Fix #544

Squashed commit of the following:

commit 1ab9b58e9f
Author: James Agnew <jamesagnew@gmail.com>
Date:   Tue Jan 24 10:46:56 2017 -0500

    Changes working now

commit 5c752cdace
Author: James <jamesagnew@gmail.com>
Date:   Tue Jan 24 08:43:04 2017 -0500

    Get JPA working with new uuid: logic

commit 127b76884a
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jan 23 21:11:18 2017 -0500

    Fix test

commit 599bbe236c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Mon Jan 23 18:42:46 2017 -0500

    Work on #544

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.model.primitive;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -202,34 +203,6 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 		return getIdPartAsBigDecimal();
 	}
 
-	private String determineLocalPrefix(String theValue) {
-		if (theValue == null || theValue.isEmpty()) {
-			return null;
-		}
-		if (theValue.startsWith("#")) {
-			return "#";
-		}
-		int lastPrefix = -1;
-		for (int i = 0; i < theValue.length(); i++) {
-			char nextChar = theValue.charAt(i);
-			if (nextChar == ':') {
-				lastPrefix = i;
-			} else if (!Character.isLetter(nextChar) || !Character.isLowerCase(nextChar)) {
-				break;
-			}
-		}
-		if (lastPrefix != -1) {
-			String candidate = theValue.substring(0, lastPrefix + 1);
-			if (candidate.startsWith("cid:") || candidate.startsWith("urn:")) {
-				return candidate;
-			} else {
-				return null;
-			}
-		} else {
-			return null;
-		}
-	}
-
 	@Override
 	public boolean equals(Object theArg0) {
 		if (!(theArg0 instanceof IdDt)) {
@@ -316,8 +289,8 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 	public String getValue() {
 		if (super.getValue() == null && myHaveComponentParts) {
 
-			if (determineLocalPrefix(myBaseUrl) != null && myResourceType == null && myUnqualifiedVersionId == null) {
+			if (isLocal() || isUrn()) {
-				return myBaseUrl + myUnqualifiedId;
+				return myUnqualifiedId;
 			}
 
 			StringBuilder b = new StringBuilder();
@@ -448,11 +421,16 @@ 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)
 	 */
 	@Override
 	public boolean isLocal() {
-		return "#".equals(myBaseUrl);
+		return defaultString(myUnqualifiedId).startsWith("#");
+	}
+
+	private boolean isUrn() {
+		return defaultString(myUnqualifiedId).startsWith("urn:");
 	}
 
 	@Override
@@ -468,6 +446,27 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 		setValue(theId.getValue());
 	}
 
+	@Override
+	public IIdType setParts(String theBaseUrl, String theResourceType, String theIdPart, String theVersionIdPart) {
+		if (isNotBlank(theVersionIdPart)) {
+			Validate.notBlank(theResourceType, "If theVersionIdPart is populated, theResourceType and theIdPart must be populated");
+			Validate.notBlank(theIdPart, "If theVersionIdPart is populated, theResourceType and theIdPart must be populated");
+		}
+		if (isNotBlank(theBaseUrl) && isNotBlank(theIdPart)) {
+			Validate.notBlank(theResourceType, "If theBaseUrl is populated and theIdPart is populated, theResourceType must be populated");
+		}
+
+		setValue(null);
+
+		myBaseUrl = theBaseUrl;
+		myResourceType = theResourceType;
+		myUnqualifiedId = theIdPart;
+		myUnqualifiedVersionId = StringUtils.defaultIfBlank(theVersionIdPart, null);
+		myHaveComponentParts = true;
+
+		return this;
+	}
+
 	/**
 	 * Set the value
 	 * 
@@ -485,8 +484,6 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 		super.setValue(theValue);
 		myHaveComponentParts = false;
 
-		String localPrefix = determineLocalPrefix(theValue);
-		
 		if (StringUtils.isBlank(theValue)) {
 			myBaseUrl = null;
 			super.setValue(null);
@@ -495,14 +492,14 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 			myResourceType = null;
 		} else if (theValue.charAt(0) == '#' && theValue.length() > 1) {
 			super.setValue(theValue);
-			myBaseUrl = "#";
+			myBaseUrl = null;
-			myUnqualifiedId = theValue.substring(1);
+			myUnqualifiedId = theValue;
 			myUnqualifiedVersionId = null;
 			myResourceType = null;
 			myHaveComponentParts = true;
-		} else if (localPrefix != null) {
+		} else if (theValue.startsWith("urn:")) {
-			myBaseUrl = localPrefix;
+			myBaseUrl = null;
-			myUnqualifiedId = theValue.substring(localPrefix.length());
+			myUnqualifiedId = theValue;
 			myUnqualifiedVersionId = null;
 			myResourceType = null;
 			myHaveComponentParts = true;
@@ -567,24 +564,33 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 	 */
 	@Override
 	public IdDt toUnqualified() {
+		if (isLocal() || isUrn()) {
+			return new IdDt(getValueAsString());
+		}
 		return new IdDt(getResourceType(), getIdPart(), getVersionIdPart());
 	}
 
 	@Override
 	public IdDt toUnqualifiedVersionless() {
-		if (isLocal()) {
+		if (isLocal() || isUrn()) {
-			return toVersionless();
+			return new IdDt(getValueAsString());
 		}
 		return new IdDt(getResourceType(), getIdPart());
 	}
 
 	@Override
 	public IdDt toVersionless() {
+		if (isLocal() || isUrn()) {
+			return new IdDt(getValueAsString());
+		}
 		return new IdDt(getBaseUrl(), getResourceType(), getIdPart(), null);
 	}
 
 	@Override
 	public IdDt withResourceType(String theResourceName) {
+		if (isLocal() || isUrn()) {
+			return new IdDt(getValueAsString());
+		}
 		return new IdDt(theResourceName, getIdPart(), getVersionIdPart());
 	}
 
@@ -600,6 +606,9 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 	 */
 	@Override
 	public IdDt withServerBase(String theServerBase, String theResourceType) {
+		if (isLocal() || isUrn()) {
+			return new IdDt(getValueAsString());
+		}
 		return new IdDt(theServerBase, theResourceType, getIdPart(), getVersionIdPart());
 	}
 
@@ -610,9 +619,14 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 	 *           The actual version string, e.g. "1"
 	 * @return A new instance of IdDt which is identical, but refers to the specific version of this resource ID noted by theVersion.
 	 */
+	@Override
 	public IdDt withVersion(String theVersion) {
 		Validate.notBlank(theVersion, "Version may not be null or empty");
 
+		if (isLocal() || isUrn()) {
+			return new IdDt(getValueAsString());
+		}
+
 		String existingValue = getValue();
 
 		int i = existingValue.indexOf(Constants.PARAM_HISTORY);
@@ -678,25 +692,4 @@ public class IdDt extends UriDt implements IPrimitiveDatatype<String>, IIdType {
 		return theIdPart.toString();
 	}
 
-	@Override
-	public IIdType setParts(String theBaseUrl, String theResourceType, String theIdPart, String theVersionIdPart) {
-		if (isNotBlank(theVersionIdPart)) {
-			Validate.notBlank(theResourceType, "If theVersionIdPart is populated, theResourceType and theIdPart must be populated");
-			Validate.notBlank(theIdPart, "If theVersionIdPart is populated, theResourceType and theIdPart must be populated");
-		}
-		if (isNotBlank(theBaseUrl) && isNotBlank(theIdPart)) {
-			Validate.notBlank(theResourceType, "If theBaseUrl is populated and theIdPart is populated, theResourceType must be populated");
-		}
-		
-		setValue(null);
-		
-		myBaseUrl = theBaseUrl;
-		myResourceType = theResourceType;
-		myUnqualifiedId = theIdPart;
-		myUnqualifiedVersionId = StringUtils.defaultIfBlank(theVersionIdPart, null);
-		myHaveComponentParts = true;
-		
-		return this;
-	}
-
 }

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

@@ -347,7 +347,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		for (BundleEntry nextEntry : theBundle.getEntries()) {
 			theEventWriter.beginObject();
 
-			if (nextEntry.getResource() != null && nextEntry.getResource().getId().getBaseUrl() != null) {
+			if (nextEntry.getResource() != null && isNotBlank(nextEntry.getResource().getIdElement().getValue()) && (nextEntry.getResource().getId().getBaseUrl() != null || nextEntry.getResource().getId().getValueAsString().startsWith("urn:"))) {
 				writeOptionalTagWithTextNode(theEventWriter, "fullUrl", nextEntry.getResource().getId().getValue());
 			}
 

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

@@ -721,7 +721,6 @@ class ParserState<T> {
 			myInstance = theInstance;
 		}
 
-		@SuppressWarnings("unchecked")
 		@Override
 		public void wereBack() {
 
@@ -2090,17 +2089,32 @@ class ParserState<T> {
 			final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
 			if (bundle) {
 
+				FhirTerser t = myContext.newTerser();
+				
+				Map<String, IBaseResource> idToResource = new HashMap<String, IBaseResource>();
+				if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
+					List<IBase> entries = t.getValues(myInstance, "Bundle.entry", IBase.class);
+					for (IBase nextEntry : entries) {
+						IPrimitiveType<?> fullUrl = t.getSingleValueOrNull(nextEntry, "fullUrl", IPrimitiveType.class);
+						if (fullUrl != null && isNotBlank(fullUrl.getValueAsString())) {
+							IBaseResource resource = t.getSingleValueOrNull(nextEntry, "resource", IBaseResource.class);
+							if (resource != null) {
+								idToResource.put(fullUrl.getValueAsString(), resource);
+							}
+						}
+					}
+				}
+				
 				/*
 				 * Stitch together resource references
 				 */
-				Map<IIdType, IBaseResource> idToResource = new HashMap<IIdType, IBaseResource>();
-				FhirTerser t = myContext.newTerser();
 				List<IBaseResource> resources = t.getAllPopulatedChildElementsOfType(myInstance, IBaseResource.class);
 				for (IBaseResource next : resources) {
 					IIdType id = next.getIdElement();
 					if (id != null && id.isEmpty() == false) {
 						String resName = myContext.getResourceDefinition(next).getName();
-						idToResource.put(id.withResourceType(resName).toUnqualifiedVersionless(), next);
+						IIdType idType = id.withResourceType(resName).toUnqualifiedVersionless();
+						idToResource.put(idType.getValueAsString(), next);
 					}
 				}
 
@@ -2108,7 +2122,8 @@ class ParserState<T> {
 					List<IBaseReference> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(next, IBaseReference.class);
 					for (IBaseReference nextRef : refs) {
 						if (nextRef.isEmpty() == false && nextRef.getReferenceElement() != null) {
-							IBaseResource target = idToResource.get(nextRef.getReferenceElement().toUnqualifiedVersionless());
+							IIdType unqualifiedVersionless = nextRef.getReferenceElement().toUnqualifiedVersionless();
+							IBaseResource target = idToResource.get(unqualifiedVersionless.getValueAsString());
 							if (target != null) {
 								nextRef.setResource(target);
 							}

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

@@ -446,7 +446,7 @@ public class XmlParser extends BaseParser implements IParser {
 
 			writeBundleResourceLink(theEventWriter, "alternate", nextEntry.getLinkAlternate());
 
-			if (nextEntry.getResource() != null && nextEntry.getResource().getId().getBaseUrl() != null) {
+			if (nextEntry.getResource() != null && isNotBlank(nextEntry.getResource().getIdElement().getValue()) && (nextEntry.getResource().getId().getBaseUrl() != null || nextEntry.getResource().getId().getValueAsString().startsWith("urn:"))) {
 				writeOptionalTagWithValue(theEventWriter, "fullUrl", nextEntry.getResource().getId().getValue());
 			}
 

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IIdType.java

@@ -130,10 +130,41 @@ public interface IIdType extends IPrimitiveType<String> {
 
 	IIdType toVersionless();
 
+	/**
+	 * Returns a copy of this object, but with a different {@link #getResourceType() resource type} 
+	 * (or if this object does not have a resource type currently, returns a copy of this object with
+	 * the given resource type).
+	 * <p>
+	 * Note that if this object represents a local reference (e.g. <code>#foo</code>) or
+	 * a URN (e.g. <code>urn:oid:1.2.3.4</code>) this method will simply return a copy
+	 * of this object with no modifications.
+	 * </p>
+	 */
 	IIdType withResourceType(String theResName);
 	
+	/**
+	 * Returns a copy of this object, but with a different {@link #getResourceType() resource type} 
+	 * and {@link #getBaseUrl() base URL}
+	 * (or if this object does not have a resource type currently, returns a copy of this object with
+	 * the given server base and resource type).
+	 * <p>
+	 * Note that if this object represents a local reference (e.g. <code>#foo</code>) or
+	 * a URN (e.g. <code>urn:oid:1.2.3.4</code>) this method will simply return a copy
+	 * of this object with no modifications.
+	 * </p>
+	 */
 	IIdType withServerBase(String theServerBase, String theResourceName);
 
+	/**
+	 * Returns a copy of this object, but with a different {@link #getVersionIdPart() version ID} 
+	 * (or if this object does not have a resource type currently, returns a copy of this object with
+	 * the given version).
+	 * <p>
+	 * Note that if this object represents a local reference (e.g. <code>#foo</code>) or
+	 * a URN (e.g. <code>urn:oid:1.2.3.4</code>) this method will simply return a copy
+	 * of this object with no modifications.
+	 * </p>
+	 */
 	IIdType withVersion(String theVersion);
 
 	/**

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

@@ -164,7 +164,7 @@ public class FhirSystemDaoDstu1 extends BaseHapiFhirSystemDao<List<IResource>, M
 				entity = toEntity(nextResource);
 				entity.setUpdated(updateTime);
 				entity.setPublished(updateTime);
-				if (nextId.isEmpty() == false && "cid:".equals(nextId.getBaseUrl())) {
+				if (nextId.getIdPart() != null && nextId.getIdPart().startsWith("cid:")) {
 					ourLog.debug("Resource in transaction has ID[{}], will replace with server assigned ID", nextId.getIdPart());
 				} else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
 					if (nextId.isEmpty() == false) {
@@ -282,7 +282,7 @@ public class FhirSystemDaoDstu1 extends BaseHapiFhirSystemDao<List<IResource>, M
 	}
 
 	private static boolean isPlaceholder(IdDt theId) {
-		if ("cid:".equals(theId.getBaseUrl())) {
+		if (theId.getIdPart() != null && theId.getIdPart().startsWith("cid:")) {
 			return true;
 		}
 		return false;

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

@@ -40,7 +40,6 @@ import java.util.Set;
 import javax.persistence.TypedQuery;
 
 import org.apache.http.NameValuePair;
-import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -634,9 +633,11 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 	}
 
 	private static boolean isPlaceholder(IdDt theId) {
-		if ("urn:oid:".equals(theId.getBaseUrl()) || "urn:uuid:".equals(theId.getBaseUrl())) {
+		if (theId.getValue() != null) {
+			if (theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:")) {
 				return true;
 			}
+		}
 		return false;
 	}
 

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

@@ -627,9 +627,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 	}
 
 	private static boolean isPlaceholder(IdType theId) {
-		if ("urn:oid:".equals(theId.getBaseUrl()) || "urn:uuid:".equals(theId.getBaseUrl())) {
+		if (theId.getValue() != null) {
+			if (theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:")) {
 				return true;
 			}
+		}
 		return false;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -1615,13 +1615,11 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
 
 		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
 		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
 		o1.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
 
 		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
 		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
 		o2.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
@@ -1760,13 +1758,11 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
 
 		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
 		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
 		o1.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
 
 		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
 		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
 		o2.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -93,7 +93,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		return null;
 	}
 
-	
 	/**
 	 * See #410
 	 */
@@ -363,7 +362,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 
 	}
 
-	
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithNoMatches() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithNoMatches";
@@ -371,7 +369,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);
 
-	
 		Observation o = new Observation();
 		o.getCode().setText("Some Observation");
 		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
@@ -385,7 +382,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
-
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";
@@ -768,7 +764,8 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 			mySystemDao.transaction(mySrd, request);
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals(e.getMessage(), "Unable to process Transaction - Request would cause multiple resources to match URL: \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateWithDuplicateMatchUrl01\". Does transaction request contain duplicates?");
+			assertEquals(e.getMessage(),
+					"Unable to process Transaction - Request would cause multiple resources to match URL: \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateWithDuplicateMatchUrl01\". Does transaction request contain duplicates?");
 		}
 	}
 
@@ -790,7 +787,8 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 			mySystemDao.transaction(mySrd, request);
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals(e.getMessage(), "Unable to process Transaction - Request would cause multiple resources to match URL: \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateWithDuplicateMatchUrl02\". Does transaction request contain duplicates?");
+			assertEquals(e.getMessage(),
+					"Unable to process Transaction - Request would cause multiple resources to match URL: \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateWithDuplicateMatchUrl02\". Does transaction request contain duplicates?");
 		}
 	}
 
@@ -1145,7 +1143,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
-
 	@Test
 	public void testTransactionDeleteMatchUrlWithZeroMatch() {
 		String methodName = "testTransactionDeleteMatchUrlWithZeroMatch";
@@ -1947,6 +1944,24 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		assertNotEquals(medOrderId1, medOrderId2);
 	}
 
+	@Test
+	public void testTransactionWIthInvalidPlaceholder() throws Exception {
+		Bundle res = new Bundle();
+		res.setType(BundleType.TRANSACTION);
+
+		Observation o1 = new Observation();
+		o1.setId("cid:observation1");
+		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
+		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
+
+		try {
+			mySystemDao.transaction(mySrd, res);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid placeholder ID found: cid:observation1 - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testTransactionWithRelativeOidIds() throws Exception {
 		Bundle res = new Bundle();
@@ -1958,13 +1973,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
 
 		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
 		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
 		o1.setSubject(new Reference("urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
 
 		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
 		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
 		o2.setSubject(new Reference("urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
@@ -2103,13 +2116,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
 
 		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
 		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
 		o1.setSubject(new Reference("Patient/urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
 
 		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
 		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
 		o2.setSubject(new Reference("Patient/urn:oid:0.1.2.3"));
 		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/model/primitive/IdDtTest.java

@@ -20,6 +20,71 @@ public class IdDtTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(IdDtTest.class);
 
+	@Test
+	public void testUuid() {
+		IdDt id = new IdDt("urn:uuid:1234-5678");
+		assertEquals("urn:uuid:1234-5678", id.getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.getIdPart());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualified().getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:uuid:1234-5678", id.withResourceType("Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withVersion("2").getValue());
+	}
+	
+	@Test
+	public void testOid() {
+		IdDt id = new IdDt("urn:oid:1.2.3.4");
+		assertEquals("urn:oid:1.2.3.4", id.getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.getIdPart());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualified().getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:oid:1.2.3.4", id.withResourceType("Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testLocal() {
+		IdDt id = new IdDt("#foo");
+		assertEquals("#foo", id.getValueAsString());
+		assertEquals("#foo", id.getIdPart());
+		assertEquals("#foo", id.toUnqualified().getValueAsString());
+		assertEquals("#foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("#foo", id.withResourceType("Patient").getValue());
+		assertEquals("#foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("#foo", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testNormal() {
+		IdDt id = new IdDt("foo");
+		assertEquals("foo", id.getValueAsString());
+		assertEquals("foo", id.getIdPart());
+		assertEquals("foo", id.toUnqualified().getValueAsString());
+		assertEquals("foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("Patient/foo", id.withResourceType("Patient").getValue());
+		assertEquals("http://foo/Patient/foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("foo/_history/2", id.withVersion("2").getValue());
+	}
+
+	
 	@Test
 	public void testDetectIsIdPartValid() {
 		assertTrue(new IdDt("0").isIdPartValid());
@@ -60,16 +125,16 @@ public class IdDtTest {
 	@Test
 	public void testDetectLocalBase() {
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("urn:uuid:", new IdDt("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdDt("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("cid:", new IdDt("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdDt("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("#180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("#", new IdDt("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdDt("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdDt("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 	}
 	
 
@@ -80,10 +145,10 @@ public class IdDtTest {
 	public void testComplicatedLocal() {
 		IdDt id = new IdDt("#Patient/cid:Patient-72/_history/1");
 		assertTrue(id.isLocal());
-		assertEquals("#", id.getBaseUrl());
+		assertEquals(null, id.getBaseUrl());
 		assertNull(id.getResourceType());
 		assertNull(id.getVersionIdPart());
-		assertEquals("Patient/cid:Patient-72/_history/1", id.getIdPart());
+		assertEquals("#Patient/cid:Patient-72/_history/1", id.getIdPart());
 		
 	}
 	

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java

@@ -561,8 +561,8 @@ public class XmlParserTest {
 		// Re-parse the bundle
 		patient = (Patient) xmlParser.parseResource(xmlParser.encodeResourceToString(patient));
 		assertEquals("#1", patient.getManagingOrganization().getReference().getValue());
-		assertEquals("#", patient.getManagingOrganization().getReference().getBaseUrl());
+		assertEquals(null, patient.getManagingOrganization().getReference().getBaseUrl());
-		assertEquals("1", patient.getManagingOrganization().getReference().getIdPart());
+		assertEquals("#1", patient.getManagingOrganization().getReference().getIdPart());
 
 		assertNotNull(patient.getManagingOrganization().getResource());
 		org = (Organization) patient.getManagingOrganization().getResource();

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/model/IdType.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.dstu2016may.model;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 /*
   Copyright (c) 2011+, HL7, Inc.
   All rights reserved.
@@ -242,34 +244,6 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     return new IdType(getValue());
   }
 
-  private String determineLocalPrefix(String theValue) {
-    if (theValue == null || theValue.isEmpty()) {
-      return null;
-    }
-    if (theValue.startsWith("#")) {
-      return "#";
-    }
-    int lastPrefix = -1;
-    for (int i = 0; i < theValue.length(); i++) {
-      char nextChar = theValue.charAt(i);
-      if (nextChar == ':') {
-        lastPrefix = i;
-      } else if (!Character.isLetter(nextChar) || !Character.isLowerCase(nextChar)) {
-        break;
-      }
-    }
-    if (lastPrefix != -1) {
-      String candidate = theValue.substring(0, lastPrefix + 1);
-      if (candidate.startsWith("cid:") || candidate.startsWith("urn:")) {
-        return candidate;
-      } else {
-        return null;
-      }
-    } else {
-      return null;
-    }
-  }
-
   @Override
   public boolean equals(Object theArg0) {
     if (!(theArg0 instanceof IdType)) {
@@ -368,8 +342,8 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     String retVal = super.getValue();
     if (retVal == null && myHaveComponentParts) {
 
-      if (determineLocalPrefix(myBaseUrl) != null && myResourceType == null && myUnqualifiedVersionId == null) {
+      if (isLocal() || isUrn()) {
-        return myBaseUrl + myUnqualifiedId;
+        return myUnqualifiedId;
       }
 
       StringBuilder b = new StringBuilder();
@@ -510,7 +484,11 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public boolean isLocal() {
-    return "#".equals(myBaseUrl);
+    return defaultString(myUnqualifiedId).startsWith("#");
+  }
+
+  private boolean isUrn() {
+    return defaultString(myUnqualifiedId).startsWith("urn:");
   }
 
   @Override
@@ -536,8 +514,6 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     super.setValue(theValue);
     myHaveComponentParts = false;
 
-    String localPrefix = determineLocalPrefix(theValue);
-
     if (StringUtils.isBlank(theValue)) {
       myBaseUrl = null;
       super.setValue(null);
@@ -546,14 +522,17 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
       myResourceType = null;
     } else if (theValue.charAt(0) == '#' && theValue.length() > 1) {
        super.setValue(theValue);
-      myBaseUrl = "#";
+       myBaseUrl = null;
-      myUnqualifiedId = theValue.substring(1);
+       myUnqualifiedId = theValue;
+       myUnqualifiedVersionId = null;
+       myResourceType = null;
+       myHaveComponentParts = true;
+     } else if (theValue.startsWith("urn:")) {
+       myBaseUrl = null;
+       myUnqualifiedId = theValue;
        myUnqualifiedVersionId = null;
        myResourceType = null;
        myHaveComponentParts = true;
-    } else if (localPrefix != null) {
-      myBaseUrl = localPrefix;
-      myUnqualifiedId = theValue.substring(localPrefix.length());
     } else {
       int vidIndex = theValue.indexOf("/_history/");
       int idIndex;
@@ -618,21 +597,33 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public IdType toUnqualified() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getResourceType(), getIdPart(), getVersionIdPart());
   }
 
   @Override
   public IdType toUnqualifiedVersionless() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getResourceType(), getIdPart());
   }
 
   @Override
   public IdType toVersionless() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getBaseUrl(), getResourceType(), getIdPart(), null);
   }
 
   @Override
   public IdType withResourceType(String theResourceName) {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(theResourceName, getIdPart(), getVersionIdPart());
   }
 
@@ -652,6 +643,9 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public IdType withServerBase(String theServerBase, String theResourceType) {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(theServerBase, theResourceType, getIdPart(), getVersionIdPart());
   }
 
@@ -667,6 +661,10 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
   public IdType withVersion(String theVersion) {
     Validate.notBlank(theVersion, "Version may not be null or empty");
 
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
+
     String existingValue = getValue();
 
     int i = existingValue.indexOf("_history");

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/model/IdTypeDstu2_1Test.java

@@ -28,6 +28,70 @@ public class IdTypeDstu2_1Test {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Test
+	public void testUuid() {
+		IdType id = new IdType("urn:uuid:1234-5678");
+		assertEquals("urn:uuid:1234-5678", id.getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.getIdPart());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualified().getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:uuid:1234-5678", id.withResourceType("Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withVersion("2").getValue());
+	}
+	
+	@Test
+	public void testOid() {
+		IdType id = new IdType("urn:oid:1.2.3.4");
+		assertEquals("urn:oid:1.2.3.4", id.getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.getIdPart());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualified().getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:oid:1.2.3.4", id.withResourceType("Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testLocal() {
+		IdType id = new IdType("#foo");
+		assertEquals("#foo", id.getValueAsString());
+		assertEquals("#foo", id.getIdPart());
+		assertEquals("#foo", id.toUnqualified().getValueAsString());
+		assertEquals("#foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("#foo", id.withResourceType("Patient").getValue());
+		assertEquals("#foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("#foo", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testNormal() {
+		IdType id = new IdType("foo");
+		assertEquals("foo", id.getValueAsString());
+		assertEquals("foo", id.getIdPart());
+		assertEquals("foo", id.toUnqualified().getValueAsString());
+		assertEquals("foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("Patient/foo", id.withResourceType("Patient").getValue());
+		assertEquals("http://foo/Patient/foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("foo/_history/2", id.withVersion("2").getValue());
+	}
+
 
 	@Test
 	public void testDetectLocal() {
@@ -55,16 +119,16 @@ public class IdTypeDstu2_1Test {
 	@Test
 	public void testDetectLocalBase() {
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("urn:uuid:", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("cid:", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("#", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 	}
 	
 
@@ -75,20 +139,20 @@ public class IdTypeDstu2_1Test {
 	public void testComplicatedLocal() {
 		IdType id = new IdType("#Patient/cid:Patient-72/_history/1");
 		assertTrue(id.isLocal());
-		assertEquals("#", id.getBaseUrl());
+		assertEquals(null, id.getBaseUrl());
 		assertNull(id.getResourceType());
 		assertNull(id.getVersionIdPart());
-		assertEquals("Patient/cid:Patient-72/_history/1", id.getIdPart());
+		assertEquals("#Patient/cid:Patient-72/_history/1", id.getIdPart());
 		
 		IdType id2 = new IdType("#Patient/cid:Patient-72/_history/1");
 		assertEquals(id, id2);
 		
 		id2 = id2.toUnqualified();
-		assertFalse(id2.isLocal());
+		assertTrue(id2.isLocal());
 		assertNull(id2.getBaseUrl());
 		assertNull(id2.getResourceType());
 		assertNull(id2.getVersionIdPart());
-		assertEquals("Patient/cid:Patient-72/_history/1", id2.getIdPart());
+		assertEquals("#Patient/cid:Patient-72/_history/1", id2.getIdPart());
 
 	}
 	

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.parser;
 
-import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
@@ -15,79 +14,31 @@ import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 import static org.mockito.Matchers.eq;
 import static org.mockito.Matchers.isNull;
-import static org.mockito.Mockito.atLeastOnce;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
-import java.io.IOException;
 import java.math.BigDecimal;
 import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.UUID;
 
 import org.apache.commons.io.IOUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.dstu2016may.model.*;
 import org.hl7.fhir.dstu2016may.model.Address.AddressUse;
 import org.hl7.fhir.dstu2016may.model.Address.AddressUseEnumFactory;
-import org.hl7.fhir.dstu2016may.model.Attachment;
-import org.hl7.fhir.dstu2016may.model.AuditEvent;
-import org.hl7.fhir.dstu2016may.model.Basic;
-import org.hl7.fhir.dstu2016may.model.Binary;
-import org.hl7.fhir.dstu2016may.model.Bundle;
 import org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu2016may.model.Bundle.BundleType;
-import org.hl7.fhir.dstu2016may.model.Claim;
-import org.hl7.fhir.dstu2016may.model.Coding;
-import org.hl7.fhir.dstu2016may.model.Communication;
-import org.hl7.fhir.dstu2016may.model.Condition;
 import org.hl7.fhir.dstu2016may.model.Condition.ConditionVerificationStatus;
-import org.hl7.fhir.dstu2016may.model.Conformance;
 import org.hl7.fhir.dstu2016may.model.Conformance.UnknownContentCode;
-import org.hl7.fhir.dstu2016may.model.Coverage;
-import org.hl7.fhir.dstu2016may.model.DateTimeType;
-import org.hl7.fhir.dstu2016may.model.DateType;
-import org.hl7.fhir.dstu2016may.model.DecimalType;
-import org.hl7.fhir.dstu2016may.model.DiagnosticReport;
-import org.hl7.fhir.dstu2016may.model.EnumFactory;
 import org.hl7.fhir.dstu2016may.model.Enumeration;
 import org.hl7.fhir.dstu2016may.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.dstu2016may.model.ExplanationOfBenefit;
-import org.hl7.fhir.dstu2016may.model.Extension;
-import org.hl7.fhir.dstu2016may.model.HumanName;
-import org.hl7.fhir.dstu2016may.model.IdType;
 import org.hl7.fhir.dstu2016may.model.Identifier.IdentifierUse;
-import org.hl7.fhir.dstu2016may.model.Linkage;
-import org.hl7.fhir.dstu2016may.model.Medication;
-import org.hl7.fhir.dstu2016may.model.MedicationOrder;
-import org.hl7.fhir.dstu2016may.model.Observation;
 import org.hl7.fhir.dstu2016may.model.Observation.ObservationStatus;
-import org.hl7.fhir.dstu2016may.model.Parameters;
-import org.hl7.fhir.dstu2016may.model.Patient;
-import org.hl7.fhir.dstu2016may.model.PrimitiveType;
-import org.hl7.fhir.dstu2016may.model.Quantity;
-import org.hl7.fhir.dstu2016may.model.QuestionnaireResponse;
-import org.hl7.fhir.dstu2016may.model.Reference;
-import org.hl7.fhir.dstu2016may.model.RelatedPerson;
-import org.hl7.fhir.dstu2016may.model.SampledData;
-import org.hl7.fhir.dstu2016may.model.SimpleQuantity;
-import org.hl7.fhir.dstu2016may.model.StringType;
-import org.hl7.fhir.dstu2016may.model.UriType;
-import org.hl7.fhir.dstu2016may.model.ValueSet;
-import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
-import org.junit.After;
+import org.junit.*;
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.Ignore;
-import org.junit.Test;
 import org.mockito.ArgumentCaptor;
-import org.mockito.Mockito;
 
 import com.google.common.collect.Sets;
 
@@ -96,11 +47,8 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
 import ca.uhn.fhir.parser.PatientWithExtendedContactDstu3.CustomContactComponent;
 import ca.uhn.fhir.parser.XmlParserDstu2_1Test.TestPatientFor327;
-import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.TestUtil;
-import ca.uhn.fhir.validation.FhirValidator;
-import ca.uhn.fhir.validation.ValidationResult;
 import net.sf.json.JSON;
 import net.sf.json.JSONSerializer;
 import net.sf.json.JsonConfig;
@@ -1430,8 +1378,8 @@ public class JsonParserDstu2_1Test {
 		ourLog.info(encoded);
 
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-		assertEquals("urn:uuid:", parsed.getEntry().get(0).getResource().getIdElement().getBaseUrl());
+		assertEquals(null, parsed.getEntry().get(0).getResource().getIdElement().getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getIdPart());
 		assertThat(encoded, not(containsString("\"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\"")));
 	}
 

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

@@ -67,6 +67,34 @@ public class JsonParserDstu2Test {
 	private static FhirContext ourCtx = FhirContext.forDstu2();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
 
+	/**
+	 * See #544
+	 */
+	@Test
+	public void testBundleStitchReferencesByUuid() throws Exception {
+		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
+		
+		DocumentManifest dm = new DocumentManifest();
+		dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+		bundle.addEntry().setResource(dm);
+		
+		Patient patient = new Patient();
+		patient.addName().addFamily("FAMILY");
+		bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+		
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
+		ourLog.info(encoded);
+		
+		bundle = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, encoded);
+		dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
+		
+		assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
+		
+		Patient subject = (Patient) dm.getSubject().getResource();
+		assertNotNull(subject);
+		assertEquals("FAMILY", subject.getNameFirstRep().getFamilyAsSingleString());
+	}
+
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();
@@ -89,6 +117,21 @@ public class JsonParserDstu2Test {
 		assertEquals("ORG", o.getName());
 	}
 
+	@Test
+	public void testEncodeBundleOldStyleContainingResourceWithUuidBase() {
+		Patient p = new Patient();
+		p.setId(IdDt.newRandomUuid());
+		p.addName().addFamily("PATIENT");
+
+		Bundle b = new Bundle();
+		b.addEntry().setResource(p);
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder("fullUrl", p.getId().getValue(), "Patient"));
+	}
+
+	
 	/**
 	 * See #308
 	 */
@@ -1242,8 +1285,8 @@ public class JsonParserDstu2Test {
 		ourLog.info(encoded);
 
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getId().getValue());
-		assertEquals("urn:uuid:", parsed.getEntry().get(0).getResource().getId().getBaseUrl());
+		assertEquals(null, parsed.getEntry().get(0).getResource().getId().getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getId().getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getId().getIdPart());
 		assertThat(encoded, not(containsString("\"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\"")));
 	}
 

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/IdType.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.dstu3.model;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 /*
   Copyright (c) 2011+, HL7, Inc.
   All rights reserved.
@@ -242,41 +244,12 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     return new IdType(getValue());
   }
 
-  private String determineLocalPrefix(String theValue) {
-    if (theValue == null || theValue.isEmpty()) {
-      return null;
-    }
-    if (theValue.startsWith("#")) {
-      return "#";
-    }
-    int lastPrefix = -1;
-    for (int i = 0; i < theValue.length(); i++) {
-      char nextChar = theValue.charAt(i);
-      if (nextChar == ':') {
-        lastPrefix = i;
-      } else if (!Character.isLetter(nextChar) || !Character.isLowerCase(nextChar)) {
-        break;
-      }
-    }
-    if (lastPrefix != -1) {
-      String candidate = theValue.substring(0, lastPrefix + 1);
-      if (candidate.startsWith("cid:") || candidate.startsWith("urn:")) {
-        return candidate;
-      } else {
-        return null;
-      }
-    } else {
-      return null;
-    }
-  }
-
   @Override
   public boolean equals(Object theArg0) {
     if (!(theArg0 instanceof IdType)) {
       return false;
     }
-    IdType id = (IdType) theArg0;
+    return StringUtils.equals(getValueAsString(), ((IdType)theArg0).getValueAsString());
-    return StringUtils.equals(getValueAsString(), id.getValueAsString());
   }
 
   /**
@@ -368,8 +341,8 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     String retVal = super.getValue();
     if (retVal == null && myHaveComponentParts) {
 
-      if (determineLocalPrefix(myBaseUrl) != null && myResourceType == null && myUnqualifiedVersionId == null) {
+      if (isLocal() || isUrn()) {
-        return myBaseUrl + myUnqualifiedId;
+        return myUnqualifiedId;
       }
 
       StringBuilder b = new StringBuilder();
@@ -510,7 +483,11 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public boolean isLocal() {
-    return "#".equals(myBaseUrl);
+    return defaultString(myUnqualifiedId).startsWith("#");
+  }
+
+  private boolean isUrn() {
+    return defaultString(myUnqualifiedId).startsWith("urn:");
   }
 
   @Override
@@ -536,8 +513,6 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
     super.setValue(theValue);
     myHaveComponentParts = false;
 
-    String localPrefix = determineLocalPrefix(theValue);
-
     if (StringUtils.isBlank(theValue)) {
       myBaseUrl = null;
       super.setValue(null);
@@ -546,14 +521,17 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
       myResourceType = null;
     } else if (theValue.charAt(0) == '#' && theValue.length() > 1) {
       super.setValue(theValue);
-      myBaseUrl = "#";
+      myBaseUrl = null;
-      myUnqualifiedId = theValue.substring(1);
+      myUnqualifiedId = theValue;
+      myUnqualifiedVersionId = null;
+      myResourceType = null;
+      myHaveComponentParts = true;
+    } else if (theValue.startsWith("urn:")) {
+      myBaseUrl = null;
+      myUnqualifiedId = theValue;
       myUnqualifiedVersionId = null;
       myResourceType = null;
       myHaveComponentParts = true;
-    } else if (localPrefix != null) {
-      myBaseUrl = localPrefix;
-      myUnqualifiedId = theValue.substring(localPrefix.length());
     } else {
       int vidIndex = theValue.indexOf("/_history/");
       int idIndex;
@@ -618,21 +596,33 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public IdType toUnqualified() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getResourceType(), getIdPart(), getVersionIdPart());
   }
 
   @Override
   public IdType toUnqualifiedVersionless() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getResourceType(), getIdPart());
   }
 
   @Override
   public IdType toVersionless() {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(getBaseUrl(), getResourceType(), getIdPart(), null);
   }
 
   @Override
   public IdType withResourceType(String theResourceName) {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(theResourceName, getIdPart(), getVersionIdPart());
   }
 
@@ -652,6 +642,9 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    */
   @Override
   public IdType withServerBase(String theServerBase, String theResourceType) {
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
     return new IdType(theServerBase, theResourceType, getIdPart(), getVersionIdPart());
   }
 
@@ -664,9 +657,14 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
    * @return A new instance of IdType which is identical, but refers to the
    *         specific version of this resource ID noted by theVersion.
    */
+  @Override
   public IdType withVersion(String theVersion) {
     Validate.notBlank(theVersion, "Version may not be null or empty");
 
+    if (isLocal() || isUrn()) {
+       return new IdType(getValueAsString());
+    }
+
     String existingValue = getValue();
 
     int i = existingValue.indexOf("_history");

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/model/IdTypeDstu3Test.java

@@ -28,6 +28,69 @@ public class IdTypeDstu3Test {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Test
+	public void testUuid() {
+		IdType id = new IdType("urn:uuid:1234-5678");
+		assertEquals("urn:uuid:1234-5678", id.getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.getIdPart());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualified().getValueAsString());
+		assertEquals("urn:uuid:1234-5678", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:uuid:1234-5678", id.withResourceType("Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:uuid:1234-5678", id.withVersion("2").getValue());
+	}
+	
+	@Test
+	public void testOid() {
+		IdType id = new IdType("urn:oid:1.2.3.4");
+		assertEquals("urn:oid:1.2.3.4", id.getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.getIdPart());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualified().getValueAsString());
+		assertEquals("urn:oid:1.2.3.4", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("urn:oid:1.2.3.4", id.withResourceType("Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("urn:oid:1.2.3.4", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testLocal() {
+		IdType id = new IdType("#foo");
+		assertEquals("#foo", id.getValueAsString());
+		assertEquals("#foo", id.getIdPart());
+		assertEquals("#foo", id.toUnqualified().getValueAsString());
+		assertEquals("#foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("#foo", id.withResourceType("Patient").getValue());
+		assertEquals("#foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("#foo", id.withVersion("2").getValue());
+	}
+
+	@Test
+	public void testNormal() {
+		IdType id = new IdType("foo");
+		assertEquals("foo", id.getValueAsString());
+		assertEquals("foo", id.getIdPart());
+		assertEquals("foo", id.toUnqualified().getValueAsString());
+		assertEquals("foo", id.toUnqualifiedVersionless().getValueAsString());
+		assertEquals(null, id.getVersionIdPart());
+		assertEquals(null, id.getResourceType());
+		assertEquals(null, id.getBaseUrl());
+		
+		assertEquals("Patient/foo", id.withResourceType("Patient").getValue());
+		assertEquals("http://foo/Patient/foo", id.withServerBase("http://foo", "Patient").getValue());
+		assertEquals("foo/_history/2", id.withVersion("2").getValue());
+	}
 
 	@Test
 	public void testDetectLocal() {
@@ -55,16 +118,16 @@ public class IdTypeDstu3Test {
 	@Test
 	public void testDetectLocalBase() {
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("urn:uuid:", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("cid:", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("cid:180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("cid:180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 
 		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getValue());
-		assertEquals("#", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
+		assertEquals(null, new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
+		assertEquals("#180f219f-97a8-486d-99d9-ed631fe4fc57", new IdType("#180f219f-97a8-486d-99d9-ed631fe4fc57").getIdPart());
 	}
 	
 
@@ -75,20 +138,20 @@ public class IdTypeDstu3Test {
 	public void testComplicatedLocal() {
 		IdType id = new IdType("#Patient/cid:Patient-72/_history/1");
 		assertTrue(id.isLocal());
-		assertEquals("#", id.getBaseUrl());
+		assertEquals(null, id.getBaseUrl());
 		assertNull(id.getResourceType());
 		assertNull(id.getVersionIdPart());
-		assertEquals("Patient/cid:Patient-72/_history/1", id.getIdPart());
+		assertEquals("#Patient/cid:Patient-72/_history/1", id.getIdPart());
 		
 		IdType id2 = new IdType("#Patient/cid:Patient-72/_history/1");
 		assertEquals(id, id2);
 		
 		id2 = id2.toUnqualified();
-		assertFalse(id2.isLocal());
+		assertTrue(id2.isLocal());
 		assertNull(id2.getBaseUrl());
 		assertNull(id2.getResourceType());
 		assertNull(id2.getVersionIdPart());
-		assertEquals("Patient/cid:Patient-72/_history/1", id2.getIdPart());
+		assertEquals("#Patient/cid:Patient-72/_history/1", id2.getIdPart());
 
 	}
 	

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java

@@ -34,52 +34,16 @@ import java.util.UUID;
 import org.apache.commons.io.IOUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Address.AddressUse;
 import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
-import org.hl7.fhir.dstu3.model.Attachment;
-import org.hl7.fhir.dstu3.model.AuditEvent;
-import org.hl7.fhir.dstu3.model.Basic;
-import org.hl7.fhir.dstu3.model.Binary;
-import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Bundle.BundleType;
-import org.hl7.fhir.dstu3.model.Claim;
-import org.hl7.fhir.dstu3.model.Coding;
-import org.hl7.fhir.dstu3.model.Communication;
-import org.hl7.fhir.dstu3.model.Condition;
 import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus;
-import org.hl7.fhir.dstu3.model.Conformance;
 import org.hl7.fhir.dstu3.model.Conformance.UnknownContentCode;
-import org.hl7.fhir.dstu3.model.Coverage;
-import org.hl7.fhir.dstu3.model.DateTimeType;
-import org.hl7.fhir.dstu3.model.DateType;
-import org.hl7.fhir.dstu3.model.DecimalType;
-import org.hl7.fhir.dstu3.model.DiagnosticReport;
-import org.hl7.fhir.dstu3.model.EnumFactory;
-import org.hl7.fhir.dstu3.model.Enumeration;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.dstu3.model.ExplanationOfBenefit;
-import org.hl7.fhir.dstu3.model.Extension;
-import org.hl7.fhir.dstu3.model.HumanName;
-import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
-import org.hl7.fhir.dstu3.model.Linkage;
-import org.hl7.fhir.dstu3.model.Medication;
-import org.hl7.fhir.dstu3.model.MedicationRequest;
-import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
-import org.hl7.fhir.dstu3.model.Parameters;
-import org.hl7.fhir.dstu3.model.Patient;
-import org.hl7.fhir.dstu3.model.PrimitiveType;
-import org.hl7.fhir.dstu3.model.Quantity;
-import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
-import org.hl7.fhir.dstu3.model.Reference;
-import org.hl7.fhir.dstu3.model.RelatedPerson;
-import org.hl7.fhir.dstu3.model.SampledData;
-import org.hl7.fhir.dstu3.model.SimpleQuantity;
-import org.hl7.fhir.dstu3.model.StringType;
-import org.hl7.fhir.dstu3.model.UriType;
-import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.junit.After;
 import org.junit.AfterClass;
@@ -115,6 +79,35 @@ public class JsonParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
+	/**
+	 * See #544
+	 */
+	@Test
+	public void testBundleStitchReferencesByUuid() throws Exception {
+		Bundle bundle = new Bundle();
+		
+		DocumentManifest dm = new DocumentManifest();
+		dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+		bundle.addEntry().setResource(dm);
+		
+		Patient patient = new Patient();
+		patient.addName().setFamily("FAMILY");
+		bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+		
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
+		ourLog.info(encoded);
+		
+		bundle = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
+		dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
+		
+		assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
+		
+		Patient subject = (Patient) dm.getSubject().getResource();
+		assertNotNull(subject);
+		assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
+	}
+
+	
 	@Test
 	public void testIncorrectJsonTypesIdAndArray() {
 		
@@ -1660,8 +1653,8 @@ public class JsonParserDstu3Test {
 		ourLog.info(encoded);
 
 		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-		assertEquals("urn:uuid:", parsed.getEntry().get(0).getResource().getIdElement().getBaseUrl());
+		assertEquals(null, parsed.getEntry().get(0).getResource().getIdElement().getBaseUrl());
-		assertEquals("180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getIdPart());
+		assertEquals("urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57", parsed.getEntry().get(0).getResource().getIdElement().getIdPart());
 		assertThat(encoded, not(containsString("\"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\"")));
 	}
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -77,153 +77,31 @@ public class XmlParserDstu3Test {
 	}
 
 	/**
-	 * See #414
+	 * See #544
 	 */
 	@Test
-	public void testParseXmlExtensionWithoutUrl() {
+	public void testBundleStitchReferencesByUuid() throws Exception {
-		//@formatter:off
+		Bundle bundle = new Bundle();
-		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-			"        <extension>\n" + 
-			"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" + 
-			"        </extension>\n" + 
-			"</Patient>";
-		//@formatter:on
 		
-		IParser parser = ourCtx.newXmlParser();
+		DocumentManifest dm = new DocumentManifest();
-		parser.setParserErrorHandler(new LenientErrorHandler());
+		dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
-		Patient parsed = (Patient) parser.parseResource(input);
+		bundle.addEntry().setResource(dm);
-		assertEquals(1, parsed.getExtension().size());
-		assertEquals(null, parsed.getExtension().get(0).getUrl());
-		assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
-
-		try {
-			parser = ourCtx.newXmlParser();
-			parser.setParserErrorHandler(new StrictErrorHandler());
-			parser.parseResource(input);
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
-		}
-		
-	}
-
-	
-	/**
-	 * See #414
-	 */
-	@Test
-	public void testParseXmlModifierExtensionWithoutUrl() {
-		//@formatter:off
-		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-			"        <modifierExtension>\n" + 
-			"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" + 
-			"        </modifierExtension>\n" + 
-			"</Patient>";
-		//@formatter:on
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new LenientErrorHandler());
-		Patient parsed = (Patient) parser.parseResource(input);
-		assertEquals(1, parsed.getModifierExtension().size());
-		assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
-		assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
-
-		try {
-			parser = ourCtx.newXmlParser();
-			parser.setParserErrorHandler(new StrictErrorHandler());
-			parser.parseResource(input);
-			fail();
-		} catch (DataFormatException e) {
-			assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
-		}
-		
-	}
-
-	@Test
-	public void testEncodeChainedContainedResourcer() {
-		Organization gp = new Organization();
-		gp.setName("grandparent");
-
-		Organization parent = new Organization();
-		parent.setName("parent");
-		parent.getPartOf().setResource(gp);
-
-		Organization child = new Organization();
-		child.setName("child");
-		child.getPartOf().setResource(parent);
 		
 		Patient patient = new Patient();
-		patient.getManagingOrganization().setResource(child);
+		patient.addName().setFamily("FAMILY");
+		bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
 		
-		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
 		ourLog.info(encoded);
 		
-		patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+		bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
+		dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
 		
-		child = (Organization) patient.getManagingOrganization().getResource();
+		assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
-		assertEquals("child", child.getName());
 		
-		parent = (Organization) child.getPartOf().getResource();
+		Patient subject = (Patient) dm.getSubject().getResource();
-		assertEquals("parent", parent.getName());
+		assertNotNull(subject);
-
+		assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
-		gp = (Organization) parent.getPartOf().getResource();
-		assertEquals("grandparent", gp.getName());
-	}
-
-	/**
-	 * If a contained resource refers to a contained resource that comes after it, it should still be successfully
-	 * woven together.
-	 */
-	@Test
-	public void testParseWovenContainedResources() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new StrictErrorHandler());
-		org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
-
-		DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
-		Observation obs = (Observation) resource.getResult().get(1).getResource();
-		assertEquals("#2", obs.getId());
-		Reference performerFirstRep = obs.getPerformerFirstRep();
-		Practitioner performer = (Practitioner) performerFirstRep.getResource();
-		assertEquals("#3", performer.getId());
-	}
-
-	@Test(expected = DataFormatException.class)
-	public void testContainedResourceWithNoId() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new StrictErrorHandler());
-		parser.parseResource(Bundle.class, string);
-	}
-
-	@Test()
-	public void testContainedResourceWithNoIdLenient() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new LenientErrorHandler());
-		parser.parseResource(Bundle.class, string);
-	}
-
-	@Test(expected = DataFormatException.class)
-	public void testParseWithInvalidLocalRef() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new StrictErrorHandler());
-		parser.parseResource(Bundle.class, string);
-	}
-
-	@Test()
-	public void testParseWithInvalidLocalRefLenient() throws IOException {
-		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
-
-		IParser parser = ourCtx.newXmlParser();
-		parser.setParserErrorHandler(new LenientErrorHandler());
-		parser.parseResource(Bundle.class, string);
 	}
 	
 	@Test
@@ -257,6 +135,7 @@ public class XmlParserDstu3Test {
 
 	}
 
+	
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();
@@ -279,6 +158,24 @@ public class XmlParserDstu3Test {
 		assertEquals("ORG", o.getName());
 	}
 
+	@Test(expected = DataFormatException.class)
+	public void testContainedResourceWithNoId() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	@Test()
+	public void testContainedResourceWithNoIdLenient() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
 	@Test
 	public void testDuration() {
 		Encounter enc = new Encounter();
@@ -1023,6 +920,37 @@ public class XmlParserDstu3Test {
 		assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport")));
 	}
 
+	@Test
+	public void testEncodeChainedContainedResourcer() {
+		Organization gp = new Organization();
+		gp.setName("grandparent");
+
+		Organization parent = new Organization();
+		parent.setName("parent");
+		parent.getPartOf().setResource(gp);
+
+		Organization child = new Organization();
+		child.setName("child");
+		child.getPartOf().setResource(parent);
+
+		Patient patient = new Patient();
+		patient.getManagingOrganization().setResource(child);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+
+		child = (Organization) patient.getManagingOrganization().getResource();
+		assertEquals("child", child.getName());
+
+		parent = (Organization) child.getPartOf().getResource();
+		assertEquals("parent", parent.getName());
+
+		gp = (Organization) parent.getPartOf().getResource();
+		assertEquals("grandparent", gp.getName());
+	}
+
 	/**
 	 * See #326
 	 */
@@ -1929,8 +1857,6 @@ public class XmlParserDstu3Test {
 		assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>"));
 	}
 
-	
-
 	@Test
 	public void testMoreExtensions() throws Exception {
 
@@ -2176,6 +2102,8 @@ public class XmlParserDstu3Test {
 
 	}
 
+	
+
 	@Test
 	public void testParseAndEncodeCommentsOnExtensions() {
 		//@formatter:off
@@ -3105,6 +3033,106 @@ public class XmlParserDstu3Test {
 		}
 	}
 
+	@Test(expected = DataFormatException.class)
+	public void testParseWithInvalidLocalRef() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	@Test()
+	public void testParseWithInvalidLocalRefLenient() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	/**
+	 * If a contained resource refers to a contained resource that comes after it, it should still be successfully
+	 * woven together.
+	 */
+	@Test
+	public void testParseWovenContainedResources() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
+
+		DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
+		Observation obs = (Observation) resource.getResult().get(1).getResource();
+		assertEquals("#2", obs.getId());
+		Reference performerFirstRep = obs.getPerformerFirstRep();
+		Practitioner performer = (Practitioner) performerFirstRep.getResource();
+		assertEquals("#3", performer.getId());
+	}
+
+	/**
+	 * See #414
+	 */
+	@Test
+	public void testParseXmlExtensionWithoutUrl() {
+		//@formatter:off
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+			"        <extension>\n" + 
+			"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" + 
+			"        </extension>\n" + 
+			"</Patient>";
+		//@formatter:on
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		Patient parsed = (Patient) parser.parseResource(input);
+		assertEquals(1, parsed.getExtension().size());
+		assertEquals(null, parsed.getExtension().get(0).getUrl());
+		assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
+
+		try {
+			parser = ourCtx.newXmlParser();
+			parser.setParserErrorHandler(new StrictErrorHandler());
+			parser.parseResource(input);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
+		}
+		
+	}
+
+	/**
+	 * See #414
+	 */
+	@Test
+	public void testParseXmlModifierExtensionWithoutUrl() {
+		//@formatter:off
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+			"        <modifierExtension>\n" + 
+			"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" + 
+			"        </modifierExtension>\n" + 
+			"</Patient>";
+		//@formatter:on
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		Patient parsed = (Patient) parser.parseResource(input);
+		assertEquals(1, parsed.getModifierExtension().size());
+		assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
+		assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
+
+		try {
+			parser = ourCtx.newXmlParser();
+			parser.setParserErrorHandler(new StrictErrorHandler());
+			parser.parseResource(input);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
+		}
+		
+	}
+
 	/**
 	 * See #339
 	 * 

src/changes/changes.xml

@@ -222,6 +222,17 @@
 				return an HTTP 404 and not a 400, per the HTTP spec. Thanks to 
 				GitHub user @CarthageKing for the pull request!
 			</action>
+			<action type="fix" issue="544">
+				When parsing a Bundle containing placeholder fullUrls and references
+				(e.g. "urn:uuid:0000-0000") the resource reference targets did not get
+				populated with the given resources. Note that as a part of this
+				change, <![CDATA[<code>IdType</code> and <code>IdDt</code>]]> have been modified
+				so that when parsing a placeholder ID, the complete placeholder including the
+				"urn:uuid:" or "urn:oid:" prefix will be placed into the ID part. Previously,
+				the prefix was treated as the base URL, which led to strange behaviour
+				like the placeholder being treated as a real IDs. Thanks to GitHub
+				user @jodue for reporting!
+			</action>
 		</release>
 		<release version="2.1" date="2016-11-11">
 			<action type="add">