If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420)

* If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5419-binaries-created-only-for-the-first-resource-entry-of-the-bundle.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5419
+title: "Previously, when `AllowAutoInflateBinaries` was enabled in `JpaStorageSettings` and bundles with multiple 
+resources were submitted, binaries were created on the disk only for the first resource entry of the bundle. 
+This has been fixed."

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.client.api.IClientInterceptor;
@@ -18,13 +19,16 @@ import ca.uhn.fhir.rest.client.api.IHttpResponse;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.HapiExtensions;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
-import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Binary;
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
@@ -32,7 +36,6 @@ import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.EnumSource;
-import org.junit.jupiter.params.provider.ValueSource;
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -62,6 +65,7 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
 	public static final byte[] FEW_BYTES = {4, 3, 2, 1};
 	public static final byte[] SOME_BYTES = {1, 2, 3, 4, 5, 6, 7, 8, 7, 6, 5, 4, 3, 2, 1, 8, 9, 0, 10, 9};
 	public static final byte[] SOME_BYTES_2 = {6, 7, 8, 7, 6, 5, 4, 3, 2, 1, 5, 5, 5, 6};
+	public static final byte[] SOME_BYTES_3 = {5, 5, 5, 6, 6, 7, 7, 7, 8, 8, 8};
 	private static final Logger ourLog = LoggerFactory.getLogger(BinaryStorageInterceptorR4Test.class);
 
 	@Autowired
@@ -381,12 +385,8 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
 
 		// Create a resource with a big enough docRef
 		DocumentReference docRef = new DocumentReference();
-		DocumentReference.DocumentReferenceContentComponent content = docRef.addContent();
+		addDocumentAttachmentData(docRef, SOME_BYTES);
-		content.getAttachment().setContentType("application/octet-stream");
+		addDocumentAttachmentData(docRef, SOME_BYTES_2);
-		content.getAttachment().setData(SOME_BYTES);
-		DocumentReference.DocumentReferenceContentComponent content2 = docRef.addContent();
-		content2.getAttachment().setContentType("application/octet-stream");
-		content2.getAttachment().setData(SOME_BYTES_2);
 		DaoMethodOutcome outcome = myDocumentReferenceDao.create(docRef, mySrd);
 
 		// Make sure it was externalized
@@ -422,18 +422,73 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testCreateBinaryAttachments_bundleWithMultipleDocumentReferences_createdAndReadBackSuccessfully() {
+		// Create Patient
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("001");
+		patient.addName().addGiven("Johnny").setFamily("Walker");
+
+		// Create first DocumentReference with a big enough attachments
+		DocumentReference docRef = new DocumentReference();
+		addDocumentAttachmentData(docRef, SOME_BYTES);
+		addDocumentAttachmentData(docRef, SOME_BYTES_2);
+
+		// Create second DocumentReference with a big enough attachment
+		DocumentReference docRef2 = new DocumentReference();
+		addDocumentAttachmentData(docRef2, SOME_BYTES_3);
+
+		// Create Bundle
+		Bundle bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.TRANSACTION);
+		// Patient entry component
+		addBundleEntry(bundle, patient, "Patient");
+		// First DocumentReference entry component
+		addBundleEntry(bundle, docRef, "DocumentReference");
+		// Second DocumentReference entry component
+		addBundleEntry(bundle, docRef2, "DocumentReference");
+
+		// Execute transaction
+		Bundle output = myClient.transaction().withBundle(bundle).execute();
+		ourLog.debug(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
+
+		// Verify bundle response
+		assertEquals(3, output.getEntry().size());
+		output.getEntry().forEach(entry -> assertEquals("201 Created", entry.getResponse().getStatus()));
+
+		// Read back and verify first DocumentReference and attachments
+		IIdType firstDocRef = new IdType(output.getEntry().get(1).getResponse().getLocation());
+		DocumentReference firstDoc = myDocumentReferenceDao.read(firstDocRef, mySrd);
+		assertEquals("application/octet-stream", firstDoc.getContentFirstRep().getAttachment().getContentType());
+		assertArrayEquals(SOME_BYTES, firstDoc.getContentFirstRep().getAttachment().getData());
+		assertEquals("application/octet-stream", firstDoc.getContent().get(1).getAttachment().getContentType());
+		assertArrayEquals(SOME_BYTES_2, firstDoc.getContent().get(1).getAttachment().getData());
+
+		// Read back and verify second DocumentReference and attachment
+		IIdType secondDocRef = new IdType(output.getEntry().get(2).getResponse().getLocation());
+		DocumentReference secondDoc = myDocumentReferenceDao.read(secondDocRef, mySrd);
+		assertEquals("application/octet-stream", secondDoc.getContentFirstRep().getAttachment().getContentType());
+		assertArrayEquals(SOME_BYTES_3, secondDoc.getContentFirstRep().getAttachment().getData());
+	}
+
+	private void addBundleEntry(Bundle theBundle, Resource theResource, String theUrl) {
+		Bundle.BundleEntryComponent getComponent = new Bundle.BundleEntryComponent();
+		Bundle.BundleEntryRequestComponent requestComponent = new Bundle.BundleEntryRequestComponent();
+		requestComponent.setMethod(Bundle.HTTPVerb.POST);
+		requestComponent.setUrl(theUrl);
+		getComponent.setRequest(requestComponent);
+		getComponent.setResource(theResource);
+		getComponent.setFullUrl(IdDt.newRandomUuid().getValue());
+		theBundle.addEntry(getComponent);
+	}
 
 	@Test
 	public void testUpdateRejectsIncorrectBinary() {
 
 		// Create a resource with a big enough docRef
 		DocumentReference docRef = new DocumentReference();
-		DocumentReference.DocumentReferenceContentComponent content = docRef.addContent();
+		addDocumentAttachmentData(docRef, SOME_BYTES);
-		content.getAttachment().setContentType("application/octet-stream");
+		addDocumentAttachmentData(docRef, SOME_BYTES_2);
-		content.getAttachment().setData(SOME_BYTES);
-		DocumentReference.DocumentReferenceContentComponent content2 = docRef.addContent();
-		content2.getAttachment().setContentType("application/octet-stream");
-		content2.getAttachment().setData(SOME_BYTES_2);
 		DaoMethodOutcome outcome = myDocumentReferenceDao.create(docRef, mySrd);
 
 		// Make sure it was externalized
@@ -449,13 +504,13 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
 		docRef = new DocumentReference();
 		docRef.setId(id.toUnqualifiedVersionless());
 		docRef.setStatus(Enumerations.DocumentReferenceStatus.CURRENT);
-		content = docRef.addContent();
+		DocumentReference.DocumentReferenceContentComponent content = docRef.addContent();
 		content.getAttachment().setContentType("application/octet-stream");
 		content.getAttachment().getDataElement().addExtension(
 			HapiExtensions.EXT_EXTERNALIZED_BINARY_ID,
 			new StringType(binaryId)
 		);
-		content2 = docRef.addContent();
+		DocumentReference.DocumentReferenceContentComponent content2 = docRef.addContent();
 		content2.getAttachment().setContentType("application/octet-stream");
 		content2.getAttachment().getDataElement().addExtension(
 			HapiExtensions.EXT_EXTERNALIZED_BINARY_ID,
@@ -497,5 +552,10 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	private void addDocumentAttachmentData(DocumentReference theDocumentReference, byte[] theData) {
+		DocumentReference.DocumentReferenceContentComponent content = theDocumentReference.addContent();
+		content.getAttachment().setContentType("application/octet-stream");
+		content.getAttachment().setData(theData);
+	}
 
 }

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/binary/interceptor/BinaryStorageInterceptor.java

@@ -251,7 +251,7 @@ public class BinaryStorageInterceptor<T extends IPrimitiveType<byte[]>> {
 						}
 						if (myBinaryStorageSvc.isValidBlobId(newBlobId)) {
 							List<DeferredBinaryTarget> deferredBinaryTargets =
-									getOrCreateDeferredBinaryStorageMap(theTransactionDetails);
+									getOrCreateDeferredBinaryStorageList(theResource);
 							DeferredBinaryTarget newDeferredBinaryTarget =
 									new DeferredBinaryTarget(newBlobId, nextTarget, data);
 							deferredBinaryTargets.add(newDeferredBinaryTarget);
@@ -289,21 +289,29 @@ public class BinaryStorageInterceptor<T extends IPrimitiveType<byte[]>> {
 	}
 
 	@Nonnull
-	private List<DeferredBinaryTarget> getOrCreateDeferredBinaryStorageMap(TransactionDetails theTransactionDetails) {
+	@SuppressWarnings("unchecked")
-		return theTransactionDetails.getOrCreateUserData(getDeferredListKey(), ArrayList::new);
+	private List<DeferredBinaryTarget> getOrCreateDeferredBinaryStorageList(IBaseResource theResource) {
+		Object deferredBinaryTargetList = theResource.getUserData(getDeferredListKey());
+		if (deferredBinaryTargetList == null) {
+			deferredBinaryTargetList = new ArrayList<>();
+			theResource.setUserData(getDeferredListKey(), deferredBinaryTargetList);
+		}
+		return (List<DeferredBinaryTarget>) deferredBinaryTargetList;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Hook(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED)
 	public void storeLargeBinariesBeforeCreatePersistence(
-			TransactionDetails theTransactionDetails, IBaseResource theResource, Pointcut thePoincut)
+			TransactionDetails theTransactionDetails, IBaseResource theResource, Pointcut thePointcut)
 			throws IOException {
-		if (theTransactionDetails == null) {
+		if (theResource == null) {
 			return;
 		}
-		List<DeferredBinaryTarget> deferredBinaryTargets = theTransactionDetails.getUserData(getDeferredListKey());
+		Object deferredBinaryTargetList = theResource.getUserData(getDeferredListKey());
-		if (deferredBinaryTargets != null) {
+
+		if (deferredBinaryTargetList != null) {
 			IIdType resourceId = theResource.getIdElement();
-			for (DeferredBinaryTarget next : deferredBinaryTargets) {
+			for (DeferredBinaryTarget next : (List<DeferredBinaryTarget>) deferredBinaryTargetList) {
 				String blobId = next.getBlobId();
 				IBinaryTarget target = next.getBinaryTarget();
 				InputStream dataStream = next.getDataStream();