Fix #241 and fix #247 - Don't encode UUID IDs on resources, and preserve

bundle type when retrieving pages

hapi-fhir-base/pom.xml

@@ -40,6 +40,11 @@
 			<artifactId>thymeleaf</artifactId>
 			<optional>true</optional>
 		</dependency>
+		<dependency>
+			<groupId>org.javassist</groupId>
+			<artifactId>javassist</artifactId>
+			<optional>true</optional>
+		</dependency>
 
 		<!-- Only required for CORS support -->
 		<dependency>

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationMethodBinding.java

@@ -186,7 +186,7 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
 	
 	@Override
 	protected BundleTypeEnum getResponseBundleType() {
-		return null;
+		return BundleTypeEnum.COLLECTION;
 	}
 
 	public List<ReturnType> getReturnParams() {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/Constants.java

@@ -150,6 +150,11 @@ public class Constants {
 	public static final String PARAM_CONTENT = "_content";
 	public static final String PARAM_TEXT = "_text";
 	
+	/**
+	 * Used in paging links
+	 */
+	public static final Object PARAM_BUNDLETYPE = "_bundletype";
+
 	static {
 		Map<String, EncodingEnum> valToEncoding = new HashMap<String, EncodingEnum>();
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -58,6 +58,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.rest.annotation.Destroy;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Initialize;
@@ -511,7 +512,13 @@ public class RestfulServer extends HttpServlet {
 		String linkSelfBase = getServerAddressStrategy().determineServerBase(getServletContext(), theRequest.getServletRequest());
 		String linkSelf = linkSelfBase + theRequest.getCompleteUrl().substring(theRequest.getCompleteUrl().indexOf('?'));
 
-		bundleFactory.initializeBundleFromBundleProvider(this, resultList, responseEncoding, theRequest.getFhirServerBase(), linkSelf, prettyPrint, start, count, thePagingAction, null, includes);
+		BundleTypeEnum bundleType = null;
+		String[] bundleTypeValues = theRequest.getParameters().get(Constants.PARAM_BUNDLETYPE);
+		if (bundleTypeValues != null) {
+			bundleType = BundleTypeEnum.VALUESET_BINDER.fromCodeString(bundleTypeValues[0]);
+		}
+		
+		bundleFactory.initializeBundleFromBundleProvider(this, resultList, responseEncoding, theRequest.getFhirServerBase(), linkSelf, prettyPrint, start, count, thePagingAction, bundleType, includes);
 
 		Bundle bundle = bundleFactory.getDstu1Bundle();
 		if (bundle != null) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java

@@ -60,6 +60,7 @@ import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.PreferReturnEnum;
 import ca.uhn.fhir.rest.api.SummaryEnum;
@@ -132,7 +133,7 @@ public class RestfulServerUtils {
 		}
 	}
 
-	public static String createPagingLink(Set<Include> theIncludes, String theServerBase, String theSearchId, int theOffset, int theCount, EncodingEnum theResponseEncoding, boolean thePrettyPrint) {
+	public static String createPagingLink(Set<Include> theIncludes, String theServerBase, String theSearchId, int theOffset, int theCount, EncodingEnum theResponseEncoding, boolean thePrettyPrint, BundleTypeEnum theBundleType) {
 		try {
 			StringBuilder b = new StringBuilder();
 			b.append(theServerBase);
@@ -173,6 +174,13 @@ public class RestfulServerUtils {
 				}
 			}
 			
+			if (theBundleType != null) {
+				b.append('&');
+				b.append(Constants.PARAM_BUNDLETYPE);
+				b.append('=');
+				b.append(theBundleType.getCode());
+			}
+
 			return b.toString();
 		} catch (UnsupportedEncodingException e) {
 			throw new Error("UTF-8 not supported", e);// should not happen

hapi-fhir-jpaserver-base/pom.xml

@@ -75,6 +75,12 @@
 			<scope>test</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>org.javassist</groupId>
+			<artifactId>javassist</artifactId>
+			<version>3.20.0-GA</version>
+		</dependency>
+
 		<dependency>
 			<groupId>com.phloc</groupId>
 			<artifactId>phloc-schematron</artifactId>
@@ -345,10 +351,7 @@
 							<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml</targetResourceSpringBeansFile>
 							<baseResourceNames></baseResourceNames>
 							<excludeResourceNames>
-								<!-- 
+								<!-- <excludeResourceName>OperationDefinition</excludeResourceName> <excludeResourceName>OperationOutcome</excludeResourceName> -->
-								<excludeResourceName>OperationDefinition</excludeResourceName>
-								<excludeResourceName>OperationOutcome</excludeResourceName>
-								-->
 							</excludeResourceNames>
 						</configuration>
 					</execution>

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

@@ -101,20 +101,20 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	protected EntityManager myEntityManager;
 
 	@Autowired
-	private PlatformTransactionManager myPlatformTransactionManager;
+	protected PlatformTransactionManager myPlatformTransactionManager;
 
 	@Autowired
 	private DaoConfig myDaoConfig;
 
 	@Autowired(required = false)
-	private ISearchDao mySearchDao;
+	protected ISearchDao mySearchDao;
 
 	private String myResourceName;
 	private Class<T> myResourceType;
 	private String mySecondaryPrimaryKeyParamName;
 
 	@Autowired()
-	private ISearchResultDao mySearchResultDao;
+	protected ISearchResultDao mySearchResultDao;
 
 	@Override
 	public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java

@@ -30,21 +30,21 @@ import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.primitive.UnsignedIntDt;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 
 public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
 
-	@Override
+	private IBundleProvider doEverythingOperation(IIdType theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
-	public IBundleProvider patientInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		if (theCount != null) {
 			paramMap.setCount(theCount.getValue());
 		}
 
-//		paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
 		paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
 		paramMap.setEverythingMode(theId != null ? EverythingModeEnum.PATIENT_INSTANCE : EverythingModeEnum.PATIENT_TYPE);
 		paramMap.setSort(theSort);
@@ -52,13 +52,28 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
 		if (theId != null) {
 			paramMap.add("_id", new StringParam(theId.getIdPart()));
 		}
-		ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
+		
-		return retVal;
+		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this);
+		builder.setType(getResourceType(), getResourceName());
+		return builder.search(paramMap);
+	}
+
+	@Override
+	public IBundleProvider patientInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
+		// Notify interceptors
+		ActionRequestDetails requestDetails = new ActionRequestDetails(null, getResourceName());
+		notifyInterceptors(RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE, requestDetails);
+
+		return doEverythingOperation(theId, theCount, theLastUpdated, theSort);
 	}
 
 	@Override
 	public IBundleProvider patientTypeEverything(HttpServletRequest theServletRequest, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
-		return patientInstanceEverything(theServletRequest, null, theCount, theLastUpdated, theSort);
+		// Notify interceptors
+		ActionRequestDetails requestDetails = new ActionRequestDetails(null, getResourceName());
+		notifyInterceptors(RestOperationTypeEnum.EXTENDED_OPERATION_TYPE, requestDetails);
+
+		return doEverythingOperation(null, theCount, theLastUpdated, theSort);
 	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -134,6 +134,38 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		myRestServer.unregisterInterceptor(interceptor);
 	}
 
+	@Test
+	public void testEverythingReturnsCorrectBundleType() throws Exception {
+		myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
+		myRestServer.setPagingProvider(new FifoMemoryPagingProvider(1).setDefaultPageSize(10));
+		ResponseHighlighterInterceptor interceptor = new ResponseHighlighterInterceptor();
+		myRestServer.registerInterceptor(interceptor);
+
+		for (int i = 0; i < 11; i++) {
+			Patient p = new Patient();
+			p.addName().addFamily("Name" + i);
+			ourClient.create().resource(p).execute();
+		}
+
+		HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");
+		get.addHeader("Accept", "application/xml+fhir");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			String response = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(response);
+			assertThat(response, not(containsString("_format")));
+			assertEquals(200, http.getStatusLine().getStatusCode());
+			
+			Bundle responseBundle = ourCtx.newXmlParser().parseResource(Bundle.class, response);
+			assertEquals(BundleTypeEnum.COLLECTION, responseBundle.getTypeElement().getValueAsEnum());
+			
+		} finally {
+			http.close();
+		}
+
+		myRestServer.unregisterInterceptor(interceptor);
+	}
+
 	@Test
 	public void testEverythingType() throws Exception {
 		HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");

hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/rest/server/Dstu1BundleFactory.java

@@ -255,11 +255,11 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 	
 			if (searchId != null) {
 				if (theOffset + numToReturn < theResult.size()) {
-					myBundle.getLinkNext().setValue(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
+					myBundle.getLinkNext().setValue(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint, theBundleType));
 				}
 				if (theOffset > 0) {
 					int start = Math.max(0, theOffset - limit);
-					myBundle.getLinkPrevious().setValue(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
+					myBundle.getLinkPrevious().setValue(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint, theBundleType));
 				}
 			}
 		}

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/PagingTest.java

@@ -73,7 +73,7 @@ public class PagingTest {
 			assertEquals(5, bundle.getEntries().size());
 			assertEquals("0", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("4", bundle.getEntries().get(4).getResource().getId().getIdPart());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=5&" + Constants.PARAM_COUNT + "=5&_format=xml&_pretty=true", bundle.getLinkNext()
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=5&" + Constants.PARAM_COUNT + "=5&_format=xml&_pretty=true&_bundletype=searchset", bundle.getLinkNext()
 					.getValue());
 			assertNull(bundle.getLinkPrevious().getValue());
 			link = bundle.getLinkNext().getValue();
@@ -90,7 +90,7 @@ public class PagingTest {
 			assertEquals("5", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("9", bundle.getEntries().get(4).getResource().getId().getIdPart());
 			assertNull(bundle.getLinkNext().getValue());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=5&_format=json&_pretty=true", bundle.getLinkPrevious()
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=5&_format=json&_pretty=true&_bundletype=searchset", bundle.getLinkPrevious()
 					.getValue());
 		}
 	}
@@ -141,7 +141,7 @@ public class PagingTest {
 			assertEquals(2, bundle.getEntries().size());
 			assertEquals("0", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("1", bundle.getEntries().get(1).getResource().getId().getIdPart());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_format=xml", bundle.getLinkNext().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_format=xml&_bundletype=searchset", bundle.getLinkNext().getValue());
 			assertNull(bundle.getLinkPrevious().getValue());
 			link = bundle.getLinkNext().getValue();
 		}
@@ -156,9 +156,9 @@ public class PagingTest {
 			assertEquals(2, bundle.getEntries().size());
 			assertEquals("2", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("3", bundle.getEntries().get(1).getResource().getId().getIdPart());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=4&" + Constants.PARAM_COUNT + "=2&_format=xml", bundle.getLinkNext().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=4&" + Constants.PARAM_COUNT + "=2&_format=xml&_bundletype=searchset", bundle.getLinkNext().getValue());
-			assertEquals(base + '/' + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_format=xml", bundle.getLinkSelf().getValue());
+			assertEquals(base + '/' + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_format=xml&_bundletype=searchset", bundle.getLinkSelf().getValue());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=2&_format=xml", bundle.getLinkPrevious().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=2&_format=xml&_bundletype=searchset", bundle.getLinkPrevious().getValue());
 		}
 	}
 	
@@ -236,7 +236,7 @@ public class PagingTest {
 			assertEquals(2, bundle.getEntries().size());
 			assertEquals("0", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("1", bundle.getEntries().get(1).getResource().getId().getIdPart());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2", bundle.getLinkNext().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_bundletype=searchset", bundle.getLinkNext().getValue());
 			assertNull(bundle.getLinkPrevious().getValue());
 			link = bundle.getLinkNext().getValue();
 		}
@@ -251,9 +251,9 @@ public class PagingTest {
 			assertEquals(2, bundle.getEntries().size());
 			assertEquals("2", bundle.getEntries().get(0).getResource().getId().getIdPart());
 			assertEquals("3", bundle.getEntries().get(1).getResource().getId().getIdPart());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=4&" + Constants.PARAM_COUNT + "=2", bundle.getLinkNext().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=4&" + Constants.PARAM_COUNT + "=2&_bundletype=searchset", bundle.getLinkNext().getValue());
-			assertEquals(base + '/' + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2", bundle.getLinkSelf().getValue());
+			assertEquals(base + '/' + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=2&" + Constants.PARAM_COUNT + "=2&_bundletype=searchset", bundle.getLinkSelf().getValue());
-			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=2", bundle.getLinkPrevious().getValue());
+			assertEquals(base + '?' + Constants.PARAM_PAGINGACTION + "=ABCD&" + Constants.PARAM_PAGINGOFFSET + "=0&" + Constants.PARAM_COUNT + "=2&_bundletype=searchset", bundle.getLinkPrevious().getValue());
 		}
 
 	}

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

@@ -349,7 +349,11 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 			}
 
 			numToReturn = Math.min(numToReturn, theResult.size() - theOffset);
+			if (numToReturn > 0) {
 				resourceList = theResult.getResources(theOffset, numToReturn + theOffset);
+			} else {
+				resourceList = Collections.emptyList();
+			}
 			RestfulServerUtils.validateResourceListNotNull(resourceList);
 
 			if (theSearchId != null) {
@@ -390,12 +394,12 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 			if (searchId != null) {
 				if (theOffset + numToReturn < theResult.size()) {
 					myBundle.addLink().setRelation(Constants.LINK_NEXT)
-							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
+							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint, theBundleType));
 				}
 				if (theOffset > 0) {
 					int start = Math.max(0, theOffset - limit);
 					myBundle.addLink().setRelation(Constants.LINK_PREVIOUS)
-							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
+							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint, theBundleType));
 				}
 			}
 		}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -1,19 +1,24 @@
 package ca.uhn.fhir.parser;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.emptyString;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
-import ca.uhn.fhir.model.dstu2.resource.*;
-import ca.uhn.fhir.model.dstu2.valueset.*;
 import org.apache.commons.io.IOUtils;
 import org.hamcrest.Matchers;
 import org.junit.Assert;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -29,7 +34,22 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Binary;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.Condition;
+import ca.uhn.fhir.model.dstu2.resource.Conformance;
+import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
+import ca.uhn.fhir.model.dstu2.resource.Medication;
+import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.QuestionnaireResponse;
+import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
+import ca.uhn.fhir.model.dstu2.valueset.ConditionVerificationStatusEnum;
+import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
+import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -1019,7 +1039,6 @@ public class JsonParserDstu2Test {
 	}
 
 	// see #241
-	@Ignore
 	@Test
 	public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception {
 		Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED);
@@ -1030,7 +1049,8 @@ public class JsonParserDstu2Test {
 		bundle.getEntry().add(entry);
 		IParser parser = ourCtx.newJsonParser();
 		String json = parser.encodeResourceToString(bundle);
+		ourLog.info(json);
 		bundle = (ca.uhn.fhir.model.dstu2.resource.Bundle) parser.parseResource(json);
-		assertTrue(bundle.getEntry().get(0).getResource().getIdElement().isEmpty());
+		assertThat(json, not(containsString("\"id\"")));
 	}
 }

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/SearchDstu2Test.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.rest.server;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.startsWith;
 import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
@@ -36,12 +37,14 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Link;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.param.DateAndListParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.util.PatternMatcher;
 import ca.uhn.fhir.util.PortUtil;
 
@@ -74,7 +77,6 @@ public class SearchDstu2Test {
 		assertEquals(400, status.getStatusLine().getStatusCode());
 	}
 
-
 	@Test
 	public void testSearchReferenceParams01() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=searchNoList&ref=123");
@@ -142,6 +144,52 @@ public class SearchDstu2Test {
 		assertEquals("2002", ourLastDateAndList.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(1).getValueAsString());
 	}
 
+	/**
+	 * See #247
+	 */
+	@Test
+	public void testSearchPagesAllHaveCorrectBundleType() throws Exception {
+		Bundle resp;
+		{
+			HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?searchHugeResults=yes&_count=10&_pretty=true");
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			IOUtils.closeQuietly(status.getEntity().getContent());
+			ourLog.info(responseContent);
+			resp = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
+			assertEquals("searchset", resp.getType());
+			assertEquals(100, resp.getTotal().intValue());
+		}
+		Link nextLink = resp.getLink("next");
+		assertThat(nextLink.getUrl(), startsWith("http://"));
+
+		// Now try the next page
+		{
+			HttpGet httpGet = new HttpGet(nextLink.getUrl());
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			IOUtils.closeQuietly(status.getEntity().getContent());
+			ourLog.info(responseContent);
+			resp = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
+			assertEquals("searchset", resp.getType());
+			assertEquals(100, resp.getTotal().intValue());
+		}
+		
+		nextLink = resp.getLink("next");
+		assertThat(nextLink.getUrl(), startsWith("http://"));
+
+		// Now try a third page
+		{
+			HttpGet httpGet = new HttpGet(nextLink.getUrl());
+			HttpResponse status = ourClient.execute(httpGet);
+			String responseContent = IOUtils.toString(status.getEntity().getContent());
+			IOUtils.closeQuietly(status.getEntity().getContent());
+			ourLog.info(responseContent);
+			resp = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
+			assertEquals("searchset", resp.getType());
+			assertEquals(100, resp.getTotal().intValue());
+		}
+	}
 
 	@Test
 	public void testSearchByPost() throws Exception {
@@ -196,7 +244,6 @@ public class SearchDstu2Test {
 
 	}
 
-	
 	@Test
 	public void testSearchBlacklist01Failing() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=searchBlacklist01&ref.black1=value");
@@ -206,6 +253,7 @@ public class SearchDstu2Test {
 		ourLog.info(responseContent);
 		assertEquals(400, status.getStatusLine().getStatusCode());
 	}
+
 	@Test
 	public void testSearchBlacklist01Passing() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=searchBlacklist01&ref.white1=value");
@@ -301,6 +349,7 @@ public class SearchDstu2Test {
 
 		ServletHandler proxyHandler = new ServletHandler();
 		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
 
 		servlet.setResourceProviders(patientProvider);
 		ServletHolder servletHolder = new ServletHolder(servlet);
@@ -320,7 +369,6 @@ public class SearchDstu2Test {
 	 */
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 
-
 		@Override
 		public Class<? extends IResource> getResourceType() {
 			return Patient.class;
@@ -359,6 +407,21 @@ public class SearchDstu2Test {
 		}
 		//@formatter:on
 
+		//@formatter:off
+		@Search()
+		public List<Patient> searchHugeResults(
+				@RequiredParam(name = "searchHugeResults") StringParam theParam) {
+			ourLastMethod = "searchHugeResults";
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+			for (int i = 0; i < 100; i++) {
+				Patient patient = new Patient();
+				patient.setId("" + i);
+				retVal.add(patient.addIdentifier(new IdentifierDt("SYSTEM", "CODE"+ i)));
+			}
+			return retVal;
+		}
+		//@formatter:on
+
 		//@formatter:off
 		@Search(queryName="searchBlacklist01")
 		public List<Patient> searchBlacklist01(
@@ -368,7 +431,7 @@ public class SearchDstu2Test {
 		}
 		//@formatter:on
 
-		@Search(queryName="searchWithBundleProvider")
+		@Search(queryName = "searchWithBundleProvider")
 		public IBundleProvider searchWithBundleProvider() {
 			return new IBundleProvider() {
 
@@ -394,7 +457,7 @@ public class SearchDstu2Test {
 			};
 		}
 
-		@Search(queryName="searchWithRef")
+		@Search(queryName = "searchWithRef")
 		public Patient searchWithRef() {
 			Patient patient = new Patient();
 			patient.setId("Patient/1/_history/1");

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2hl7org/Dstu2Hl7OrgBundleFactory.java

@@ -364,12 +364,12 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
       if (searchId != null) {
         if (theOffset + numToReturn < theResult.size()) {
           myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theIncludes,
-              theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
+              theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint, theBundleType));
         }
         if (theOffset > 0) {
           int start = Math.max(0, theOffset - limit);
           myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(
-              theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
+              theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint, theBundleType));
         }
       }
     }

pom.xml

@@ -224,9 +224,8 @@
 		<apache_httpclient_version>4.4</apache_httpclient_version>
 		<apache_httpcore_version>4.4</apache_httpcore_version>
 		<derby_version>10.12.1.1</derby_version>
-		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this 
+		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this version with caution! Also note that if 
-			version with caution! Also note that if you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration 
+			you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration for that plugin... -->
-			for that plugin... -->
 		<hibernate_version>5.0.2.Final</hibernate_version>
 		<hibernate_validator_version>5.2.1.Final</hibernate_validator_version>
 		<jetty_version>9.3.4.v20151007</jetty_version>
@@ -245,11 +244,7 @@
 		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 		<xmlunit_version>1.6</xmlunit_version>
 
-		<!--
+		<!-- We are aiming to still work on a very old version of SLF4j even though we depend on the newest, just to be nice to users of the API. This version is tested in the hapi-fhir-cobertura. -->
-		We are aiming to still work on a very old version of SLF4j even though
-		we depend on the newest, just to be nice to users of the API. This version
-		is tested in the hapi-fhir-cobertura. 
-		-->
 		<slf4j_target_version>1.6.0</slf4j_target_version>
 
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
@@ -502,6 +497,11 @@
 				<artifactId>hibernate-validator</artifactId>
 				<version>${hibernate_validator_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.javassist</groupId>
+				<artifactId>javassist</artifactId>
+				<version>3.20.0-GA</version>
+			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-android</artifactId>
@@ -923,43 +923,43 @@
 						<configuration>
 							<target>
 								<copy todir="target/site/apidocs">
-									<fileset dir="hapi-fhir-base/target/site/apidocs" />
+									<fileset dir="hapi-fhir-base/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-dstu">
-									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-hl7org-dstu2">
-									<fileset dir="hapi-fhir-structures-hl7org-dstu2/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-hl7org-dstu2/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-dstu2">
-									<fileset dir="hapi-fhir-structures-dstu2/target/site/apidocs" />
+									<fileset dir="hapi-fhir-structures-dstu2/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/apidocs-jpaserver">
-									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs" />
+									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs"/>
 								</copy>
 								<copy todir="target/site/xref-jpaserver">
-									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref" />
+									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref"/>
 								</copy>
 								<copy todir="target/site/xref-base">
-									<fileset dir="hapi-fhir-base/target/site/xref" />
+									<fileset dir="hapi-fhir-base/target/site/xref"/>
 								</copy>
 								<!-- <copy todir="target/site/cobertura"> <fileset dir="hapi-fhir-cobertura/target/site/cobertura" /> </copy> -->
 								<copy todir="target/site">
-									<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*" />
+									<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*"/>
 								</copy>
 								<echo>Fixing Checkstyle Report</echo>
 								<replace dir="target/site" summary="true">
-									<include name="checkstyle.html" />
+									<include name="checkstyle.html"/>
 									<replacetoken>"../../</replacetoken>
 									<replacevalue>"./</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken>http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css</replacetoken>
 									<replacevalue>./css/bootstrap-responsive.min.css</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="index.html" />
+									<include name="index.html"/>
 									<replacetoken><![CDATA[<h2 id="Welcome">Welcome</h2>]]></replacetoken>
 									<replacevalue><![CDATA[<div class="jumbotron subhead">
 		<div class="row" id="banner">
@@ -988,33 +988,33 @@
 							<target>
 								<echo>Adding Fontawesome</echo>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
 									<replacevalue><![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
 									<replacevalue><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Test Servers <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Documentation <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
-									<include name="*.html" />
+									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Get Help <]]></replacetoken>
 									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
 								</replace>
 								<echo>Changing Breadcrumbs</echo>
 								<replace dir="target/site" summary="true">
-									<include name="doc_*.html" />
+									<include name="doc_*.html"/>
 									<replacetoken><![CDATA[<li class="divider">/</li>]]></replacetoken>
 									<replacevalue><![CDATA[<li  class="divider">/</li>
 			<li><a href="docindex.html" title="Documentation">Documentation</a></li>
@@ -1065,8 +1065,8 @@
 								<echo>Adding Google analytics in target/site for &lt;body&gt;</echo>
 								<replace dir="target/site" summary="true">
 									<include name="**/*.html"></include>
-									<replacefilter token="#build#" value="${label}" />
+									<replacefilter token="#build#" value="${label}"/>
-									<replacefilter token="#version#" value="${project.version}" />
+									<replacefilter token="#version#" value="${project.version}"/>
 									<replacetoken><![CDATA[</body>]]></replacetoken>
 									<replacevalue><![CDATA[
 <script>
@@ -1204,9 +1204,8 @@
 
 	<reporting>
 		<plugins>
-			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> 
+			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> </reportSet> 
-				</reportSet> </reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> 
+				</reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> </plugin> -->
-				</plugin> -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-changes-plugin</artifactId>
@@ -1281,9 +1280,8 @@
 			</modules>
 			<build>
 				<plugins>
-					<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> 
+					<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> <goals> <goal>single</goal> </goals> 
-						<goals> <goal>single</goal> </goals> <configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> 
+						<configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> </descriptors> </configuration> </execution> </executions> </plugin> -->
-						</descriptors> </configuration> </execution> </executions> </plugin> -->
 				</plugins>
 			</build>
 

src/changes/changes.xml

@@ -212,7 +212,7 @@
 				<![CDATA[<a href="./apidocs-jpaserver/ca/uhn/fhir/jpa/dao/IJpaServerInterceptor.html">IJpaServerInterceptor</a>]]>
 				interceptors for JPA server which can be used for more fine grained operations.
 			</action>
-			<action type="fix">
+			<action type="fix" issue="241">
 				Parser (XML and JSON) shouldn't encode an ID tag in resources
 				which are part of a bundle when the resource has a UUID/OID
 				ID.
@@ -222,6 +222,11 @@
 				to declare that it should allow even parameters it doesn't 
 				understand.
 			</action>
+			<action type="fix" issue="247">
+				Correctly set the Bundle.type value on all pages of a search result in
+				the server, and correcltly set the same value in JPA server $everything
+				results.
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">