodeMissingSystem=Invalid token specified for parameter {0} - No system specified: {1}|{2}
+ca.uhn.fhir.jpa.dao.SearchBuilder.invalidCodeMissingCode=Invalid token specified for parameter {0} - No code specified: {1}|{2}
 
 ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.matchesFound=Matches found!
 ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.noMatchesFound=No matches found!

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

@@ -1857,9 +1857,11 @@ public class SearchBuilder implements ISearchBuilder {
 				codes.addAll(myTerminologySvc.expandValueSet(code));
 			} else if (modifier == TokenParamModifier.ABOVE) {
 				system = determineSystemIfMissing(theParamName, code, system);
+				validateHaveSystemAndCodeForToken(theParamName, code, system);
 				codes.addAll(myTerminologySvc.findCodesAbove(system, code));
 			} else if (modifier == TokenParamModifier.BELOW) {
 				system = determineSystemIfMissing(theParamName, code, system);
+				validateHaveSystemAndCodeForToken(theParamName, code, system);
 				codes.addAll(myTerminologySvc.findCodesBelow(system, code));
 			} else {
 				codes.add(new VersionIndependentConcept(system, code));
@@ -1902,6 +1904,19 @@ public class SearchBuilder implements ISearchBuilder {
 		return retVal;
 	}
 
+	private void validateHaveSystemAndCodeForToken(String theParamName, String theCode, String theSystem) {
+		String systemDesc = defaultIfBlank(theSystem, "(missing)");
+		String codeDesc = defaultIfBlank(theCode, "(missing)");
+		if (isBlank(theCode)) {
+			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "invalidCodeMissingSystem", theParamName, systemDesc, codeDesc);
+			throw new InvalidRequestException(msg);
+		}
+		if (isBlank(theSystem)) {
+			String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "invalidCodeMissingCode", theParamName, systemDesc, codeDesc);
+			throw new InvalidRequestException(msg);
+		}
+	}
+
 	private Predicate addPredicateToken(String theResourceName, String theParamName, CriteriaBuilder theBuilder, From<?, ResourceIndexedSearchParamToken> theFrom, List<VersionIndependentConcept> theTokens, TokenParamModifier theModifier, TokenModeEnum theTokenMode) {
 		if (myDontUseHashesForSearch) {
 			final Path<String> systemExpression = theFrom.get("mySystem");
@@ -2056,6 +2071,7 @@ public class SearchBuilder implements ISearchBuilder {
 				outerQuery.multiselect(myBuilder.countDistinct(myResourceTableRoot));
 			} else {
 				outerQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
+				outerQuery.distinct(true);
 			}
 
 		}
@@ -3125,6 +3141,8 @@ public class SearchBuilder implements ISearchBuilder {
 
 		private final SearchRuntimeDetails mySearchRuntimeDetails;
 		private final RequestDetails myRequest;
+		private final boolean myHaveRawSqlHooks;
+		private final boolean myHavePerftraceFoundIdHook;
 		private boolean myFirst = true;
 		private IncludesIterator myIncludesIterator;
 		private Long myNext;
@@ -3143,13 +3161,16 @@ public class SearchBuilder implements ISearchBuilder {
 			if (myParams.getEverythingMode() != null) {
 				myStillNeedToFetchIncludes = true;
 			}
+
+			myHavePerftraceFoundIdHook =JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID, myInterceptorBroadcaster, myRequest);
+			myHaveRawSqlHooks = JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_RAW_SQL, myInterceptorBroadcaster, myRequest);
+
 		}
 
 		private void fetchNext() {
 
-			boolean haveRawSqlHooks = JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_RAW_SQL, myInterceptorBroadcaster, myRequest);
 			try {
-				if (haveRawSqlHooks) {
+				if (myHaveRawSqlHooks) {
 					CurrentThreadCaptureQueriesListener.startCapturing();
 				}
 
@@ -3190,6 +3211,13 @@ public class SearchBuilder implements ISearchBuilder {
 					if (myNext == null) {
 						while (myResultsIterator.hasNext()) {
 							Long next = myResultsIterator.next();
+							if (myHavePerftraceFoundIdHook) {
+								HookParams params = new HookParams()
+									.add(Integer.class, System.identityHashCode(this))
+									.add(Object.class, next);
+								JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID, params);
+							}
+
 							if (next != null) {
 								if (myPidSet.add(next)) {
 									myNext = next;
@@ -3228,7 +3256,7 @@ public class SearchBuilder implements ISearchBuilder {
 				mySearchRuntimeDetails.setFoundMatchesCount(myPidSet.size());
 
 			} finally {
-				if (haveRawSqlHooks) {
+				if (myHaveRawSqlHooks) {
 					SqlQueryList capturedQueries = CurrentThreadCaptureQueriesListener.getCurrentQueueAndStopCapturing();
 					HookParams params = new HookParams()
 						.add(RequestDetails.class, myRequest)

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java

@@ -145,10 +145,9 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
 
 			} else {
 
-				FHIRPathEngine fhirPathEngine = new FHIRPathEngine(new HapiWorkerContext(theContext, VALIDATION_SUPPORT));
 				try {
-					fhirPathEngine.parse(theExpression);
+					theContext.newFluentPath().parse(theExpression);
-				} catch (FHIRLexer.FHIRLexerException e) {
+				} catch (Exception e) {
 					throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + theExpression + "\": " + e.getMessage());
 				}
 

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

@@ -1,31 +0,0 @@
-package ca.uhn.fhir.jpa.provider;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * 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.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-/**
- * @deprecated Use ca.uhn.fhir.jpa.binstore.BinaryAccessProvider instead
- */
-@Deprecated
-public class BinaryAccessProvider extends ca.uhn.fhir.jpa.binstore.BinaryAccessProvider {
-
-	// FIXME: JA delete before 4.0.0
-
-}

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

@@ -233,6 +233,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				ourLog.trace("Going to try to start next search");
 				Optional<Search> newSearch = mySearchCacheSvc.tryToMarkSearchAsInProgress(search);
 				if (newSearch.isPresent()) {
+					ourLog.trace("Launching new search");
 					search = newSearch.get();
 					String resourceType = search.getResourceType();
 					SearchParameterMap params = search.getSearchParameterMap().orElseThrow(() -> new IllegalStateException("No map in PASSCOMPLET search"));
@@ -1113,7 +1114,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						throw newResourceGoneException(getSearch().getUuid());
 					}
 
-					ourLog.debug("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
+					ourLog.trace("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
 					setPreviouslyAddedResourcePids(previouslyAddedResourcePids);
 					return null;
 				});

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -2,10 +2,15 @@ package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.data.ISearchDao;
-import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.entity.Search;
-import ca.uhn.fhir.jpa.model.entity.*;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
+import ca.uhn.fhir.jpa.model.entity.ResourceLink;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@@ -34,7 +39,11 @@ import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
-import org.junit.*;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -45,11 +54,29 @@ import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.math.BigDecimal;
 import java.nio.charset.StandardCharsets;
-import java.util.*;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
 import java.util.stream.Collectors;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.contains;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.hasItem;
+import static org.hamcrest.Matchers.hasItems;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 
 @SuppressWarnings({"unchecked", "Duplicates"})
@@ -1978,6 +2005,52 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSearchOnCodesWithBelow() {
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.addConcept().setCode("111-1")
+			.addConcept().setCode("111-2");
+		cs.addConcept().setCode("222-1")
+			.addConcept().setCode("222-2");
+		myCodeSystemDao.create(cs);
+
+		Observation obs1 = new Observation();
+		obs1.getCode().addCoding().setSystem("http://foo").setCode("111-1");
+		String id1 = myObservationDao.create(obs1).getId().toUnqualifiedVersionless().getValue();
+
+		Observation obs2 = new Observation();
+		obs2.getCode().addCoding().setSystem("http://foo").setCode("111-2");
+		String id2 = myObservationDao.create(obs2).getId().toUnqualifiedVersionless().getValue();
+
+
+		IBundleProvider result;
+
+		result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Observation.SP_CODE, new TokenParam("http://foo", "111-1")));
+		assertThat(toUnqualifiedVersionlessIds(result).toString(), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1));
+
+		result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Observation.SP_CODE, new TokenParam("http://foo", "111-1").setModifier(TokenParamModifier.BELOW)));
+		assertThat(toUnqualifiedVersionlessIds(result).toString(), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1, id2));
+
+		try {
+			myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Observation.SP_CODE, new TokenParam(null, "111-1").setModifier(TokenParamModifier.BELOW)));
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid token specified for parameter code - No code specified: (missing)|111-1", e.getMessage());
+		}
+
+		try {
+			myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(Observation.SP_CODE, new TokenParam("111-1", null).setModifier(TokenParamModifier.BELOW)));
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid token specified for parameter code - No system specified: 111-1|(missing)", e.getMessage());
+		}
+	}
+
+
 	@Test
 	public void testSearchParamChangesType() {
 		String name = "testSearchParamChangesType";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java

@@ -1,19 +1,26 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
+import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.BundleUtil;
 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.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent;
@@ -30,25 +37,32 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderCustomSearchParamR4Test.class);
 
+
 	@Override
 	@After
 	public void after() throws Exception {
 		super.after();
 
 		myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
+
 	}
 
 	@Override
@@ -66,7 +80,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	}
 
 	private Map<String, CapabilityStatementRestResourceSearchParamComponent> extractSearchParams(CapabilityStatement conformance, String resType) {
-		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = new HashMap<String, CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent>();
+		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = new HashMap<>();
 		for (CapabilityStatementRestComponent nextRest : conformance.getRest()) {
 			for (CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
 				if (!resType.equals(nextResource.getType())) {
@@ -81,7 +95,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	}
 
 	@Test
-	public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
+	public void saveCreateSearchParamInvalidWithMissingStatus() {
 		SearchParameter sp = new SearchParameter();
 		sp.setCode("foo");
 		sp.setExpression("Patient.gender");
@@ -431,6 +445,127 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 
 	}
 
+	/**
+	 * See #1300
+	 */
+	@Test
+	public void testCustomParameterMatchingManyValues() {
+
+		List<String> found = new ArrayList<>();
+
+		class Interceptor {
+			@Hook(Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID)
+			public void foundId(Integer theSearchId, Object theId) {
+				found.add(theSearchId + "/" + theId);
+			}
+		}
+		Interceptor interceptor = new Interceptor();
+		myInterceptorRegistry.registerInterceptor(interceptor);
+		try {
+			myDaoConfig.setAllowContainsSearches(true);
+
+			// Add a custom search parameter
+			SearchParameter fooSp = new SearchParameter();
+			fooSp.addBase("Questionnaire");
+			fooSp.setCode("item-text");
+			fooSp.setName("item-text");
+			fooSp.setType(Enumerations.SearchParamType.STRING);
+			fooSp.setTitle("FOO SP");
+			fooSp.setExpression("Questionnaire.item.text | Questionnaire.item.item.text | Questionnaire.item.item.item.text");
+			fooSp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
+			fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
+			mySearchParameterDao.create(fooSp, mySrd);
+			mySearchParamRegistry.forceRefresh();
+
+			int textIndex = 0;
+			List<Long> ids = new ArrayList<>();
+			for (int i = 0; i < 200; i++) {
+				//Lots and lots of matches
+				Questionnaire q = new Questionnaire();
+				q
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++));
+				q
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++));
+				q
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++));
+				q
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++));
+				q
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++))
+					.addItem()
+					.setText("Section " + (textIndex++));
+				ids.add(myQuestionnaireDao.create(q).getId().getIdPartAsLong());
+			}
+
+			int foundCount = 0;
+			Bundle bundle = null;
+			List<Long> actualIds = new ArrayList<>();
+			do {
+
+				if (bundle == null) {
+					bundle = ourClient
+						.search()
+						.byUrl(ourServerBase + "/Questionnaire?item-text=Section")
+						.returnBundle(Bundle.class)
+						.execute();
+				} else {
+					bundle = ourClient
+						.loadPage()
+						.next(bundle)
+						.execute();
+				}
+				List<IBaseResource> resources = BundleUtil.toListOfResources(myFhirCtx, bundle);
+				resources.forEach(t -> actualIds.add(t.getIdElement().getIdPartAsLong()));
+				foundCount += resources.size();
+
+			} while (bundle.getLink("next") != null);
+
+			ourLog.info("Found: {}", found);
+
+			runInTransaction(() -> {
+
+				List<Search> searches = mySearchEntityDao.findAll();
+				assertEquals(1, searches.size());
+				Search search = searches.get(0);
+				String message = "\nWanted: " + (ids) + "\n" +
+					"Actual: " + (actualIds) + "\n" +
+					"Found : " + (found) + "\n" +
+					search.toString();
+				assertEquals(message, 200, search.getNumFound());
+				assertEquals(message, 200, search.getTotalCount().intValue());
+				assertEquals(message, SearchStatusEnum.FINISHED, search.getStatus());
+			});
+
+			assertEquals(200, foundCount);
+		} finally {
+			myInterceptorRegistry.unregisterInterceptor(interceptor);
+		}
+	}
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java

@@ -7,7 +7,13 @@ import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
 import ca.uhn.fhir.util.TestUtil;
 import com.google.common.collect.Lists;
-import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.dstu3.model.CodeType;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.Parameters;
+import org.hl7.fhir.dstu3.model.PrimitiveType;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.dstu3.model.Type;
+import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.junit.After;
 import org.junit.AfterClass;
@@ -24,8 +30,13 @@ import java.util.Set;
 import java.util.stream.Collectors;
 
 import static org.awaitility.Awaitility.await;
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
 
 public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 
@@ -116,9 +127,7 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 
 		myTerminologyDeferredStorageSvc.saveDeferred();
 
-		runInTransaction(() -> {
+		await().until(() -> runInTransaction(() -> myTermConceptMapDao.count()), greaterThan(0L));
-			await().until(() -> myTermConceptMapDao.count(), greaterThan(0L));
-		});
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/resources/r4/impact-sp.json

@@ -0,0 +1,29 @@
+{
+	"resourceType": "SearchParameter",
+	"id": "54805",
+	"meta": {
+		"versionId": "1",
+		"lastUpdated": "2019-11-04T18:33:47.918+00:00",
+		"source": "#pt4ERkOO6LGm5ZoA"
+	},
+	"text": {
+		"status": "generated",
+		"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Search for a questionnaire by item.text nested field - up to 3 levels.</div>"
+	},
+	"url": "https://impact-fhir.mitre.org/r4/SearchParameter/QuestionnaireItemText",
+	"version": "0.0.1",
+	"name": "QuestionnaireItemText",
+	"status": "active",
+	"date": "2019-10-25T15:38:45-04:00",
+	"description": "Search for a questionnaire by item.text nested field - up to 3 levels.",
+	"code": "item-text",
+	"base": [
+		"Questionnaire"
+	],
+	"type": "string",
+	"expression": "Questionnaire.item.text | Questionnaire.item.item.text | Questionnaire.item.item.item.text",
+	"xpathUsage": "normal",
+	"modifier": [
+		"contains"
+	]
+}

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/fluentpath/FluentPathDstu3.java

@@ -49,4 +49,9 @@ public class FluentPathDstu3 implements IFluentPath {
     return evaluate(theInput, thePath, theReturnType).stream().findFirst();
   }
 
+  @Override
+  public void parse(String theExpression) {
+    myEngine.parse(theExpression);
+  }
+
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/fluentpath/FluentPathR4.java

@@ -49,5 +49,10 @@ public class FluentPathR4 implements IFluentPath {
     return evaluate(theInput, thePath, theReturnType).stream().findFirst();
   }
 
+  @Override
+  public void parse(String theExpression) {
+    myEngine.parse(theExpression);
+  }
+
 
 }

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/fhirpath/FhirPathR5.java

@@ -49,5 +49,10 @@ public class FhirPathR5 implements IFluentPath {
     return evaluate(theInput, thePath, theReturnType).stream().findFirst();
   }
 
+	@Override
+	public void parse(String theExpression) {
+		myEngine.parse(theExpression);
+	}
+
 
 }

src/changes/changes.xml

@@ -501,6 +501,18 @@
 				A NullPointerException in the XML Parser was fixed when serializing a resource containing an extension
 				on a primitive datatype that was missing a URL declaration.
 			</action>
+			<action type="fix">
+				When using the _filter search parameter in the JPA server with an untyped resource ID, the
+				filter could bring in search results of the wrong type. Thanks to Anthony Sute for the Pull
+				Request and Jens Villadsen for reporting!
+			</action>
+			<action type="fix" issue="1300">
+				In some cases where where a single search parameter matches the same resource many times with 
+				different distinct values (e.g. a search by Patient:name where there are hundreds of patients having
+				hundreds of distinct names each) the Search Coordinator would end up in an infinite loop and never
+				return all of the possible results. Thanks to @imranmoezkhan for reporting, and to 
+				Tim Shaffer for providing a reproducible test case!
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">

src/site/xdoc/index.xml

@@ -17,9 +17,9 @@
 				<br/>
 				<iframe src="https://ghbtns.com/github-btn.html?user=jamesagnew&amp;repo=hapi-fhir&amp;type=fork&amp;count=true&amp;v=2" frameborder="0" scrolling="0" width="100px" height="20px"></iframe>
 				<br/>
-				<a href="https://travis-ci.org/jamesagnew/hapi-fhir"><img src="https://travis-ci.org/jamesagnew/hapi-fhir.svg?branch=master" alt="Build Status"/></a>
+				<a href="https://dev.azure.com/jamesagnew214/jamesagnew214/_build/latest?definitionId=1&branchName=master"><img src="https://dev.azure.com/jamesagnew214/jamesagnew214/_apis/build/status/jamesagnew.hapi-fhir?branchName=master" alt="Build Status"/></a>
 				<br/>
-				<a href="https://coveralls.io/r/jamesagnew/hapi-fhir?branch=master"><img src="https://coveralls.io/repos/jamesagnew/hapi-fhir/badge.svg?branch=master" alt="Coverage Status"/></a>
+				<a href="https://codecov.io/gh/jamesagnew/hapi-fhir"><img src="https://codecov.io/gh/jamesagnew/hapi-fhir/branch/master/graph/badge.svg" alt="Coverage Status"/></a>
 				<br/>
 				<a href="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg"><img src="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg" alt="Maven Central"/></a>
 				<br/>