More perf work

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

@@ -46,6 +46,7 @@ import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
+import org.springframework.util.CollectionUtils;
 import org.springframework.web.servlet.ThemeResolver;
 
 import com.google.common.collect.Lists;
@@ -100,7 +101,7 @@ public class SearchBuilder {
 	private Root<ResourceTable> myResourceTableRoot;
 	private ArrayList<Predicate> myPredicates;
 	private CriteriaBuilder myBuilder;
-	private CriteriaQuery<Tuple> myResourceTableQuery;
+	private AbstractQuery<Long> myResourceTableQuery;
 	private PlatformTransactionManager myPlatformTransactionManager;
 
 	public SearchBuilder(FhirContext theFhirContext, EntityManager theEntityManager, PlatformTransactionManager thePlatformTransactionManager, IFulltextSearchSvc theFulltextSearchSvc,
@@ -1257,19 +1258,20 @@ public class SearchBuilder {
 			throw new InvalidRequestException("This server does not support _sort specifications of type " + param.getParamType() + " - Can't serve _sort=" + theSort.getParamName());
 		}
 
-		From<?, ?> stringJoin = theFrom.join(joinAttrName, JoinType.INNER);
+		From<?, ?> join = theFrom.join(joinAttrName, JoinType.LEFT);
 
 		if (param.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
-			thePredicates.add(stringJoin.get("mySourcePath").as(String.class).in(param.getPathsSplit()));
+			thePredicates.add(join.get("mySourcePath").as(String.class).in(param.getPathsSplit()));
 		} else {
-			thePredicates.add(theBuilder.equal(stringJoin.get("myParamName"), theSort.getParamName()));
+			Predicate joinParam1 = theBuilder.equal(join.get("myParamName"), theSort.getParamName());
+			thePredicates.add(joinParam1);
 		}
 
 		for (String next : sortAttrName) {
 			if (theSort.getOrder() == null || theSort.getOrder() == SortOrderEnum.ASC) {
-				theOrders.add(theBuilder.asc(stringJoin.get(next)));
+				theOrders.add(theBuilder.asc(join.get(next)));
 			} else {
-				theOrders.add(theBuilder.desc(stringJoin.get(next)));
+				theOrders.add(theBuilder.desc(join.get(next)));
 			}
 		}
 
@@ -1470,27 +1472,53 @@ public class SearchBuilder {
 
 	public List<Long> loadSearchPage(SearchParameterMap theParams, int theFromIndex, int theToIndex) {
 
-		// if (myFulltextSearchSvc == null) {
-		// if (theParams.containsKey(Constants.PARAM_TEXT)) {
-		// throw new InvalidRequestException("Fulltext search is not enabled on this service, can not process parameter: " + Constants.PARAM_TEXT);
-		// } else if (theParams.containsKey(Constants.PARAM_CONTENT)) {
-		// throw new InvalidRequestException("Fulltext search is not enabled on this service, can not process parameter: " + Constants.PARAM_CONTENT);
-		// }
-		// } else {
-		// // FIXME: add from and to
-		// List<Long> searchResultPids = myFulltextSearchSvc.search(myResourceName, theParams);
-		// if (searchResultPids != null) {
-		// if (searchResultPids.isEmpty()) {
-		// return Collections.emptyList();
-		// }
-		// return searchResultPids;
-		// }
-		// }
-
 		myBuilder = myEntityManager.getCriteriaBuilder();
-		myResourceTableQuery = myBuilder.createTupleQuery();
+		CriteriaQuery<Long> outerQuery = null;
+		
+		/*
+		 * Sort
+		 * 
+		 * If we have a sort, we wrap the criteria search (the search that actually
+		 * finds the appropriate resources) in an outer search which is then sorted
+		 */
+		if (theParams.getSort() != null) {
+
+			outerQuery = myBuilder.createQuery(Long.class);
+			Root<ResourceTable> outerQueryFrom = outerQuery.from(ResourceTable.class);
+			
+			List<Order> orders = Lists.newArrayList();
+			List<Predicate> predicates = Lists.newArrayList();
+			
+			createSort(myBuilder, outerQueryFrom, theParams.getSort(), orders, predicates);
+			if (orders.size() > 0) {
+				outerQuery.orderBy(orders);
+			}
+			
+			Subquery<Long> subQ = outerQuery.subquery(Long.class);
+			Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
+			
+			myResourceTableQuery = subQ;
+			myResourceTableRoot = subQfrom;
+			
+			Expression<Long> selectExpr = subQfrom.get("myId").as(Long.class);
+			subQ.select(selectExpr);
+			
+			predicates.add(0, myBuilder.in(outerQueryFrom.get("myId").as(Long.class)).value(subQ));
+			
+			outerQuery.multiselect(outerQueryFrom.get("myId").as(Long.class));
+			outerQuery.where(predicates.toArray(new Predicate[0]));
+			
+		} else {
+			
+			outerQuery = myBuilder.createQuery(Long.class);
+			myResourceTableQuery = outerQuery;
+			myResourceTableRoot = myResourceTableQuery.from(ResourceTable.class);
+			outerQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
+			
+		}
+
+		
 		myResourceTableQuery.distinct(true);
-		myResourceTableRoot = myResourceTableQuery.from(ResourceTable.class);
 		myPredicates = new ArrayList<Predicate>();
 		if (theParams.getEverythingMode() == null) {
 			myPredicates.add(myBuilder.equal(myResourceTableRoot.get("myResourceType"), myResourceName));
@@ -1509,7 +1537,9 @@ public class SearchBuilder {
 				Long pid = BaseHapiFhirDao.translateForcedIdToPid(myResourceName, idParm.getValue(), myForcedIdDao);
 				myPredicates.add(myBuilder.equal(join.get("myTargetResourcePid").as(Long.class), pid));
 			} else {
-				myPredicates.add(myBuilder.equal(join.get("myTargetResourceType").as(String.class), myResourceName));
+				Predicate targetTypePredicate = myBuilder.equal(join.get("myTargetResourceType").as(String.class), myResourceName);
+				Predicate sourceTypePredicate = myBuilder.equal(myResourceTableRoot.get("myResourceType").as(String.class), myResourceName);
+				myPredicates.add(myBuilder.or(sourceTypePredicate, targetTypePredicate));
 			}
 
 		} else {
@@ -1539,14 +1569,19 @@ public class SearchBuilder {
 
 		myResourceTableQuery.where(myBuilder.and(SearchBuilder.toArray(myPredicates)));
 
-		myResourceTableQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
+		/*
-		TypedQuery<Tuple> query = myEntityManager.createQuery(myResourceTableQuery);
+		 * Now perform the search
+		 */
+		TypedQuery<Long> query = myEntityManager.createQuery(outerQuery);
 		query.setFirstResult(theFromIndex);
 		query.setMaxResults(theToIndex - theFromIndex);
 
 		List<Long> pids = new ArrayList<Long>();
-		for (Tuple next : query.getResultList()) {
+		
-			pids.add(next.get(0, Long.class));
+		for (Long next : query.getResultList()) {
+			if (next != null) {
+				pids.add(next);
+			}
 		}
 
 		return pids;
@@ -1889,6 +1924,10 @@ public class SearchBuilder {
 			return;
 		}
 
+		// Dupes will cause a crash later anyhow, but this is expensive so only do it
+		// when running asserts
+		assert new HashSet<Long>(theIncludePids).size() == theIncludePids.size() : "PID list contains duplicates: " + theIncludePids;
+		
 		Map<Long, Integer> position = new HashMap<Long, Integer>();
 		for (Long next : theIncludePids) {
 			position.put(next, theResourceListToPopulate.size());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -77,11 +77,11 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 				entitiesToSave.add(present);
 			}
 
-			mySearchParamPresentDao.deleteInBatch(entitiesToDelete);
-			mySearchParamPresentDao.save(entitiesToSave);
-
 		}
 
+		mySearchParamPresentDao.deleteInBatch(entitiesToDelete);
+		mySearchParamPresentDao.save(entitiesToSave);
+		
 	}
 
 	@Override

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

@@ -32,6 +32,7 @@ import org.springframework.transaction.support.TransactionTemplate;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
+import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
@@ -190,7 +191,7 @@ public abstract class BaseJpaTest {
 		return bundleStr;
 	}
 
-	public static void purgeDatabase(final EntityManager entityManager, PlatformTransactionManager theTxManager) {
+	public static void purgeDatabase(final EntityManager entityManager, PlatformTransactionManager theTxManager, ISearchParamPresenceSvc theSearchParamPresenceSvc) {
 		TransactionTemplate txTemplate = new TransactionTemplate(theTxManager);
 		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
 		txTemplate.execute(new TransactionCallback<Void>() {
@@ -255,6 +256,7 @@ public abstract class BaseJpaTest {
 				return null;
 			}
 		});
+		theSearchParamPresenceSvc.flushCachesForUnitTest();
 	}
 
 	public static Set<String> toCodes(Set<TermConcept> theConcepts) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java

@@ -26,12 +26,14 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.AnnotationConfigApplicationContext;
 import org.springframework.transaction.PlatformTransactionManager;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu1Config;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.IResource;
@@ -61,10 +63,11 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest {
 	private static IFhirResourceDao<Patient> ourPatientDao;
 	private static IFhirSystemDao<List<IResource>, MetaDt> ourSystemDao;
 	private static PlatformTransactionManager ourTxManager;
+	private static ISearchParamPresenceSvc ourSearchParamPresenceSvc;
 
 	@Before
 	public void before() {
-		super.purgeDatabase(ourEntityManager, ourTxManager);
+		super.purgeDatabase(ourEntityManager, ourTxManager, ourSearchParamPresenceSvc);
 	}
 
 	@Override
@@ -493,6 +496,7 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest {
 		ourSystemDao = ourCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
 		ourEntityManager = ourCtx.getBean(EntityManager.class);
 		ourTxManager = ourCtx.getBean(PlatformTransactionManager.class);
+		ourSearchParamPresenceSvc = ourCtx.getBean(ISearchParamPresenceSvc.class);
 	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
+import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@@ -147,6 +148,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myValueSetDaoDstu2")
 	protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
+	@Autowired
+	protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
+
 	@Before
 	public void beforeCreateInterceptor() {
 		myInterceptor = mock(IServerInterceptor.class);
@@ -167,7 +171,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Transactional()
 	public void beforePurgeDatabase() {
 		final EntityManager entityManager = this.myEntityManager;
-		purgeDatabase(entityManager, myTxManager);
+		purgeDatabase(entityManager, myTxManager, mySearchParamPresenceSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -1307,15 +1307,15 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 
 		SearchParameterMap params;
 		
+		params = new SearchParameterMap();
+		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(pid1, pid3));
+
 		params = new SearchParameterMap();
 		params.add(Patient.SP_NAME, new StringParam("FAMILY1"));
 		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
 		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(pid1));
 
-		params = new SearchParameterMap();
-		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
-		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(pid1, pid3));
-
 		params = new SearchParameterMap();
 		params.add(Patient.SP_NAME, new StringParam("FAMILY9999"));
 		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));

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

@@ -224,8 +224,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Transactional()
 	public void beforePurgeDatabase() {
 		final EntityManager entityManager = this.myEntityManager;
-		purgeDatabase(entityManager, myTxManager);
+		purgeDatabase(entityManager, myTxManager, mySearchParamPresenceSvc);
-		mySearchParamPresenceSvc.flushCachesForUnitTest();
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -108,7 +108,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 	@Test
 	public void testEverythingTimings() throws Exception {
-		String methodName = "testEverythingIncludesBackReferences";
+		String methodName = "testEverythingTimings";
 
 		Organization org = new Organization();
 		org.setName(methodName);
@@ -124,7 +124,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
 
 		Patient pat2 = new Patient();
-		pat2.addAddress().addLine(methodName);
+		pat2.addAddress().addLine(methodName + "2");
 		pat2.getManagingOrganization().setReferenceElement(orgId);
 		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
 
@@ -2862,6 +2862,125 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 	}
 
+	@Test
+	public void testSortOnPopulatedField() throws Exception {
+		Patient pBA = new Patient();
+		pBA.setId("BA");
+		pBA.setActive(true);
+		pBA.setGender(AdministrativeGender.MALE);
+		pBA.addName().setFamily("B").addGiven("A");
+		myPatientDao.update(pBA);
+
+		Patient pBB = new Patient();
+		pBB.setId("BB");
+		pBB.setActive(true);
+		pBB.setGender(AdministrativeGender.MALE);
+		pBB.addName().setFamily("B").addGiven("B");
+		pBB.addName().setFamily("Z").addGiven("Z");
+		myPatientDao.update(pBB);
+
+		Patient pAB = new Patient();
+		pAB.setId("AB");
+		pAB.setActive(true);
+		pAB.setGender(AdministrativeGender.MALE);
+		pAB.addName().setFamily("A").addGiven("B");
+		myPatientDao.update(pAB);
+		
+		Patient pAA = new Patient();
+		pAA.setId("AA");
+		pAA.setActive(true);
+		pAA.setGender(AdministrativeGender.MALE);
+		pAA.addName().setFamily("A").addGiven("A");
+		myPatientDao.update(pAA);
+
+		SearchParameterMap map;
+		List<String> ids;
+
+		map = new SearchParameterMap();
+		map.setSort(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC)));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+		
+		map = new SearchParameterMap();
+		map.setSort(new SortSpec("gender").setChain(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC))));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		ourLog.info("IDS: {}", ids);
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+
+		map = new SearchParameterMap();
+		map.add(Patient.SP_ACTIVE, new TokenParam(null, "true"));
+		map.setSort(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC)));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+	}
+
+	@Test
+	public void testSort() throws Exception {
+		Patient pBA = new Patient();
+		pBA.setId("BA");
+		pBA.setActive(true);
+		pBA.setGender(AdministrativeGender.MALE);
+		pBA.addName().setFamily("B").addGiven("A");
+		myPatientDao.update(pBA);
+
+		Patient pBB = new Patient();
+		pBB.setId("BB");
+		pBB.setActive(true);
+		pBB.setGender(AdministrativeGender.MALE);
+		pBB.addName().setFamily("B").addGiven("B");
+		myPatientDao.update(pBB);
+
+		Patient pAB = new Patient();
+		pAB.setId("AB");
+		pAB.setActive(true);
+		pAB.setGender(AdministrativeGender.MALE);
+		pAB.addName().setFamily("A").addGiven("B");
+		myPatientDao.update(pAB);
+		
+		Patient pAA = new Patient();
+		pAA.setId("AA");
+		pAA.setActive(true);
+		pAA.setGender(AdministrativeGender.MALE);
+		pAA.addName().setFamily("A").addGiven("A");
+		myPatientDao.update(pAA);
+
+		Patient pCA = new Patient();
+		pCA.setId("CA");
+		pCA.setActive(false);
+		pCA.addName().setFamily("C").addGiven("A");
+		pCA.addName().setFamily("Z").addGiven("A");
+		myPatientDao.update(pCA);
+
+		SearchParameterMap map;
+		List<String> ids;
+
+		// Sort across all resources
+		map = new SearchParameterMap();
+		map.setSort(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC)));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB", "Patient/CA"));
+		
+		// A sort on a field that isn't populated in all cases
+		map = new SearchParameterMap();
+		map.setSort(new SortSpec("gender"));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		ourLog.info("IDS: {}", ids);
+		assertThat(ids, containsInAnyOrder("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB", "Patient/CA"));
+		
+		map = new SearchParameterMap();
+		map.setSort(new SortSpec("gender").setChain(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC))));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		ourLog.info("IDS: {}", ids);
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB", "Patient/CA"));
+
+		// Sort 
+		map = new SearchParameterMap();
+		map.add(Patient.SP_ACTIVE, new TokenParam(null, "true"));
+		map.setSort(new SortSpec("family", SortOrderEnum.ASC).setChain(new SortSpec("given", SortOrderEnum.ASC)));
+		ids = toUnqualifiedVersionlessIdValues(myPatientDao.search(map));
+		assertThat(ids, contains("Patient/AA", "Patient/AB", "Patient/BA", "Patient/BB"));
+	}
+
 	@Test
 	public void testSearchWithUriParamAbove() throws Exception {
 		ValueSet vs1 = new ValueSet();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java

@@ -23,6 +23,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu3WithoutLuceneConfig;
 import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -139,6 +140,8 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
 
 	@Autowired
 	protected PlatformTransactionManager myTxManager;
+	@Autowired
+	protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
 
 	@Autowired
 	@Qualifier("myJpaValidationSupportChainDstu3")
@@ -148,7 +151,7 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
 	@Transactional()
 	public void beforePurgeDatabase() {
 		final EntityManager entityManager = this.myEntityManager;
-		purgeDatabase(entityManager, myTxManager);
+		purgeDatabase(entityManager, myTxManager, mySearchParamPresenceSvc);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu1Test.java

@@ -39,6 +39,7 @@ import ca.uhn.fhir.jpa.dao.BaseJpaTest;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
@@ -87,6 +88,7 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 	private static CloseableHttpClient ourHttpClient;
 	private static EntityManager ourEntityManager;
 	private static PlatformTransactionManager ourTxManager;
+	private static ISearchParamPresenceSvc ourSearchParamPresenceSvc;
 
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
@@ -551,6 +553,7 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 		ourOrganizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDaoDstu1", IFhirResourceDao.class);
 		ourEntityManager = ourAppCtx.getBean(EntityManager.class);
 		ourTxManager = ourAppCtx.getBean(PlatformTransactionManager.class);
+		ourSearchParamPresenceSvc = ourAppCtx.getBean(ISearchParamPresenceSvc.class);
 		
 		List<IResourceProvider> rpsDev = (List<IResourceProvider>) ourAppCtx.getBean("myResourceProvidersDstu1", List.class);
 		restServer.setResourceProviders(rpsDev);
@@ -593,7 +596,7 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 	
 	@Before
 	public void before() {
-		super.purgeDatabase(ourEntityManager, ourTxManager);
+		super.purgeDatabase(ourEntityManager, ourTxManager, ourSearchParamPresenceSvc);
 	}
 
 }

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

@@ -2169,7 +2169,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 	}
 
-
 	@Test
 	public void testSaveAndRetrieveExistingNarrativeJson() {
 		Patient p1 = new Patient();
@@ -3046,41 +3045,37 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		p.addName().addGiven("Sarah").setFamily("Graham");
 		ourClient.create().resource(p).execute();
 
-		//@formatter:off
 		Bundle resp = ourClient
-			.search()
+				.search()
-			.forResource(Patient.class)
+				.forResource(Patient.class)
-			.where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", methodName))
+				.where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", methodName))
-			.sort().ascending(Patient.FAMILY)
+				.sort().ascending(Patient.FAMILY)
-			.sort().ascending(Patient.GIVEN)
+				.sort().ascending(Patient.GIVEN)
-			.count(100)
+				.count(100)
-			.returnBundle(Bundle.class)
+				.returnBundle(Bundle.class)
-			.execute();
+				.execute();
-		//@formatter:on
 
 		List<String> names = toNameList(resp);
 
 		ourLog.info(StringUtils.join(names, '\n'));
 
-		//@formatter:off
 		assertThat(names, contains( // this matches in order only
-			"Daniel Adams",
+				"Daniel Adams",
-			"Aaron Alexis",
+				"Aaron Alexis",
-			"Carol Allen",
+				"Carol Allen",
-			"Ruth Black",
+				"Ruth Black",
-			"Brian Brooks",
+				"Brian Brooks",
-			"Amy Clark",
+				"Amy Clark",
-			"Susan Clark",
+				"Susan Clark",
-			"Anthony Coleman",
+				"Anthony Coleman",
-			"Lisa Coleman",
+				"Lisa Coleman",
-			"Steven Coleman",
+				"Steven Coleman",
-			"Ruth Cook",
+				"Ruth Cook",
-			"Betty Davis",
+				"Betty Davis",
-			"Joshua Diaz",
+				"Joshua Diaz",
-			"Brian Gracia",
+				"Brian Gracia",
-			"Sarah Graham",
+				"Sarah Graham",
-			"Stephan Graham"));
+				"Stephan Graham"));
-		//@formatter:om
 
 	}
 
@@ -3118,7 +3113,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		CloseableHttpResponse resp = ourHttpClient.execute(post);
 		try {
 			assertEquals(200, resp.getStatusLine().getStatusCode());
-			String output= IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
+			String output = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(output);
 		} finally {
 			resp.close();
@@ -3157,7 +3152,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
-			assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Can not update resource, request URL must contain an ID element for update (PUT) operation (it must be of the form [base]/[resource type]/[id])"));
+			assertThat(oo.getIssue().get(0).getDiagnostics(),
+					containsString("Can not update resource, request URL must contain an ID element for update (PUT) operation (it must be of the form [base]/[resource type]/[id])"));
 		} finally {
 			response.close();
 		}
@@ -3234,13 +3230,16 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		try {
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newJsonParser().parseResource(OperationOutcome.class, new InputStreamReader(response.getEntity().getContent()));
-			assertEquals("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"FOO\" does not match URL ID of \"" + p1id.getIdPart() + "\"", oo.getIssue().get(0).getDiagnostics());
+			assertEquals(
+					"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"FOO\" does not match URL ID of \""
+							+ p1id.getIdPart() + "\"",
+					oo.getIssue().get(0).getDiagnostics());
 		} finally {
 			response.close();
 		}
 
 		// Try to update with the no ID in the resource body
-		p1.setId((String)null);
+		p1.setId((String) null);
 
 		encoded = myFhirCtx.newJsonParser().encodeResourceToString(p1);
 		put = new HttpPut(ourServerBase + "/Patient/" + p1id.getIdPart());
@@ -3270,7 +3269,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 
 	}
 
-
 	@Test
 	public void testUpdateRejectsInvalidTypes() throws InterruptedException {
 

hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml

@@ -38,7 +38,7 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 	<!-- Set to 'trace' to enable SQL Value logging -->
-	<logger name="org.hibernate.type" additivity="false" level="trace">
+	<logger name="org.hibernate.type" additivity="false" level="info">
 		<appender-ref ref="STDOUT" />
 	</logger>