Revert change to make IdDt#isLocal() return true if the base is "urn:". This caused all kinds of regressions and was obviously a bad idea.

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdDt.java

@@ -401,15 +401,11 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 	}
 
 	/**
-	 * Returns <code>true</code> if the ID is a local reference (in other words, it begins with the '#' character
+	 * Returns <code>true</code> if the ID is a local reference (in other words, it begins with the '#' character)
-	 * or it begins with "cid:" or "urn:")
 	 */
 	@Override
 	public boolean isLocal() {
-		if (myBaseUrl == null) {
+		return "#".equals(myBaseUrl);
-			return false;
-		}
-		return "#".equals(myBaseUrl) || myBaseUrl.equals("cid:") || myBaseUrl.startsWith("urn:");
 	}
 
 	/**

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java

@@ -1672,6 +1672,16 @@ class ParserState<T> {
 			myExtension = theExtension;
 		}
 
+		@Override
+		public void attributeValue(String theName, String theValue) throws DataFormatException {
+			if ("url".equals(theName)) {
+				// The URL attribute is handles in the XML loop as a special case since it is "url" instead
+				// of "value" like every single other place
+				return;
+			}
+			super.attributeValue(theName, theValue);
+		}
+
 		@Override
 		public void endingElement() throws DataFormatException {
 			if (myExtension.getValue() != null && myExtension.getExtension().size() > 0) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java

@@ -85,8 +85,8 @@ public class ReferenceParam extends IdDt implements IQueryParameterType {
 		if (myBase.getMissing()!=null) {
 			return myBase.getValueAsQueryToken();
 		}
-		if (isLocal()) {
+		if (isBlank(getResourceType())) {
-			return getValue();
+			return getValue(); // e.g. urn:asdjd or 123 or cid:wieiuru or #1
 		} else {
 			return getIdPart();
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1.java

@@ -50,6 +50,11 @@ import ca.uhn.fhir.util.FhirTerser;
 public class FhirSystemDaoDstu1 extends BaseFhirSystemDao<List<IResource>> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu1.class);
 
+	@Override
+	public MetaDt metaGetOperation() {
+		throw new NotImplementedOperationException("meta not supported in DSTU1");
+	}
+
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public List<IResource> transaction(List<IResource> theResources) {
@@ -60,14 +65,14 @@ public class FhirSystemDaoDstu1 extends BaseFhirSystemDao<List<IResource>> {
 
 		for (int i = 0; i < theResources.size(); i++) {
 			IResource res = theResources.get(i);
-			if (res.getId().hasIdPart() && !res.getId().hasResourceType() && !res.getId().isLocal()) {
+			if (res.getId().hasIdPart() && !res.getId().hasResourceType() && !isPlaceholder(res.getId())) {
 				res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
 			}
 
 			/*
 			 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
 			 */
-			if (res.getId().isLocal()) {
+			if (isPlaceholder(res.getId())) {
 				if (!allIds.add(res.getId())) {
 					throw new InvalidRequestException("Transaction bundle contains multiple resources with ID: " + res.getId());
 				}
@@ -138,7 +143,7 @@ public class FhirSystemDaoDstu1 extends BaseFhirSystemDao<List<IResource>> {
 				} else {
 					throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionOperationWithMultipleMatchFailure", nextResouceOperationIn.name(), matchUrl, candidateMatches.size()));
 				}
-			} else if (nextId.isEmpty() || nextId.isLocal()) {
+			} else if (nextId.isEmpty() || isPlaceholder(nextId)) {
 				entity = null;
 			} else {
 				entity = tryToLoadEntity(nextId);
@@ -213,7 +218,7 @@ public class FhirSystemDaoDstu1 extends BaseFhirSystemDao<List<IResource>> {
 				if (nextId.toUnqualifiedVersionless().equals(newId)) {
 					ourLog.info("Transaction resource ID[{}] is being updated", newId);
 				} else {
-					if (nextId.isLocal()) {
+					if (isPlaceholder(nextId)) {
 						// nextId = new IdDt(resourceName, nextId.getIdPart());
 						ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
 						idConversions.put(nextId, newId);
@@ -267,10 +272,11 @@ public class FhirSystemDaoDstu1 extends BaseFhirSystemDao<List<IResource>> {
 		return retVal;
 	}
 
-	@Override
+	private static boolean isPlaceholder(IdDt theId) {
-	public MetaDt metaGetOperation() {
+		if ("cid:".equals(theId.getBaseUrl())) {
-		throw new NotImplementedOperationException("meta not supported in DSTU1");
+			return true;
+		}
+		return false;
 	}
 
-
 }

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

@@ -24,7 +24,6 @@ import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.Date;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
@@ -60,6 +59,26 @@ import ca.uhn.fhir.util.FhirTerser;
 public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2.class);
 
+	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
+		String url = nextEntry.getTransaction().getUrl();
+		if (isBlank(url)) {
+			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionMissingUrl", verb.name()));
+		}
+		return url;
+	}
+
+	@Override
+	public MetaDt metaGetOperation() {
+
+		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t)";
+		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
+		List<TagDefinition> tagDefinitions = q.getResultList();
+
+		MetaDt retVal = super.toMetaDt(tagDefinitions);
+
+		return retVal;
+	}
+
 	private UrlParts parseUrl(String theAction, String theUrl) {
 		UrlParts retVal = new UrlParts();
 
@@ -151,7 +170,7 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 			if (res != null) {
 
 				nextResourceId = res.getId();
-				if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !nextResourceId.isLocal()) {
+				if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
 					nextResourceId = new IdDt(toResourceName(res.getClass()), nextResourceId.getIdPart());
 					res.setId(nextResourceId);
 				}
@@ -159,7 +178,7 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 				/*
 				 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
 				 */
-				if (nextResourceId.isLocal()) {
+				if (isPlaceholder(nextResourceId)) {
 					if (!allIds.add(nextResourceId)) {
 						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
 					}
@@ -317,33 +336,13 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 		return response;
 	}
 
-	@Override
-	public MetaDt metaGetOperation() {
-
-		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t)";
-		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
-		List<TagDefinition> tagDefinitions = q.getResultList();
-
-		MetaDt retVal = super.toMetaDt(tagDefinitions);
-
-		return retVal;
-	}
-
-	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
-		String url = nextEntry.getTransaction().getUrl();
-		if (isBlank(url)) {
-			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseFhirSystemDao.class, "transactionMissingUrl", verb.name()));
-		}
-		return url;
-	}
-
 	private static void handleTransactionCreateOrUpdateOutcome(Map<IdDt, IdDt> idSubstitutions, Map<IdDt, DaoMethodOutcome> idToPersistedOutcome, IdDt nextResourceId, DaoMethodOutcome outcome,
 			Entry newEntry, String theResourceType) {
 		IdDt newId = outcome.getId().toUnqualifiedVersionless();
-		IdDt resourceId = nextResourceId.isLocal() ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
+		IdDt resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
 		if (newId.equals(resourceId) == false) {
 			idSubstitutions.put(resourceId, newId);
-			if (resourceId.isLocal()) {
+			if (isPlaceholder(resourceId)) {
 				/*
 				 * The correct way for substitution IDs to be is to be with no resource type, but we'll accept the qualified kind too just to be lenient.
 				 */
@@ -360,6 +359,13 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 		newEntry.getTransactionResponse().setEtag(outcome.getId().getVersionIdPart());
 	}
 
+	private static boolean isPlaceholder(IdDt theId) {
+		if ("urn:oid:".equals(theId.getBaseUrl()) || "urn:uuid:".equals(theId.getBaseUrl())) {
+			return true;
+		}
+		return false;
+	}
+
 	private static class UrlParts {
 		private IFhirResourceDao<? extends IResource> myDao;
 		private String myParams;

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -39,6 +39,7 @@ import ca.uhn.fhir.model.dstu2.resource.AllergyIntolerance;
 import ca.uhn.fhir.model.dstu2.resource.Binary;
 import ca.uhn.fhir.model.dstu2.resource.Composition;
 import ca.uhn.fhir.model.dstu2.resource.DataElement;
+import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
 import ca.uhn.fhir.model.dstu2.resource.Medication;
 import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
@@ -55,6 +56,8 @@ import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 
 public class XmlParserDstu2Test {
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
@@ -129,6 +132,8 @@ public class XmlParserDstu2Test {
 	}
 
 
+	
+	
 	@Test
 	public void testEncodeAndParseBundleWithoutResourceIds() {
 		Organization org = new Organization();
@@ -143,6 +148,42 @@ public class XmlParserDstu2Test {
 		assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
 	}
 
+	public static void main(String[] args) {
+		IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
+//		c.registerInterceptor(new LoggingInterceptor(true));
+		c.read().resource("Patient").withId("324").execute();
+	}
+	
+	@Test
+	public void testEncodeBundleWithContained() {
+		DiagnosticReport rpt = new DiagnosticReport();
+		rpt.addResult().setResource(new Observation().setCode(new CodeableConceptDt().setText("Sharp1")).setId("#1"));
+		rpt.addResult().setResource(new Observation().setCode(new CodeableConceptDt().setText("Uuid1")).setId("urn:uuid:UUID1"));
+		
+		ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle();
+		b.addEntry().setResource(rpt);
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
+		ourLog.info(encoded);
+		
+		assertThat(encoded, stringContainsInOrder(
+				"<DiagnosticReport",
+				"<contained",
+				"<Observation",
+				"<text value=\"Sharp1\"",
+				"</DiagnosticReport"
+				));
+		assertThat(encoded, not(stringContainsInOrder(
+				"<DiagnosticReport",
+				"<contained",
+				"<Observation",
+				"<contained",
+				"<Observation",
+				"</DiagnosticReport"
+				)));
+	}
+	
+	
 	@Test
 	public void testEncodeAndParseContained() {
 		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);