Clean up handling of searches nested in batch and transaction

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

@@ -1744,9 +1744,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
 			if (tagList != null) {
 				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+				totalMetaCount += tagList.size();
+			}
+			List<IdDt> profileList = ResourceMetadataKeyEnum.PROFILES.get(res);
+			if (profileList != null) {
+				totalMetaCount += profileList.size();
 			}
-			totalMetaCount += tagList.size();
-			totalMetaCount += ResourceMetadataKeyEnum.PROFILES.get(res).size();
 		} else {
 			IAnyResource res = (IAnyResource) theResource;
 			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);

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

@@ -29,6 +29,7 @@ import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
 
+import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.instance.model.api.*;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -926,9 +927,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			notifyInterceptors(RestOperationTypeEnum.SEARCH_TYPE, requestDetails);
 		
 			if (theRequestDetails.isSubRequest()) {
-				theParams.setLoadSynchronous(true);
+				Integer max =  myDaoConfig.getMaximumSearchResultCountInTransaction();
-				int max =  myDaoConfig.getMaximumSearchResultCountInTransaction();
+				if (max != null) {
-				theParams.setLoadSynchronousUpTo(myDaoConfig.getMaximumSearchResultCountInTransaction());
+					Validate.inclusiveBetween(1, Integer.MAX_VALUE, max.intValue(), "Maximum search result count in transaction ust be a positive integer");
+					theParams.setLoadSynchronousUpTo(myDaoConfig.getMaximumSearchResultCountInTransaction());
+				}
 			}
 
 			if (!isPagingProviderDatabaseBacked(theRequestDetails)) {

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

@@ -57,7 +57,7 @@ public class DaoConfig {
 	 * 
 	 * @see #setMaximumSearchResultCountInTransaction(int)
 	 */
-	private static final int DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = 500;
+	private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
 
 	/**
 	 * Default value for {@link #setReuseCachedSearchResultsForMillis(Long)}: 60000ms (one minute)
@@ -110,7 +110,7 @@ public class DaoConfig {
 	 * update setter javadoc if default changes
 	 */
 	private int myMaximumExpansionSize = 5000;
-	private int myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
+	private Integer myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
 	private ResourceEncodingEnum myResourceEncoding = ResourceEncodingEnum.JSONC;
 	/**
 	 * update setter javadoc if default changes
@@ -233,14 +233,17 @@ public class DaoConfig {
 	}
 
 	/**
-	 * Provides the maximum number of results which may be returned by a search within a FHIR <code>transaction</code>
+	 * Provides the maximum number of results which may be returned by a search (HTTP GET) which
-	 * operation. For example, if this value is set to <code>100</code> and a FHIR transaction is processed with a sub-request
+	 * is executed as a sub-operation within within a FHIR <code>transaction</code> or
-	 * for <code>Patient?gender=male</code>, the server will throw an error (and the transaction will fail) if there are more than
+	 * <code>batch</code> operation. For example, if this value is set to <code>100</code> and 
+	 * a FHIR transaction is processed with a sub-request for <code>Patient?gender=male</code>,
+	 * the server will throw an error (and the transaction will fail) if there are more than
 	 * 100 resources on the server which match this query.
-	 * 
+	 * <p>
-	 * @see #DEFAULT_LOGICAL_BASE_URLS The default value for this setting
+	 * The default value is <code>null</code>, which means that there is no limit.
+	 * </p>  
 	 */
-	public int getMaximumSearchResultCountInTransaction() {
+	public Integer getMaximumSearchResultCountInTransaction() {
 		return myMaximumSearchResultCountInTransaction;
 	}
 
@@ -699,14 +702,17 @@ public class DaoConfig {
 	}
 
 	/**
-	 * Provides the maximum number of results which may be returned by a search within a FHIR <code>transaction</code>
+	 * Provides the maximum number of results which may be returned by a search (HTTP GET) which
-	 * operation. For example, if this value is set to <code>100</code> and a FHIR transaction is processed with a sub-request
+	 * is executed as a sub-operation within within a FHIR <code>transaction</code> or
-	 * for <code>Patient?gender=male</code>, the server will throw an error (and the transaction will fail) if there are more than
+	 * <code>batch</code> operation. For example, if this value is set to <code>100</code> and 
+	 * a FHIR transaction is processed with a sub-request for <code>Patient?gender=male</code>,
+	 * the server will throw an error (and the transaction will fail) if there are more than
 	 * 100 resources on the server which match this query.
-	 * 
+	 * <p>
-	 * @see #DEFAULT_LOGICAL_BASE_URLS The default value for this setting
+	 * The default value is <code>null</code>, which means that there is no limit.
+	 * </p>  
 	 */
-	public void setMaximumSearchResultCountInTransaction(int theMaximumSearchResultCountInTransaction) {
+	public void setMaximumSearchResultCountInTransaction(Integer theMaximumSearchResultCountInTransaction) {
 		myMaximumSearchResultCountInTransaction = theMaximumSearchResultCountInTransaction;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -106,8 +106,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 		Bundle resp = new Bundle();
 		resp.setType(BundleTypeEnum.BATCH_RESPONSE);
-		OperationOutcome ooResp = new OperationOutcome();
-		resp.addEntry().setResource(ooResp);
 
 		/*
 		 * For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
@@ -163,7 +161,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 		long delay = System.currentTimeMillis() - start;
 		ourLog.info("Batch completed in {}ms", new Object[] { delay });
-		ooResp.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDiagnostics("Batch completed in " + delay + "ms");
 
 		return resp;
 	}

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

@@ -114,8 +114,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 		Bundle resp = new Bundle();
 		resp.setType(BundleType.BATCHRESPONSE);
-		OperationOutcome ooResp = new OperationOutcome();
-		resp.addEntry().setResource(ooResp);
 
 		/*
 		 * For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
@@ -171,7 +169,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 		long delay = System.currentTimeMillis() - start;
 		ourLog.info("Batch completed in {}ms", new Object[] { delay });
-		ooResp.addIssue().setSeverity(IssueSeverity.INFORMATION).setDiagnostics("Batch completed in " + delay + "ms");
 
 		return resp;
 	}

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

@@ -77,7 +77,6 @@ public class DatabaseBackedPagingProvider extends BasePagingProvider implements
 	@Override
 	public synchronized String storeResultList(IBundleProvider theList) {
 		String uuid = theList.getUuid();
-		Validate.notNull(uuid);
 		return uuid;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -40,7 +40,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 		DataSource dataSource = ProxyDataSourceBuilder
 				.create(retVal)
-				.multiline()
 				.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
 				.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
 				.countQuery()
@@ -70,7 +69,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		extraProperties.put("hibernate.jdbc.batch_size", "50");
-		extraProperties.put("hibernate.format_sql", "true");
+		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
 		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");

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.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
@@ -75,7 +76,6 @@ import ca.uhn.fhir.util.TestUtil;
 @ContextConfiguration(classes= {TestDstu2Config.class, ca.uhn.fhir.jpa.config.WebsocketDstu2DispatcherConfig.class})
 //@formatter:on
 public abstract class BaseJpaDstu2Test extends BaseJpaTest {
-
 	@Autowired
 	protected ApplicationContext myAppCtx;
 	@Autowired
@@ -114,18 +114,18 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myLocationDaoDstu2")
 	protected IFhirResourceDao<Location> myLocationDao;
+	@Autowired
+		@Qualifier("myMediaDaoDstu2")
+		protected IFhirResourceDao<Media> myMediaDao;
 	
 @Autowired
-	@Qualifier("myMediaDaoDstu2")
+@Qualifier("myMedicationAdministrationDaoDstu2")
-	protected IFhirResourceDao<Media> myMediaDao;
+protected IFhirResourceDao<MedicationAdministration> myMedicationAdministrationDao;
 	
 	@Autowired
 	@Qualifier("myMedicationDaoDstu2")
 	protected IFhirResourceDao<Medication> myMedicationDao;
 	@Autowired
-	@Qualifier("myMedicationAdministrationDaoDstu2")
-	protected IFhirResourceDao<MedicationAdministration> myMedicationAdministrationDao;
-	@Autowired
 	@Qualifier("myMedicationOrderDaoDstu2")
 	protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
 	@Autowired
@@ -135,6 +135,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myOrganizationDaoDstu2")
 	protected IFhirResourceDao<Organization> myOrganizationDao;
 	@Autowired
+	protected DatabaseBackedPagingProvider myPagingProvider;
+	@Autowired
 	@Qualifier("myPatientDaoDstu2")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired
@@ -150,8 +152,12 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myResourceProvidersDstu2")
 	protected Object myResourceProviders;
 	@Autowired
+	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
+	@Autowired
 	protected IFulltextSearchSvc mySearchDao;
 	@Autowired
+	protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
+	@Autowired
 	@Qualifier("myStructureDefinitionDaoDstu2")
 	protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
 	@Autowired
@@ -171,10 +177,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myValueSetDaoDstu2")
 	protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
-	@Autowired
-	protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
-	@Autowired
-	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
 
 	@Before
 	public void beforeCreateInterceptor() {

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

@@ -86,8 +86,7 @@ import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
-import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
+import ca.uhn.fhir.jpa.search.*;
-import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
@@ -108,13 +107,13 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
-	//	@Autowired
+	// @Autowired
-//	protected HapiWorkerContext myHapiWorkerContext;
+	// protected HapiWorkerContext myHapiWorkerContext;
 	@Autowired
 	@Qualifier("myAllergyIntoleranceDaoDstu3")
 	protected IFhirResourceDao<AllergyIntolerance> myAllergyIntoleranceDao;
 	@Autowired
-	protected ApplicationContext myAppCtx;	
+	protected ApplicationContext myAppCtx;
 	@Autowired
 	@Qualifier("myAppointmentDaoDstu3")
 	protected IFhirResourceDao<Appointment> myAppointmentDao;
@@ -124,7 +123,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myBundleDaoDstu3")
 	protected IFhirResourceDao<Bundle> myBundleDao;
-@Autowired
+	@Autowired
 	@Qualifier("myCarePlanDaoDstu3")
 	protected IFhirResourceDao<CarePlan> myCarePlanDao;
 	@Autowired
@@ -195,6 +194,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myOrganizationDaoDstu3")
 	protected IFhirResourceDao<Organization> myOrganizationDao;
 	@Autowired
+	protected DatabaseBackedPagingProvider myPagingProvider;
+	@Autowired
 	@Qualifier("myPatientDaoDstu3")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTransactionSearchDstu2Test.java

@@ -0,0 +1,304 @@
+package ca.uhn.fhir.jpa.provider;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.nullValue;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.*;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
+import ca.uhn.fhir.jpa.rp.dstu2.*;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.valueset.*;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.util.TestUtil;
+
+public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
+
+	private static RestfulServer myRestServer;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu2Test.class);
+	private static Server ourServer;
+	private static String ourServerBase;
+	private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
+	
+
+
+	
+	@SuppressWarnings("deprecation")
+	@After
+	public void after() {
+		myRestServer.setUseBrowserFriendlyContentTypes(true);
+		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
+		myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
+	}
+
+	@Before
+	public void before() {
+		mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
+		ourClient.registerInterceptor(mySimpleHeaderInterceptor);
+	}
+	
+	@Before
+	public void beforeStartServer() throws Exception {
+		if (myRestServer == null) {
+			PatientResourceProvider patientRp = new PatientResourceProvider();
+			patientRp.setDao(myPatientDao);
+
+			QuestionnaireResourceProviderDstu2 questionnaireRp = new QuestionnaireResourceProviderDstu2();
+			questionnaireRp.setDao(myQuestionnaireDao);
+
+			ObservationResourceProvider observationRp = new ObservationResourceProvider();
+			observationRp.setDao(myObservationDao);
+
+			OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
+			organizationRp.setDao(myOrganizationDao);
+
+			RestfulServer restServer = new RestfulServer(ourCtx);
+			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
+
+			restServer.setPlainProviders(mySystemProvider);
+
+			int myPort = RandomServerPortProvider.findFreePort();
+			ourServer = new Server(myPort);
+
+			ServletContextHandler proxyHandler = new ServletContextHandler();
+			proxyHandler.setContextPath("/");
+
+			ourServerBase = "http://localhost:" + myPort + "/fhir/context";
+
+			ServletHolder servletHolder = new ServletHolder();
+			servletHolder.setServlet(restServer);
+			proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+
+			ourCtx = FhirContext.forDstu2();
+			restServer.setFhirContext(ourCtx);
+
+			ourServer.setHandler(proxyHandler);
+			ourServer.start();
+
+			ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
+			ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+			myRestServer = restServer;
+		}
+		
+		myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
+		myRestServer.setPagingProvider(myPagingProvider);
+	}
+	
+
+	private List<String> create20Patients() {
+		List<String> ids = new ArrayList<String>();
+		for (int i = 0; i < 20; i++) {
+			Patient patient = new Patient();
+			patient.setGender(AdministrativeGenderEnum.MALE);
+			patient.addIdentifier().setSystem("urn:foo").setValue("A");
+			patient.addName().addFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
+			String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
+			ids.add(id);
+		}
+		return ids;
+	}
+
+	@Test
+	public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.BATCH);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerbEnum.GET)
+			.setUrl("Patient?_count=5");
+		
+		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		assertEquals(null, respBundle.getLink("next"));
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+	}
+	
+	@Test
+	public void testBatchWithGetNormalSearch() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.BATCH);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerbEnum.GET)
+			.setUrl("Patient?_count=5&_sort=name");
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		
+		String nextPageLink = respBundle.getLink("next").getUrl();
+		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
+		respBundle = output;
+		assertEquals(5, respBundle.getEntry().size());
+		actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
+	}
+
+	/**
+	 * 30 searches in one batch! Whoa!
+	 */
+	@Test
+	public void testBatchWithManyGets() throws Exception {
+		List<String> ids = create20Patients();
+
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.BATCH);
+		for (int i = 0; i < 30; i++) {
+			input
+				.addEntry()
+				.getRequest()
+				.setMethod(HTTPVerbEnum.GET)
+				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
+		}
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(30, output.getEntry().size());
+		for (int i = 0; i < 30; i++) {
+			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
+			assertEquals(5, respBundle.getEntry().size());
+			assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
+			List<String> actualIds = toIds(respBundle);
+			assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		}
+	}
+
+	@Test
+	public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.TRANSACTION);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerbEnum.GET)
+			.setUrl("Patient?_count=5");
+		
+		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		assertEquals(null, respBundle.getLink("next"));
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+	}
+	
+	@Test
+	public void testTransactionWithGetNormalSearch() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.TRANSACTION);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerbEnum.GET)
+			.setUrl("Patient?_count=5&_sort=name");
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		
+		String nextPageLink = respBundle.getLink("next").getUrl();
+		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
+		respBundle = output;
+		assertEquals(5, respBundle.getEntry().size());
+		actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
+	}
+
+	/**
+	 * 30 searches in one Transaction! Whoa!
+	 */
+	@Test
+	public void testTransactionWithManyGets() throws Exception {
+		List<String> ids = create20Patients();
+
+		
+		Bundle input = new Bundle();
+		input.setType(BundleTypeEnum.TRANSACTION);
+		for (int i = 0; i < 30; i++) {
+			input
+				.addEntry()
+				.getRequest()
+				.setMethod(HTTPVerbEnum.GET)
+				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
+		}
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(30, output.getEntry().size());
+		for (int i = 0; i < 30; i++) {
+			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
+			assertEquals(5, respBundle.getEntry().size());
+			assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
+			List<String> actualIds = toIds(respBundle);
+			assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		}
+	}
+
+	private List<String> toIds(Bundle theRespBundle) {
+		ArrayList<String> retVal = new ArrayList<String>();
+		for (Entry next : theRespBundle.getEntry()) {
+			retVal.add(next.getResource().getIdElement().toUnqualifiedVersionless().getValue());
+		}
+		return retVal;
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java

@@ -58,6 +58,7 @@ import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.jpa.rp.dstu3.ObservationResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.OrganizationResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu3.PatientResourceProvider;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
@@ -202,7 +203,6 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 			organizationRp.setDao(myOrganizationDao);
 
 			RestfulServer restServer = new RestfulServer(ourCtx);
-			restServer.setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(10));
 			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
 
 			restServer.setPlainProviders(mySystemProvider);
@@ -237,6 +237,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
 		}
 		
 		myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
+		myRestServer.setPagingProvider(myPagingProvider);
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java

@@ -0,0 +1,358 @@
+package ca.uhn.fhir.jpa.provider.dstu3;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.nullValue;
+import static org.hamcrest.Matchers.startsWith;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.Header;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Bundle.*;
+import org.hl7.fhir.dstu3.model.DecimalType;
+import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.OperationDefinition;
+import org.hl7.fhir.dstu3.model.OperationOutcome;
+import org.hl7.fhir.dstu3.model.Organization;
+import org.hl7.fhir.dstu3.model.Parameters;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
+import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
+import ca.uhn.fhir.jpa.rp.dstu3.ObservationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu3.OrganizationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu3.PatientResourceProvider;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+
+public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
+
+	private static RestfulServer myRestServer;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx;
+	private static CloseableHttpClient ourHttpClient;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu3Test.class);
+	private static Server ourServer;
+	private static String ourServerBase;
+	private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
+
+
+	
+	@SuppressWarnings("deprecation")
+	@After
+	public void after() {
+		myRestServer.setUseBrowserFriendlyContentTypes(true);
+		ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
+		myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
+	}
+
+	@Before
+	public void before() {
+		mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
+		ourClient.registerInterceptor(mySimpleHeaderInterceptor);
+	}
+	
+	@Before
+	public void beforeStartServer() throws Exception {
+		if (myRestServer == null) {
+			PatientResourceProvider patientRp = new PatientResourceProvider();
+			patientRp.setDao(myPatientDao);
+
+			QuestionnaireResourceProviderDstu3 questionnaireRp = new QuestionnaireResourceProviderDstu3();
+			questionnaireRp.setDao(myQuestionnaireDao);
+
+			ObservationResourceProvider observationRp = new ObservationResourceProvider();
+			observationRp.setDao(myObservationDao);
+
+			OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
+			organizationRp.setDao(myOrganizationDao);
+
+			RestfulServer restServer = new RestfulServer(ourCtx);
+			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
+
+			restServer.setPlainProviders(mySystemProvider);
+
+			int myPort = RandomServerPortProvider.findFreePort();
+			ourServer = new Server(myPort);
+
+			ServletContextHandler proxyHandler = new ServletContextHandler();
+			proxyHandler.setContextPath("/");
+
+			ourServerBase = "http://localhost:" + myPort + "/fhir/context";
+
+			ServletHolder servletHolder = new ServletHolder();
+			servletHolder.setServlet(restServer);
+			proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+
+			ourCtx = FhirContext.forDstu3();
+			restServer.setFhirContext(ourCtx);
+
+			ourServer.setHandler(proxyHandler);
+			ourServer.start();
+
+			PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+			HttpClientBuilder builder = HttpClientBuilder.create();
+			builder.setConnectionManager(connectionManager);
+			ourHttpClient = builder.build();
+
+			ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
+			ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+			ourClient.setLogRequestAndResponse(true);
+			myRestServer = restServer;
+		}
+		
+		myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
+		myRestServer.setPagingProvider(myPagingProvider);
+	}
+	
+
+	private List<String> create20Patients() {
+		List<String> ids = new ArrayList<String>();
+		for (int i = 0; i < 20; i++) {
+			Patient patient = new Patient();
+			patient.setGender(AdministrativeGender.MALE);
+			patient.addIdentifier().setSystem("urn:foo").setValue("A");
+			patient.addName().setFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
+			String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
+			ids.add(id);
+		}
+		return ids;
+	}
+
+	@Test
+	public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.BATCH);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerb.GET)
+			.setUrl("Patient?_count=5");
+		
+		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		assertEquals(null, respBundle.getLink("next"));
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+	}
+	
+	@Test
+	public void testBatchWithGetNormalSearch() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.BATCH);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerb.GET)
+			.setUrl("Patient?_count=5&_sort=name");
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		
+		String nextPageLink = respBundle.getLink("next").getUrl();
+		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
+		respBundle = output;
+		assertEquals(5, respBundle.getEntry().size());
+		actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
+	}
+
+	/**
+	 * 30 searches in one batch! Whoa!
+	 */
+	@Test
+	public void testBatchWithManyGets() throws Exception {
+		List<String> ids = create20Patients();
+
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.BATCH);
+		for (int i = 0; i < 30; i++) {
+			input
+				.addEntry()
+				.getRequest()
+				.setMethod(HTTPVerb.GET)
+				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
+		}
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(30, output.getEntry().size());
+		for (int i = 0; i < 30; i++) {
+			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
+			assertEquals(5, respBundle.getEntry().size());
+			assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
+			List<String> actualIds = toIds(respBundle);
+			assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		}
+	}
+
+	@Test
+	public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.TRANSACTION);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerb.GET)
+			.setUrl("Patient?_count=5");
+		
+		myDaoConfig.setMaximumSearchResultCountInTransaction(100);
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		assertEquals(null, respBundle.getLink("next"));
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+	}
+	
+	@Test
+	public void testTransactionWithGetNormalSearch() throws Exception {
+		List<String> ids = create20Patients();
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.TRANSACTION);
+		input
+			.addEntry()
+			.getRequest()
+			.setMethod(HTTPVerb.GET)
+			.setUrl("Patient?_count=5&_sort=name");
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(1, output.getEntry().size());
+		Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
+		assertEquals(5, respBundle.getEntry().size());
+		List<String> actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		
+		String nextPageLink = respBundle.getLink("next").getUrl();
+		output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
+		respBundle = output;
+		assertEquals(5, respBundle.getEntry().size());
+		actualIds = toIds(respBundle);
+		assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
+	}
+
+	/**
+	 * 30 searches in one Transaction! Whoa!
+	 */
+	@Test
+	public void testTransactionWithManyGets() throws Exception {
+		List<String> ids = create20Patients();
+
+		
+		Bundle input = new Bundle();
+		input.setType(BundleType.TRANSACTION);
+		for (int i = 0; i < 30; i++) {
+			input
+				.addEntry()
+				.getRequest()
+				.setMethod(HTTPVerb.GET)
+				.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
+		}
+		
+		Bundle output = ourClient.transaction().withBundle(input).execute();
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+		
+		assertEquals(30, output.getEntry().size());
+		for (int i = 0; i < 30; i++) {
+			Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
+			assertEquals(5, respBundle.getEntry().size());
+			assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
+			List<String> actualIds = toIds(respBundle);
+			assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
+		}
+	}
+
+	private List<String> toIds(Bundle theRespBundle) {
+		ArrayList<String> retVal = new ArrayList<String>();
+		for (BundleEntryComponent next : theRespBundle.getEntry()) {
+			retVal.add(next.getResource().getIdElement().toUnqualifiedVersionless().getValue());
+		}
+		return retVal;
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.rest.server.provider.dstu2;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
 /*
  * #%L
  * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@@ -10,7 +11,7 @@ package ca.uhn.fhir.rest.server.provider.dstu2;
  * 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
+ * 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,
@@ -62,6 +63,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu2BundleFactory.class);
 
 	private Bundle myBundle;
 	private FhirContext myContext;
@@ -223,7 +225,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 				entry.getRequest().getMethodElement().setValueAsString(httpVerb.getCode());
 			}
 			populateBundleEntryFullUrl(next, entry);
-			
+
 			BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
 			if (searchMode != null) {
 				entry.getSearch().getModeElement().setValue(searchMode.getCode());
@@ -257,7 +259,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 	public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated) {
 
 		myBase = theServerBase;
-		
+
 		if (myBundle.getId().isEmpty()) {
 			myBundle.setId(UUID.randomUUID().toString());
 		}
@@ -302,7 +304,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 	public void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
 			boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
 		myBase = theServerBase;
-		
+
 		int numToReturn;
 		String searchId = null;
 		List<IBaseResource> resourceList;
@@ -327,7 +329,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 			if (numTotalResults != null) {
 				numToReturn = Math.min(numToReturn, numTotalResults - theOffset);
 			}
-			
+
 			if (numToReturn > 0) {
 				resourceList = theResult.getResources(theOffset, numToReturn + theOffset);
 			} else {
@@ -340,7 +342,9 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 			} else {
 				if (numTotalResults == null || numTotalResults > numToReturn) {
 					searchId = pagingProvider.storeResultList(theResult);
-					Validate.notNull(searchId, "Paging provider returned null searchId");
+					if (isBlank(searchId)) {
+						ourLog.info("Found {} results but paging provider did not provide an ID to use for paging", numTotalResults);
+					}
 				}
 			}
 		}

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/rest/server/Dstu3BundleFactory.java

@@ -1,5 +1,6 @@
 package org.hl7.fhir.dstu3.hapi.rest.server;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
 /*
  * #%L
  * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@@ -44,7 +45,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
-
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu3BundleFactory.class);
   private Bundle myBundle;
   private FhirContext myContext;
   private String myBase;
@@ -336,7 +337,9 @@ public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
       } else {
         if (numTotalResults == null || numTotalResults > numToReturn) {
           searchId = pagingProvider.storeResultList(theResult);
-          Validate.notNull(searchId, "Paging provider returned null searchId");
+          if (isBlank(searchId)) {
+            ourLog.info("Found {} results but paging provider did not provide an ID to use for paging", numTotalResults);
+          }
         }
       }
     }

src/changes/changes.xml

@@ -85,6 +85,23 @@
 				(tags, profiles, and security labels) on an individual resource. The default
 				is 1000.
 			</action>
+			<action type="add">
+				When executing a search (HTTP GET) as a nested operation in in a transaction or 
+				batch operation, the search now returns a normal page of results with a link to
+				the next page, like any other search would. Previously the search would return
+				a small number of results with no paging performed, so this change brings transaction
+				and batch processing in line with other types of search.
+			</action>
+			<action type="add">
+				JPA server no longer returns an OperationOutcome resource as the first resource
+				in the Bundle for a response to a batch operation. This behaviour was previously
+				present, but was not specified in the FHIR specification so it caused confusion and
+				was inconsistent with behaviour in other servers.
+			</action>
+			<action type="fix">
+				Fix a regression in HAPI FHIR 2.5 JPA server where executing a search in a
+				transaction or batch operation caused an exception.
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">