Merge branch 'philips-3.6.0'

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

@@ -65,6 +65,15 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
 		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
 		List<IBaseResource> retVal = txTemplate.execute(theStatus -> toResourceList(mySearchBuilder, pids));
 
+		int totalCountWanted = theToIndex - theFromIndex;
+		if (retVal.size() < totalCountWanted) {
+			if (mySearch.getStatus() == SearchStatusEnum.PASSCMPLET) {
+				int remainingWanted = totalCountWanted - retVal.size();
+				int fromIndex = theToIndex - remainingWanted;
+				List<IBaseResource> remaining = super.getResources(fromIndex, theToIndex);
+				retVal.addAll(remaining);
+			}
+		}
 		ourLog.trace("Loaded resources to return");
 
 		return retVal;

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

@@ -229,17 +229,19 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 			txTemplate.afterPropertiesSet();
 			return txTemplate.execute(t -> {
-				myEntityManager.refresh(theSearch);
+				Search search = mySearchDao.findById(theSearch.getId()).orElse(theSearch);
-				if (theSearch.getStatus() != SearchStatusEnum.PASSCMPLET) {
+
+				if (search.getStatus() != SearchStatusEnum.PASSCMPLET) {
 					throw new IllegalStateException("Can't change to LOADING because state is " + theSearch.getStatus());
 				}
-				theSearch.setStatus(SearchStatusEnum.LOADING);
+				search.setStatus(SearchStatusEnum.LOADING);
-				Search newSearch = mySearchDao.save(theSearch);
+				Search newSearch = mySearchDao.save(search);
 				return Optional.of(newSearch);
 			});
 		} catch (Exception e) {
 			ourLog.warn("Failed to activate search: {}", e.toString());
-			ourLog.trace("Failed to activate search", e);
+			// FIXME: aaaaa
+			ourLog.info("Failed to activate search", e);
 			return Optional.empty();
 		}
 	}
@@ -511,9 +513,10 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 								 * user has requested resources 0-60, then they would get 0-50 back but the search
 								 * coordinator would then stop searching.SearchCoordinatorSvcImplTest
 								 */
-								List<Long> remainingResources = SearchCoordinatorSvcImpl.this.getResources(mySearch.getUuid(), mySyncedPids.size(), theToIndex);
+								// FIXME: aaaaaaaa
-								ourLog.debug("Adding {} resources to the existing {} synced resource IDs", remainingResources.size(), mySyncedPids.size());
+//								List<Long> remainingResources = SearchCoordinatorSvcImpl.this.getResources(mySearch.getUuid(), mySyncedPids.size(), theToIndex);
-								mySyncedPids.addAll(remainingResources);
+//								ourLog.debug("Adding {} resources to the existing {} synced resource IDs", remainingResources.size(), mySyncedPids.size());
+//								mySyncedPids.addAll(remainingResources);
 								keepWaiting = false;
 								break;
 							case FAILED:

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -176,6 +176,70 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 		return null;
 	}
 	
+	@Test
+	public void testTransactionReSavesPreviouslyDeletedResources() {
+
+		{
+			Bundle input = new Bundle();
+			input.setType(BundleType.TRANSACTION);
+
+			Patient pt = new Patient();
+			pt.setId("pt");
+			pt.setActive(true);
+			input
+				.addEntry()
+				.setResource(pt)
+				.getRequest()
+				.setUrl("Patient/pt")
+				.setMethod(HTTPVerb.PUT);
+
+			Observation obs = new Observation();
+			obs.setId("obs");
+			obs.getSubject().setReference("Patient/pt");
+			input
+				.addEntry()
+				.setResource(obs)
+				.getRequest()
+				.setUrl("Observation/obs")
+				.setMethod(HTTPVerb.PUT);
+
+			mySystemDao.transaction(null, input);
+		}
+
+		myObservationDao.delete(new IdType("Observation/obs"));
+		myPatientDao.delete(new IdType("Patient/pt"));
+
+		{
+			Bundle input = new Bundle();
+			input.setType(BundleType.TRANSACTION);
+
+			Patient pt = new Patient();
+			pt.setId("pt");
+			pt.setActive(true);
+			input
+				.addEntry()
+				.setResource(pt)
+				.getRequest()
+				.setUrl("Patient/pt")
+				.setMethod(HTTPVerb.PUT);
+
+			Observation obs = new Observation();
+			obs.setId("obs");
+			obs.getSubject().setReference("Patient/pt");
+			input
+				.addEntry()
+				.setResource(obs)
+				.getRequest()
+				.setUrl("Observation/obs")
+				.setMethod(HTTPVerb.PUT);
+
+			mySystemDao.transaction(null, input);
+		}
+
+		myPatientDao.read(new IdType("Patient/pt"));
+	}
+	
+
 	@Test
 	public void testResourceCounts() {
 		Patient p = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -34,7 +34,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
-import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.transaction.PlatformTransactionManager;
 
@@ -52,6 +51,7 @@ import static org.mockito.Mockito.*;
 @RunWith(MockitoJUnitRunner.class)
 public class SearchCoordinatorSvcImplTest {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSvcImplTest.class);
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 	@Captor
 	ArgumentCaptor<Iterable<SearchResult>> mySearchResultIterCaptor;
@@ -69,7 +69,6 @@ public class SearchCoordinatorSvcImplTest {
 	@Mock
 	private ISearchResultDao mySearchResultDao;
 	private SearchCoordinatorSvcImpl mySvc;
-
 	@Mock
 	private PlatformTransactionManager myTxManager;
 	private DaoConfig myDaoConfig;
@@ -159,7 +158,7 @@ public class SearchCoordinatorSvcImplTest {
 		}
 
 	}
-private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSvcImplTest.class);
+
 	@Test
 	public void testAsyncSearchLargeResultSetBigCountSameCoordinator() {
 		SearchParameterMap params = new SearchParameterMap();
@@ -174,7 +173,7 @@ private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSv
 			List<Long> returnedValues = iter.getReturnedValues();
 			Pageable page = (Pageable) t.getArguments()[1];
 			int offset = (int) page.getOffset();
-			int end = (int)(page.getOffset() + page.getPageSize());
+			int end = (int) (page.getOffset() + page.getPageSize());
 			end = Math.min(end, returnedValues.size());
 			offset = Math.min(offset, returnedValues.size());
 			ourLog.info("findWithSearchUuid {} - {} out of {} values", offset, end, returnedValues.size());
@@ -214,7 +213,7 @@ private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSv
 		assertEquals(10, allResults.get(0).getResourcePid().longValue());
 		assertEquals(799, allResults.get(789).getResourcePid().longValue());
 
-		myExpectedNumberOfSearchBuildersCreated = 3;
+		myExpectedNumberOfSearchBuildersCreated = 4;
 	}
 
 	@Test

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java

@@ -223,16 +223,6 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 				int start = Math.max(0, theOffset - theLimit);
 				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
 			}
-//			int offset = theOffset + resourceList.size();
-//
-//			// We're doing offset pages
-//			if (numTotalResults == null || offset < numTotalResults) {
-//				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, offset, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
-//			}
-//			if (theOffset > 0) {
-//				int start = Math.max(0, theOffset - theLimit);
-//				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
-//			}
 		}
 
 		bundleFactory.addRootPropertiesToBundle(theResult.getUuid(), serverBase, theLinkSelf, linkPrev, linkNext, theResult.size(), theBundleType, theResult.getPublished());

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/util/FhirTerserDstu3Test.java

@@ -27,6 +27,35 @@ public class FhirTerserDstu3Test {
 
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 
+	@Test
+	public void testCloneIntoBundle() {
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.TRANSACTION);
+
+		Patient pt = new Patient();
+		pt.setId("pt");
+		pt.setActive(true);
+		input
+			.addEntry()
+			.setResource(pt)
+			.getRequest()
+			.setUrl("Patient/pt")
+			.setMethod(Bundle.HTTPVerb.PUT);
+
+		Observation obs = new Observation();
+		obs.setId("obs");
+		obs.getSubject().setReference("Patient/pt");
+		input
+			.addEntry()
+			.setResource(obs)
+			.getRequest()
+			.setUrl("Observation/obs")
+			.setMethod(Bundle.HTTPVerb.PUT);
+
+		Bundle ionputClone = new Bundle();
+		ourCtx.newTerser().cloneInto(input, ionputClone, false);
+	}
+
 	@Test
 	public void testCloneIntoComposite() {
 		Quantity source = new Quantity();