Implement JPA transaction deletion operation

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

@@ -811,7 +811,7 @@ public abstract class BaseFhirDao implements IDao {
 		}
 	}
 
-	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, boolean theDelete) {
+	protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory, Date theDeletedTimestampOrNull) {
 		if (entity.getPublished() == null) {
 			entity.setPublished(new Date());
 		}
@@ -843,7 +843,7 @@ public abstract class BaseFhirDao implements IDao {
 		final List<ResourceIndexedSearchParamQuantity> quantityParams;
 		final List<ResourceIndexedSearchParamDate> dateParams;
 		final List<ResourceLink> links;
-		if (theDelete) {
+		if (theDeletedTimestampOrNull != null) {
 
 			stringParams = Collections.emptyList();
 			tokenParams = Collections.emptyList();
@@ -851,8 +851,8 @@ public abstract class BaseFhirDao implements IDao {
 			quantityParams = Collections.emptyList();
 			dateParams = Collections.emptyList();
 			links = Collections.emptyList();
-			entity.setDeleted(new Date());
+			entity.setDeleted(theDeletedTimestampOrNull);
-			entity.setUpdated(new Date());
+			entity.setUpdated(theDeletedTimestampOrNull);
 
 		} else {
 

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.dao;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
@@ -68,9 +69,6 @@ import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
 import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
-import ca.uhn.fhir.model.dstu.composite.CodingDt;
-import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
-import ca.uhn.fhir.model.dstu.composite.QuantityDt;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
 import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
@@ -163,7 +161,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 
 		}
 
-		updateEntity(theResource, entity, false, false);
+		updateEntity(theResource, entity, false, null);
 
 		MethodOutcome outcome = toMethodOutcome(entity);
 		notifyWriteCompleted();
@@ -179,7 +177,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 			throw new InvalidRequestException("Trying to update " + theId + " but this is not the current version");
 		}
 
-		ResourceTable savedEntity = updateEntity(null, entity, true, true);
+		ResourceTable savedEntity = updateEntity(null, entity, true, new Date());
 
 		notifyWriteCompleted();
 
@@ -490,7 +488,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 
 						// Execute the query and make sure we return distinct results
 						List<IResource> retVal = new ArrayList<IResource>();
-						loadResourcesByPid(pidsSubList, retVal);
+						loadResourcesByPid(pidsSubList, retVal, BundleEntryStatusEnum.MATCH);
 
 						// Load _include resources
 						if (theParams.getIncludes() != null && theParams.getIncludes().isEmpty() == false) {
@@ -748,7 +746,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 			throw new InvalidRequestException("Trying to update " + theId + " but this is not the current version");
 		}
 
-		ResourceTable savedEntity = updateEntity(theResource, entity, true, false);
+		ResourceTable savedEntity = updateEntity(theResource, entity, true, null);
 
 		notifyWriteCompleted();
 		ourLog.info("Processed update on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
@@ -1423,7 +1421,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 		createSort(theBuilder, theFrom, theSort.getChain(), theOrders, thePredicates);
 	}
 
-	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IResource> theResourceListToPopulate) {
+	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IResource> theResourceListToPopulate, BundleEntryStatusEnum theBundleEntryStatus) {
 		if (theIncludePids.isEmpty()) {
 			return;
 		}
@@ -1450,6 +1448,9 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 				ourLog.warn("Got back unexpected resource PID {}", next.getId());
 				continue;
 			}
+			
+			ResourceMetadataKeyEnum.ENTRY_STATUS.put(resource, theBundleEntryStatus);
+
 			theResourceListToPopulate.set(index, resource);
 		}
 	}

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

@@ -3,8 +3,10 @@ package ca.uhn.fhir.jpa.dao;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -20,12 +22,15 @@ import org.springframework.transaction.annotation.Transactional;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
 import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.FhirTerser;
 
@@ -41,11 +46,24 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
 		ourLog.info("Beginning transaction with {} resources", theResources.size());
 		long start = System.currentTimeMillis();
 
+		Set<IdDt> allIds = new HashSet<IdDt>();
+		
 		for (int i =0; i <theResources.size();i++) {
 			IResource res = theResources.get(i);
 			if(res.getId().hasIdPart() && !res.getId().hasResourceType()) {
 				res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
 			}
+			
+			/*
+			 * Ensure that the bundle doesn't have any duplicates, since this causes all
+			 * kinds of weirdness
+			 */
+			if (res.getId().hasResourceType() && res.getId().hasIdPart()) {
+				IdDt nextId = res.getId().toUnqualifiedVersionless();
+				if (!allIds.add(nextId)) {
+					throw new InvalidRequestException("Transaction bundle contains multiple resources with ID: " + nextId);
+				}
+			}
 		}
 		
 		FhirTerser terser = getContext().newTerser();
@@ -65,12 +83,6 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
 
 			String resourceName = toResourceName(nextResource);
 
-			// IFhirResourceDao<? extends IResource> dao = getDao(nextResource.getClass());
-			// if (dao == null) {
-			// throw new InvalidRequestException("This server is not able to handle resources of type: " +
-			// nextResource.getResourceId().getResourceType());
-			// }
-
 			ResourceTable entity;
 			if (nextId.isEmpty()) {
 				entity = null;
@@ -150,7 +162,9 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
 		for (int i = 0; i < theResources.size(); i++) {
 			IResource resource = theResources.get(i);
 			ResourceTable table = persistedResources.get(i);
-			updateEntity(resource, table, table.getId() != null, false);
+			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
+			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
+			updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull);
 		}
 
 		long delay = System.currentTimeMillis() - start;

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

@@ -1,7 +1,16 @@
 package ca.uhn.fhir.jpa.dao;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.equalToIgnoringCase;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
 
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -11,13 +20,11 @@ import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.io.IOUtils;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 
-import ch.qos.logback.core.pattern.color.BlackCompositeConverter;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
@@ -25,16 +32,16 @@ import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.dev.composite.IdentifierDt;
 import ca.uhn.fhir.model.dev.composite.QuantityDt;
-import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dev.resource.Device;
 import ca.uhn.fhir.model.dev.resource.DiagnosticReport;
 import ca.uhn.fhir.model.dev.resource.Location;
 import ca.uhn.fhir.model.dev.resource.Observation;
 import ca.uhn.fhir.model.dev.resource.Organization;
 import ca.uhn.fhir.model.dev.resource.Patient;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
-import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
@@ -214,6 +221,67 @@ public class FhirSystemDaoTest {
 
 	}
 
+	@Test
+	public void testTransactionWithDelete() throws Exception {
+		
+		/*
+		 * Create 3
+		 */
+		
+		List<IResource> res;
+		res = new ArrayList<IResource>();
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p1);
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p2);
+
+		Patient p3 = new Patient();
+		p3.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
+		res.add(p3);
+
+		ourSystemDao.transaction(res);
+
+		/*
+		 * Verify
+		 */
+		
+		IBundleProvider results = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
+		assertEquals(3, results.size());
+		
+		/*
+		 * Now delete 2
+		 */
+		
+		res = new ArrayList<IResource>();
+		List<IResource> existing = results.getResources(0, 3);
+
+		p1 = new Patient();
+		p1.setId(existing.get(0).getId());
+		ResourceMetadataKeyEnum.DELETED_AT.put(p1, InstantDt.withCurrentTime());
+		res.add(p1);
+		
+		p2 = new Patient();
+		p2.setId(existing.get(1).getId());
+		ResourceMetadataKeyEnum.DELETED_AT.put(p2, InstantDt.withCurrentTime());
+		res.add(p2);
+		
+		ourSystemDao.transaction(res);
+		
+		/*
+		 * Verify
+		 */
+		
+		IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
+		assertEquals(1, results2.size());
+		List<IResource> existing2 = results2.getResources(0, 1);
+		assertEquals(existing2.get(0).getId(), existing.get(2).getId());
+		
+	}
+
 	/**
 	 * Issue #55
 	 */
@@ -233,7 +301,7 @@ public class FhirSystemDaoTest {
 		res.add(o1);
 
 		Observation o2 = new Observation();
-		o2.setId("cid:observation1");
+		o2.setId("cid:observation2");
 		o2.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds03");
 		o2.setSubject(new ResourceReferenceDt("Patient/cid:patient1"));
 		res.add(o2);
@@ -321,6 +389,19 @@ public class FhirSystemDaoTest {
 
 	}
 
+	@Test(expected=InvalidRequestException.class)
+	public void testTransactionFailsWithDuplicateIds() {
+		Patient patient1 = new Patient();
+		patient1.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient1.addIdentifier().setSystem("urn:system").setValue( "testPersistWithSimpleLinkP01");
+
+		Patient patient2 = new Patient();
+		patient2.setId(new IdDt("Patient/testTransactionFailsWithDusplicateIds"));
+		patient2.addIdentifier().setSystem("urn:system").setValue( "testPersistWithSimpleLinkP02");
+
+		ourSystemDao.transaction(Arrays.asList((IResource) patient1, patient2));
+	}
+
 	@Test
 	public void testGetResourceCounts() {
 		Observation obs = new Observation();

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/CompleteResourceProviderTest.java

@@ -396,6 +396,7 @@ public class CompleteResourceProviderTest {
 		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSearchByIdentifier01")).encodedJson().prettyPrint().execute();
 		assertEquals(1, actual.size());
 		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getResource().getId().getIdPart());
+		assertEquals(BundleEntryStatusEnum.MATCH, actual.getEntries().get(0).getStatus().getValueAsEnum());
 	}
 
 	@Test

src/changes/changes.xml

@@ -89,6 +89,9 @@
 				appropriate configuration on the 
 				RestfulClientConfig. Thanks to Grahame Grieve for the suggestion!
 			</action>
+			<action type="add">
+			    JPA module now supports deleting resource via transaction
+			</action>
 		</release>
 		<release version="0.8" date="2014-Dec-17">
 			<action type="add">