Correctly update versions on transactipn update

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

@@ -378,12 +378,13 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 	 * 
 	 * @throws DataFormatException
 	 */
-	public void setPrecision(TemporalPrecisionEnum thePrecision) throws DataFormatException {
+	public BaseDateTimeDt setPrecision(TemporalPrecisionEnum thePrecision) throws DataFormatException {
 		if (thePrecision == null) {
 			throw new NullPointerException("Precision may not be null");
 		}
 		myPrecision = thePrecision;
 		updateStringValue();
+		return this;
 	}
 
 	private BaseDateTimeDt setTimeZone(String theWholeValue, String theValue) {

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

@@ -369,7 +369,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		// Perform actual DB update
-		updateEntity(theResource, entity, null, thePerformIndexing, true, theUpdateTime);
+		updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, theUpdateTime);
 		theResource.setId(entity.getIdDt());
 
 		// Notify JPA interceptors
@@ -1080,7 +1080,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		// Perform update
-		ResourceTable savedEntity = updateEntity(theResource, entity, null, thePerformIndexing, true, new Date());
+		ResourceTable savedEntity = updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, new Date());
 
 		// Notify interceptors
 		if (theRequestDetails != null) {

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

@@ -185,10 +185,12 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 
 	@Override
 	public IBundleProvider history(Date theSince, Date theUntil, RequestDetails theRequestDetails) {
-		// Notify interceptors
+		if (theRequestDetails != null) {
-		ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
+			// Notify interceptors
-		notifyInterceptors(RestOperationTypeEnum.HISTORY_SYSTEM, requestDetails);
+			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
-
+			notifyInterceptors(RestOperationTypeEnum.HISTORY_SYSTEM, requestDetails);
+		}
+		
 		StopWatch w = new StopWatch();
 		IBundleProvider retVal = super.history(null, null, theSince, theUntil);
 		ourLog.info("Processed global history in {}ms", w.getMillisAndRestart());

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

@@ -29,6 +29,7 @@ import java.util.Collections;
 import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.LinkedHashSet;
@@ -39,6 +40,7 @@ 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;
@@ -315,7 +317,9 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		
 		List<IIdType> deletedResources = new ArrayList<IIdType>();
 		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
-		
+		Map<Entry, ResourceTable> entriesToProcess = new IdentityHashMap<Entry, ResourceTable>();
+		Set<ResourceTable> nonUpdatedEntities = new HashSet<ResourceTable>();
+
 		/*
 		 * Loop through the request and process any entries of type
 		 * PUT, POST or DELETE
@@ -381,6 +385,10 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				DaoMethodOutcome outcome;
 				outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails);
 				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+				entriesToProcess.put(nextRespEntry, outcome.getEntity());
+				if (outcome.getCreated() == false) {
+					nonUpdatedEntities.add(outcome.getEntity());
+				}
 				break;
 			}
 			case DELETE: {
@@ -426,6 +434,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				}
 
 				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				break;
 			}
 			}
@@ -474,7 +483,8 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
-			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, updateTime);
+			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
+			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, shouldUpdate, updateTime);
 		}
 
 		myEntityManager.flush();
@@ -578,6 +588,11 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		ourLog.info("Flushing context after {}", theActionName);
 		myEntityManager.flush();
 		
+		for (java.util.Map.Entry<Entry, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
+			nextEntry.getKey().getResponse().setLocation(nextEntry.getValue().getIdDt().toUnqualified().getValue());
+			nextEntry.getKey().getResponse().setEtag(nextEntry.getValue().getIdDt().getVersionIdPart());
+		}
+		
 		long delay = System.currentTimeMillis() - start;
 		int numEntries = theRequest.getEntry().size();
 		long delayPer = delay / numEntries;
@@ -606,8 +621,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		} else {
 			newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
 		}
-		newEntry.getResponse().setLocation(outcome.getId().toUnqualified().getValue());
-		newEntry.getResponse().setEtag(outcome.getId().getVersionIdPart());
 		newEntry.getResponse().setLastModified(ResourceMetadataKeyEnum.UPDATED.get(theRes));
 	}
 

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

@@ -35,6 +35,7 @@ import java.util.Iterator;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
 
 import javax.persistence.TypedQuery;
@@ -264,9 +265,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
-		ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
+		if (theRequestDetails != null) {
-		notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
+			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
-
+			notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
+		}
+		
 		String actionName = "Transaction";
 		return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
 	}
@@ -329,6 +332,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		
 		Set<String> deletedResources = new HashSet<String>();
 		List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
+		Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<BundleEntryComponent, ResourceTable>();
+		Set<ResourceTable> nonUpdatedEntities = new HashSet<ResourceTable>();
 		
 		/*
 		 * Loop through the request and process any entries of type
@@ -392,6 +397,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				DaoMethodOutcome outcome;
 				outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails);
 				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+				entriesToProcess.put(nextRespEntry, outcome.getEntity());
+				if (outcome.getCreated() == false) {
+					nonUpdatedEntities.add(outcome.getEntity());
+				}
+
 				break;
 			}
 			case DELETE: {
@@ -426,10 +436,10 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				@SuppressWarnings("rawtypes")
 				IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
 
-				DaoMethodOutcome outcome;
 
 				String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
 
+				DaoMethodOutcome outcome;
 				UrlParts parts = UrlUtil.parseUrl(url);
 				if (isNotBlank(parts.getResourceId())) {
 					res.setId(new IdType(parts.getResourceType(), parts.getResourceId()));
@@ -440,6 +450,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 				}
 
 				handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+				entriesToProcess.put(nextRespEntry, outcome.getEntity());
 				break;
 			}
 			}
@@ -481,6 +492,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 					IdType newId = idSubstitutions.get(nextId);
 					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
 					nextRef.setReference(newId.getValue());
+				} else if (nextId.getValue().startsWith("urn:")) {
+					throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
 				} else {
 					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
 				}
@@ -488,7 +501,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 			IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
 			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
-			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, updateTime);
+			boolean shouldUpdate = !nonUpdatedEntities.contains(nextOutcome.getEntity());
+			updateEntity(nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, shouldUpdate, shouldUpdate, updateTime);
 		}
 
 		myEntityManager.flush();
@@ -589,6 +603,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 		}
 		
+		for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
+			nextEntry.getKey().getResponse().setLocation(nextEntry.getValue().getIdDt().toUnqualified().getValue());
+			nextEntry.getKey().getResponse().setEtag(nextEntry.getValue().getIdDt().getVersionIdPart());
+		}
+		
 		long delay = System.currentTimeMillis() - start;
 		ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
 
@@ -615,8 +634,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 		} else {
 			newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
 		}
-		newEntry.getResponse().setLocation(outcome.getId().toUnqualified().getValue());
-		newEntry.getResponse().setEtag(outcome.getId().getVersionIdPart());
 		newEntry.getResponse().setLastModified(((Resource)theRes).getMeta().getLastUpdated());
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java

@@ -72,6 +72,11 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	@OneToMany(mappedBy = "myResourceHistory", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
 	private Collection<ResourceHistoryTag> myTags;
 
+	public ResourceHistoryTable() {
+		super();
+	}
+	
+	
 	public void addTag(ResourceHistoryTag theTag) {
 		for (ResourceHistoryTag next : getTags()) {
 			if (next.getTag().equals(theTag)) {

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

@@ -16,6 +16,7 @@ import javax.persistence.EntityManager;
 import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.Search;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -78,6 +79,14 @@ public abstract class BaseJpaTest {
 		return theSearch.getResources(0, theSearch.size());
 	}
 
+	protected org.hl7.fhir.dstu3.model.Bundle toBundle(IBundleProvider theSearch) {
+		org.hl7.fhir.dstu3.model.Bundle bundle = new org.hl7.fhir.dstu3.model.Bundle();
+		for (IBaseResource next : theSearch.getResources(0, theSearch.size())) {
+			bundle.addEntry().setResource((Resource) next);
+		}
+		return bundle;
+	}
+
 	protected abstract FhirContext getContext();
 	
 	protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {

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

@@ -1262,13 +1262,15 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 		Bundle resp = mySystemDao.transaction(mySrd, request);
 		assertEquals(2, resp.getEntry().size());
+		
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
 
 		Entry nextEntry = resp.getEntry().get(0);
 		assertEquals("200 OK", nextEntry.getResponse().getStatus());
 		assertThat(nextEntry.getResponse().getLocation(), not(containsString("test")));
 		assertEquals(id.toVersionless(), p.getId().toVersionless());
-		assertNotEquals(id, p.getId());
 		assertThat(p.getId().toString(), endsWith("/_history/2"));
+		assertNotEquals(id, p.getId());
 
 		nextEntry = resp.getEntry().get(0);
 		assertEquals(Constants.STATUS_HTTP_200_OK + " OK", nextEntry.getResponse().getStatus());

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

@@ -24,6 +24,8 @@ import java.io.UnsupportedEncodingException;
 import java.nio.charset.StandardCharsets;
 import java.util.List;
 
+import javax.mail.Quota.Resource;
+
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.Appointment;
 import org.hl7.fhir.dstu3.model.Bundle;
@@ -98,7 +100,59 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(mo));
 	}
 
+	@Test
+	public void testTransactionDoesNotAllowDanglingTemporaryIds() throws Exception {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/cdr-bundle.json"), StandardCharsets.UTF_8);
+		Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		
+		BundleEntryComponent entry = bundle.addEntry();
+		Patient p = new Patient();
+		p.getManagingOrganization().setReference("urn:uuid:30ce60cf-f7cb-4196-961f-cadafa8b7ff5");
+		entry.setResource(p);
+		entry.getRequest().setMethod(HTTPVerb.POST);
+		entry.getRequest().setUrl("Patient");
+		
+		try {
+			mySystemDao.transaction(mySrd, bundle);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Unable to satisfy placeholder ID: urn:uuid:30ce60cf-f7cb-4196-961f-cadafa8b7ff5", e.getMessage());
+		}
+	}
 	
+	@Test
+	public void testTransactionDoesNotLeavePlaceholderIds() throws Exception {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/cdr-bundle.json"), StandardCharsets.UTF_8);
+		Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		mySystemDao.transaction(mySrd, bundle);
+		
+		IBundleProvider history = mySystemDao.history(null, null, null);
+		Bundle list = toBundle(history);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(list));
+		
+		assertEquals(6, list.getEntry().size());
+		
+		Patient p = find(list, Patient.class, 0);
+		assertTrue(p.getIdElement().isIdPartValidLong());
+		assertTrue(p.getGeneralPractitionerFirstRep().getReferenceElement().isIdPartValidLong());
+	}
+	
+	@SuppressWarnings("unchecked")
+	private <T extends org.hl7.fhir.dstu3.model.Resource> T find(Bundle theBundle, Class<T> theType, int theIndex) {
+		int count = 0;
+		for (BundleEntryComponent nextEntry : theBundle.getEntry()) {
+			if (nextEntry.getResource() != null && theType.isAssignableFrom(nextEntry.getResource().getClass())) {
+				if (count == theIndex) {
+					T t = (T) nextEntry.getResource();
+					return t;
+				}
+				count++;
+			}
+		}
+		fail();
+		return null;
+	}
+
 	@Test
 	public void testTransactionFromBundle2() throws Exception {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/transaction-bundle.xml"), StandardCharsets.UTF_8);

hapi-fhir-jpaserver-base/src/test/resources/cdr-bundle.json

@@ -0,0 +1,319 @@
+ {
+	"resourceType": "Bundle",
+	"entry": [
+		{
+			"fullUrl": "urn:uuid:7079b926-3bc9-4848-874b-da066b3b0ceb",
+			"resource": {
+				"resourceType": "Practitioner",
+				"identifier": [
+					{
+						"system": "http://acme.org/clinicians",
+						"value": "777"
+					}
+				],
+				"name": [
+					{
+						"family": [
+							"Jones"
+						],
+						"given": [
+							"Lisa",
+							"Frances"
+						]
+					}
+				],
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "1(837)555-1978",
+						"use": "work"
+					}
+				],
+				"address": [
+					{
+						"use": "work",
+						"line": [
+							"123 Brewer Street"
+						],
+						"city": "Buffalo",
+						"state": "NY",
+						"postalCode": "98765",
+						"country": "USA"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C777"
+			}
+		},
+		{
+			"fullUrl": "urn:uuid:47521791-e0f9-4eb4-b65d-be4ec2b602bf",
+			"resource": {
+				"resourceType": "Patient",
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://hl7.org/fhir/v2/0203",
+									"code": "MR"
+								}
+							]
+						},
+						"system": "http://acme.org/mrns",
+						"value": "7000135"
+					},
+					{
+						"use": "secondary",
+						"type": {
+							"coding": [
+								{
+									"system": "http://hl7.org/fhir/v2/0203",
+									"code": "SB"
+								}
+							]
+						},
+						"system": "http://acme.org/secondaryIds",
+						"value": "01238638267"
+					}
+				],
+				"name": [
+					{
+						"use": "official",
+						"family": [
+							"Smith"
+						],
+						"given": [
+							"John",
+							"Q"
+						],
+						"suffix": [
+							"Jr"
+						]
+					}
+				],
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "1(333)555-1234",
+						"use": "home"
+					}
+				],
+				"gender": "male",
+				"birthDate": "1965-03-22",
+				"deceasedBoolean": false,
+				"address": [
+					{
+						"use": "home",
+						"line": [
+							"342 Evergreen Terrace",
+							"2nd Floor"
+						],
+						"city": "Springfield",
+						"state": "NI",
+						"postalCode": "12345",
+						"country": "USA"
+					}
+				],
+				"generalPractitioner": [
+					{
+						"reference": "urn:uuid:7079b926-3bc9-4848-874b-da066b3b0ceb"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "/Patient?identifier=http%253A%252F%252Facme.org%252Fmrns%257C7000135"
+			}
+		},
+		{
+			"fullUrl": "urn:uuid:fd42a622-66ce-4a76-bbb6-573c018e29ed",
+			"resource": {
+				"resourceType": "Encounter",
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://hl7.org/fhir/v2/0203",
+									"code": "VN"
+								}
+							]
+						},
+						"system": "http://acme.org/visitNumbers",
+						"value": "4736455"
+					}
+				],
+				"class": {
+					"system": "http://hl7.org/fhir/v3/ActCode",
+					"code": "IMP",
+					"display": "Inpatient"
+				},
+				"patient": {
+					"reference": "urn:uuid:47521791-e0f9-4eb4-b65d-be4ec2b602bf"
+				},
+				"participant": [
+					{
+						"type": [
+							{
+								"coding": [
+									{
+										"system": "http://hl7.org/fhir/v3/ParticipationType",
+										"code": "ADM",
+										"display": "admitter"
+									}
+								]
+							}
+						],
+						"individual": {
+							"reference": "urn:uuid:5e0a848f-0b14-4068-8618-aa3c08c242ab"
+						}
+					},
+					{
+						"type": [
+							{
+								"coding": [
+									{
+										"system": "http://hl7.org/fhir/v3/ParticipationType",
+										"code": "ATND",
+										"display": "attender"
+									}
+								]
+							}
+						],
+						"individual": {
+							"reference": "urn:uuid:2cc6e9d3-0abb-4544-9b8e-3892f22b533b"
+						}
+					}
+				],
+				"period": {
+					"start": "2016-01-22T09:44:30-04:00",
+					"end": "2016-01-22T09:44:31-04:00"
+				},
+				"location": [
+					{
+						"location": {
+							"reference": "urn:uuid:76f243bc-49f2-40da-9064-379fcbc151d2"
+						}
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "/Encounter?identifier=http%253A%252F%252Facme.org%252FvisitNumbers%257C4736455"
+			}
+		},
+		{
+			"fullUrl": "urn:uuid:76f243bc-49f2-40da-9064-379fcbc151d2",
+			"resource": {
+				"resourceType": "Location",
+				"identifier": [
+					{
+						"system": "http://acme.org/beds",
+						"value": "124 6"
+					}
+				],
+				"name": "6",
+				"description": "124 Bed 6"
+			},
+			"request": {
+				"method": "POST",
+				"url": "/Location",
+				"ifNoneExist": "Location?name=6"
+			}
+		},
+		{
+			"fullUrl": "urn:uuid:5e0a848f-0b14-4068-8618-aa3c08c242ab",
+			"resource": {
+				"resourceType": "Practitioner",
+				"identifier": [
+					{
+						"system": "http://acme.org/clinicians",
+						"value": "3622"
+					}
+				],
+				"name": [
+					{
+						"family": [
+							"Hawkins"
+						],
+						"given": [
+							"Finnie"
+						]
+					}
+				],
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "1(837)555-2133",
+						"use": "work"
+					}
+				],
+				"address": [
+					{
+						"use": "work",
+						"line": [
+							"20 Canal St"
+						],
+						"city": "Buffalo",
+						"state": "NY",
+						"postalCode": "98222",
+						"country": "USA"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C3622"
+			}
+		},
+		{
+			"fullUrl": "urn:uuid:2cc6e9d3-0abb-4544-9b8e-3892f22b533b",
+			"resource": {
+				"resourceType": "Practitioner",
+				"identifier": [
+					{
+						"system": "http://acme.org/clinicians",
+						"value": "7452"
+					}
+				],
+				"name": [
+					{
+						"family": [
+							"May"
+						],
+						"given": [
+							"Sadie"
+						]
+					}
+				],
+				"telecom": [
+					{
+						"system": "phone",
+						"value": "1(837)555-6624",
+						"use": "work"
+					}
+				],
+				"address": [
+					{
+						"use": "work",
+						"line": [
+							"313 Fleet Street"
+						],
+						"city": "Cheektowaga",
+						"state": "NY",
+						"postalCode": "28366",
+						"country": "USA"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "/Practitioner?identifier=http%253A%252F%252Facme.org%252Fclinicians%257C7452"
+			}
+		}
+	]
+}

hapi-fhir-structures-dstu3/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,95 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=warning
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=warning
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=warning
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=error
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=warning
+org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
+org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
+org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
+org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
+org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
+org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
+org.eclipse.jdt.core.compiler.problem.nullReference=error
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
+org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=warning
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
+org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullCheck=warning
+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
+org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
+org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
+org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
+org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
+org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
+org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
+org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
+org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=warning
+org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=warning
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
+org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
+org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
+org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/utils/FluentPathEngine.java

@@ -649,7 +649,7 @@ public class FluentPathEngine {
         ExpressionNode node = group;
         focus = group.getOpNext();
         if (focus != null) { 
-          while (focus == null && !ops.contains(focus.getOperation())) {
+          while (focus != null && !ops.contains(focus.getOperation())) {
             node = focus;
             focus = focus.getOpNext();
           }

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/validation/InstanceValidator.java

@@ -690,7 +690,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     else if (fixed == null && focus != null)
       rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Unexpected element " + focus.getName());
     else if (fixed != null && focus == null)
-      rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Mising element " + propName);
+      rule(errors, IssueType.VALUE, 0, 0, path, false, "Mising element " + propName);
     else {
       String value = focus.primitiveValue();
       if (fixed instanceof org.hl7.fhir.dstu3.model.BooleanType)

hapi-fhir-structures-hl7org-dstu2/.settings/org.eclipse.jdt.core.prefs

@@ -1,10 +1,103 @@
 eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
 org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=warning
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=warning
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=warning
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=warning
+org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
+org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
+org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
+org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
+org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
+org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
+org.eclipse.jdt.core.compiler.problem.nullReference=error
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
+org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=warning
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
+org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
+org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullCheck=warning
+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
+org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
+org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
+org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
+org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
+org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
+org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
+org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
+org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=warning
+org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=warning
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
+org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
+org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
+org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
 org.eclipse.jdt.core.compiler.source=1.6
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/validation/InstanceValidator.java

@@ -464,7 +464,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     else if (fixed == null && focus != null)
       rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Unexpected element " + focus.getName());
     else if (fixed != null && focus == null)
-      rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, "Mising element " + propName);
+      rule(errors, IssueType.VALUE, 0, 0, path, false, "Mising element " + propName);
     else {
       String value = focus.getAttribute("value");
       if (fixed instanceof org.hl7.fhir.instance.model.BooleanType)

src/changes/changes.xml

@@ -210,6 +210,13 @@
 				Parser failed to parse resources containing an extension with a value type of
 				"id". Thanks to Raphael Mäder for reporting!  
 			</action>
+			<action type="fix">
+				When committing a transaction in JPA server
+				where the transaction contained placeholder IDs
+				for references between bundles, the placeholder
+				IDs were not substituted with viewing
+				resources using the _history operation
+			</action>
 		</release>
 		<release version="1.6" date="2016-07-07">
 			<action type="fix">