Allow JPA server to restore resources and link to them in a single

transaction

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

@@ -1253,6 +1253,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IBaseResource oldResource = toResource(entity, false);
 
+		/*
+		 * Mark the entity as not deleted - This is also done in the actual updateInternal()
+		 * method later on so it usually doesn't matter whether we do it here, but in the
+		 * case of a transaction with multiple PUTs we don't get there until later so
+		 * having this here means that a transaction can have a reference in one
+		 * resource to another resource in the same transaction that is being
+		 * un-deleted by the transaction. Wacky use case, sure. But it's real.
+		 *
+		 * See SystemProviderR4Test#testTransactionReSavesPreviouslyDeletedResources
+		 * for a test that needs this.
+		 */
+		entity.setDeleted(null);
+
 		/*
 		 * If we aren't indexing, that means we're doing this inside a transaction.
 		 * The transaction will do the actual storage to the database a bit later on,

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -1,12 +1,25 @@
 package ca.uhn.fhir.jpa.provider;
 
-import static org.hamcrest.Matchers.*;
+import ca.uhn.fhir.context.FhirContext;
-import static org.junit.Assert.*;
+import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
-
+import ca.uhn.fhir.jpa.rp.dstu2.*;
-import java.io.InputStream;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
-import java.nio.charset.StandardCharsets;
+import ca.uhn.fhir.model.dstu2.resource.*;
-import java.util.concurrent.TimeUnit;
+import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
-
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import ca.uhn.fhir.model.primitive.DecimalDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
@@ -17,46 +30,32 @@ import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.IdType;
 import org.junit.AfterClass;
 import org.junit.Before;
-import org.junit.Test;
 import org.junit.Ignore;
+import org.junit.Test;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
-import ca.uhn.fhir.context.FhirContext;
+import java.io.IOException;
-import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
+import java.io.InputStream;
-import ca.uhn.fhir.jpa.rp.dstu2.*;
+import java.nio.charset.StandardCharsets;
-import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
+import java.util.concurrent.TimeUnit;
-import ca.uhn.fhir.model.dstu2.resource.*;
+
-import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
+import static org.hamcrest.Matchers.*;
-import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.model.primitive.*;
-import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.client.api.IGenericClient;
-import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import ca.uhn.fhir.util.TestUtil;
 
 public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderDstu2Test.class);
 	private static RestfulServer myRestServer;
 	private static IGenericClient ourClient;
 	private static FhirContext ourCtx;
 	private static CloseableHttpClient ourHttpClient;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderDstu2Test.class);
 	private static Server ourServer;
 	private static String ourServerBase;
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		ourServer.stop();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 	@Before
 	public void beforeStartServer() throws Exception {
 		if (myRestServer == null) {
@@ -72,9 +71,23 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 			OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
 			organizationRp.setDao(myOrganizationDao);
 
+			LocationResourceProvider locationRp = new LocationResourceProvider();
+			locationRp.setDao(myLocationDao);
+
+			BinaryResourceProvider binaryRp = new BinaryResourceProvider();
+			binaryRp.setDao(myBinaryDao);
+
+			DiagnosticReportResourceProvider diagnosticReportRp = new DiagnosticReportResourceProvider();
+			diagnosticReportRp.setDao(myDiagnosticReportDao);
+			DiagnosticOrderResourceProvider diagnosticOrderRp = new DiagnosticOrderResourceProvider();
+			diagnosticOrderRp.setDao(myDiagnosticOrderDao);
+			PractitionerResourceProvider practitionerRp = new PractitionerResourceProvider();
+			practitionerRp.setDao(myPractitionerDao);
+
+
 			RestfulServer restServer = new RestfulServer(ourCtx);
 			restServer.setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(10));
-			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
+			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp, binaryRp, locationRp, diagnosticReportRp, diagnosticOrderRp, practitionerRp);
 
 			restServer.setPlainProviders(mySystemProvider);
 
@@ -179,7 +192,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
-	@Transactional(propagation=Propagation.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	@Test
 	public void testSuggestKeywords() throws Exception {
 
@@ -269,6 +282,44 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		assertEquals("get-resource-counts", op.getCode());
 	}
 
+	@Test
+	public void testTransactionReSavesPreviouslyDeletedResources() throws IOException {
+
+		for (int i = 0; i < 10; i++) {
+			ourLog.info("** Beginning pass {}", i);
+
+			Bundle input = myFhirCtx.newJsonParser().parseResource(Bundle.class, IOUtils.toString(getClass().getResourceAsStream("/dstu2/createdeletebundle.json"), Charsets.UTF_8));
+			ourClient.transaction().withBundle(input).execute();
+
+			myPatientDao.read(new IdType("Patient/Patient1063259"));
+
+			deleteAllOfType("Binary");
+			deleteAllOfType("Location");
+			deleteAllOfType("DiagnosticReport");
+			deleteAllOfType("Observation");
+			deleteAllOfType("DiagnosticOrder");
+			deleteAllOfType("Practitioner");
+			deleteAllOfType("Patient");
+			deleteAllOfType("Organization");
+
+			try {
+				myPatientDao.read(new IdType("Patient/Patient1063259"));
+				fail();
+			} catch (ResourceGoneException e) {
+				// good
+			}
+
+		}
+
+	}
+
+	private void deleteAllOfType(String theType) {
+		BundleUtil.toListOfResources(myFhirCtx, ourClient.search().forResource(theType).execute())
+			.forEach(t -> {
+				ourClient.delete().resourceById(t.getIdElement()).execute();
+			});
+	}
+
 	@Test
 	public void testTransactionFromBundle() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
@@ -372,7 +423,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 
 	@Test
 	public void testTransactionSearch() throws Exception {
-		for (int i = 0; i < 20; i ++) {
+		for (int i = 0; i < 20; i++) {
 			Patient p = new Patient();
 			p.addName().addFamily("PATIENT_" + i);
 			myPatientDao.create(p, mySrd);
@@ -385,7 +436,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
 
 		assertEquals(1, resp.getEntry().size());
-		Bundle respSub = (Bundle)resp.getEntry().get(0).getResource();
+		Bundle respSub = (Bundle) resp.getEntry().get(0).getResource();
 		assertEquals("self", respSub.getLink().get(0).getRelation());
 		assertEquals(ourServerBase + "/Patient", respSub.getLink().get(0).getUrl());
 		assertEquals("next", respSub.getLink().get(1).getRelation());
@@ -396,7 +447,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 
 	@Test
 	public void testTransactionCount() throws Exception {
-		for (int i = 0; i < 20; i ++) {
+		for (int i = 0; i < 20; i++) {
 			Patient p = new Patient();
 			p.addName().addFamily("PATIENT_" + i);
 			myPatientDao.create(p, mySrd);
@@ -409,7 +460,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
 
 		assertEquals(1, resp.getEntry().size());
-		Bundle respSub = (Bundle)resp.getEntry().get(0).getResource();
+		Bundle respSub = (Bundle) resp.getEntry().get(0).getResource();
 		assertEquals(20, respSub.getTotal().intValue());
 		assertEquals(0, respSub.getEntry().size());
 	}
@@ -423,9 +474,16 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 			ourLog.info(output);
 			assertEquals(200, http.getStatusLine().getStatusCode());
 		} finally {
-			IOUtils.closeQuietly(http);;
+			IOUtils.closeQuietly(http);
+			;
 		}
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java

@@ -3,9 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
-import ca.uhn.fhir.jpa.rp.r4.ObservationResourceProvider;
+import ca.uhn.fhir.jpa.rp.r4.*;
-import ca.uhn.fhir.jpa.rp.r4.OrganizationResourceProvider;
-import ca.uhn.fhir.jpa.rp.r4.PatientResourceProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -17,8 +15,10 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
+import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.Header;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -42,6 +42,7 @@ import org.junit.*;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.concurrent.TimeUnit;
@@ -88,8 +89,21 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
 			OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
 			organizationRp.setDao(myOrganizationDao);
 
+			LocationResourceProvider locationRp = new LocationResourceProvider();
+			locationRp.setDao(myLocationDao);
+
+			BinaryResourceProvider binaryRp = new BinaryResourceProvider();
+			binaryRp.setDao(myBinaryDao);
+
+			DiagnosticReportResourceProvider diagnosticReportRp = new DiagnosticReportResourceProvider();
+			diagnosticReportRp.setDao(myDiagnosticReportDao);
+			ServiceRequestResourceProvider diagnosticOrderRp = new ServiceRequestResourceProvider();
+			diagnosticOrderRp.setDao(myServiceRequestDao);
+			PractitionerResourceProvider practitionerRp = new PractitionerResourceProvider();
+			practitionerRp.setDao(myPractitionerDao);
+
 			RestfulServer restServer = new RestfulServer(ourCtx);
-			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
+			restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp, locationRp, binaryRp, diagnosticReportRp, diagnosticOrderRp, practitionerRp);
 
 			restServer.setPlainProviders(mySystemProvider);
 
@@ -385,6 +399,45 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
 		assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
 	}
 
+
+	@Test
+	public void testTransactionReSavesPreviouslyDeletedResources() throws IOException {
+
+		for (int i = 0; i < 10; i++) {
+			ourLog.info("** Beginning pass {}", i);
+
+			Bundle input = myFhirCtx.newJsonParser().parseResource(Bundle.class, IOUtils.toString(getClass().getResourceAsStream("/r4/createdeletebundle.json"), Charsets.UTF_8));
+			ourClient.transaction().withBundle(input).execute();
+
+			myPatientDao.read(new IdType("Patient/Patient1063259"));
+
+			deleteAllOfType("Binary");
+			deleteAllOfType("Location");
+			deleteAllOfType("DiagnosticReport");
+			deleteAllOfType("Observation");
+			deleteAllOfType("ServiceRequest");
+			deleteAllOfType("Practitioner");
+			deleteAllOfType("Patient");
+			deleteAllOfType("Organization");
+
+			try {
+				myPatientDao.read(new IdType("Patient/Patient1063259"));
+				fail();
+			} catch (ResourceGoneException e) {
+				// good
+			}
+
+		}
+
+	}
+
+	private void deleteAllOfType(String theType) {
+		BundleUtil.toListOfResources(myFhirCtx, ourClient.search().forResource(theType).execute())
+			.forEach(t -> {
+				ourClient.delete().resourceById(t.getIdElement()).execute();
+			});
+	}
+
 	@Test
 	public void testTransactionDeleteWithDuplicateDeletes() throws Exception {
 		myDaoConfig.setAllowInlineMatchUrlReferences(true);

hapi-fhir-jpaserver-base/src/test/resources/r4/createdeletebundle.json

@@ -0,0 +1,37 @@
+{
+	"resourceType": "Bundle",
+	"type": "transaction",
+	"entry": [
+		{
+			"fullUrl": "Patient/Patient1063259",
+			"resource": {
+				"resourceType": "Patient",
+				"id": "Patient1063259",
+				"identifier": [
+					{
+						"system": "http://www.foo.com/fhir/identifier-type/EnterpriseId",
+						"value": "1063259"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Patient/Patient1063259"
+			}
+		},
+		{
+			"fullUrl": "DiagnosticReport/ReportSPATH",
+			"resource": {
+				"resourceType": "DiagnosticReport",
+				"id": "ReportSPATH",
+				"subject": {
+					"reference": "Patient/Patient1063259"
+				}
+			},
+			"request": {
+				"method": "PUT",
+				"url": "DiagnosticReport/ReportSPATH"
+			}
+		}
+	]
+}

src/changes/changes.xml

@@ -104,6 +104,11 @@
 				The JPA server version migrator tool now runs in a multithreaded way, allowing it to
 				upgrade th database faster when migration tasks require data updates.
 			</action>
+			<action type="fix">
+				A bug in the JPA server was fixed: When a resource was previously deleted,
+				a transaction could not be posted that both restored the deleted resource but
+				also contained references to the now-restored resource.
+			</action>
 		</release>
 
 		<release version="3.5.0" date="2018-09-17">