Add utility method to convert Bundle into transaction (#5945)

* Add utility method to convert Bundle into transaction

* Add utility method

* Spotless

* Build fix

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java

@@ -39,6 +39,7 @@ import ca.uhn.fhir.util.bundle.SearchBundleEntryParts;
 import com.google.common.collect.Sets;
 import jakarta.annotation.Nonnull;
 import jakarta.annotation.Nullable;
+import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
@@ -59,6 +60,7 @@ import java.util.Set;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_PREV;
@@ -67,6 +69,12 @@ import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_PREV;
  * Fetch resources from a bundle
  */
 public class BundleUtil {
+
+	/** Non instantiable */
+	private BundleUtil() {
+		// nothing
+	}
+
 	private static final Logger ourLog = LoggerFactory.getLogger(BundleUtil.class);
 
 	private static final String PREVIOUS = LINK_PREV;
@@ -339,6 +347,66 @@ public class BundleUtil {
 		TerserUtil.setField(theContext, "entry", theBundle, retVal.toArray(new IBase[0]));
 	}
 
+	/**
+	 * Converts a Bundle containing resources into a FHIR transaction which
+	 * creates/updates the resources. This method does not modify the original
+	 * bundle, but returns a new copy.
+	 * <p>
+	 * This method is mostly intended for test scenarios where you have a Bundle
+	 * containing search results or other sourced resources, and want to upload
+	 * these resources to a server using a single FHIR transaction.
+	 * </p>
+	 * <p>
+	 * The Bundle is converted using the following logic:
+	 * <ul>
+	 *     <li>Bundle.type is changed to <code>transaction</code></li>
+	 *     <li>Bundle.request.method is changed to <code>PUT</code></li>
+	 *     <li>Bundle.request.url is changed to <code>[resourceType]/[id]</code></li>
+	 *     <li>Bundle.fullUrl is changed to <code>[resourceType]/[id]</code></li>
+	 * </ul>
+	 * </p>
+	 *
+	 * @param theContext The FhirContext to use with the bundle
+	 * @param theBundle The Bundle to modify. All resources in the Bundle should have an ID.
+	 * @param thePrefixIdsOrNull If not <code>null</code>, all resource IDs and all references in the Bundle will be
+	 *                           modified to such that their IDs contain the given prefix. For example, for a value
+	 *                           of "A", the resource "Patient/123" will be changed to be "Patient/A123". If set to
+	 *                           <code>null</code>, resource IDs are unchanged.
+	 * @since 7.4.0
+	 */
+	public static <T extends IBaseBundle> T convertBundleIntoTransaction(
+			@Nonnull FhirContext theContext, @Nonnull T theBundle, @Nullable String thePrefixIdsOrNull) {
+		String prefix = defaultString(thePrefixIdsOrNull);
+
+		BundleBuilder bb = new BundleBuilder(theContext);
+
+		FhirTerser terser = theContext.newTerser();
+		List<IBase> entries = terser.getValues(theBundle, "Bundle.entry");
+		for (var entry : entries) {
+			IBaseResource resource = terser.getSingleValueOrNull(entry, "resource", IBaseResource.class);
+			if (resource != null) {
+				Validate.isTrue(resource.getIdElement().hasIdPart(), "Resource in bundle has no ID");
+				String newId = theContext.getResourceType(resource) + "/" + prefix
+						+ resource.getIdElement().getIdPart();
+
+				IBaseResource resourceClone = terser.clone(resource);
+				resourceClone.setId(newId);
+
+				if (isNotBlank(prefix)) {
+					for (var ref : terser.getAllResourceReferences(resourceClone)) {
+						var refElement = ref.getResourceReference().getReferenceElement();
+						ref.getResourceReference()
+								.setReference(refElement.getResourceType() + "/" + prefix + refElement.getIdPart());
+					}
+				}
+
+				bb.addTransactionUpdateEntry(resourceClone);
+			}
+		}
+
+		return bb.getBundleTyped();
+	}
+
 	private static void validatePartsNotNull(LinkedHashSet<IBase> theDeleteParts) {
 		if (theDeleteParts == null) {
 			throw new IllegalStateException(

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5945-add-bundleutil-utility-transaction-converter-method.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 5945
+title: "A new utility method has been added to `BundleUtil` which converts a FHIR Bundle
+  containing resources (e.g. a search result bundle) into a FHIR transaction bundle which
+  could be used to upload those resources to a server."

hapi-fhir-jpaserver-ips/src/test/java/ca/uhn/fhir/jpa/ips/generator/IpsGenerationR4Test.java

@@ -47,6 +47,7 @@ import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import static ca.uhn.fhir.util.BundleUtil.convertBundleIntoTransaction;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.stringContainsInOrder;
@@ -81,11 +82,7 @@ public class IpsGenerationR4Test extends BaseResourceProviderR4Test {
 	@Test
 	public void testGenerateLargePatientSummary() throws IOException {
 		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/large-patient-everything.json.gz");
-		sourceData.setType(Bundle.BundleType.TRANSACTION);
+		sourceData = convertBundleIntoTransaction(myFhirContext, sourceData, null);
-		for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
-			nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
-			nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
-		}
 		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
 		ourLog.info("Created {} resources", outcome.getEntry().size());
 
@@ -119,11 +116,7 @@ public class IpsGenerationR4Test extends BaseResourceProviderR4Test {
 		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
 
 		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/large-patient-everything-2.json.gz");
-		sourceData.setType(Bundle.BundleType.TRANSACTION);
+		sourceData = convertBundleIntoTransaction(myFhirContext, sourceData, null);
-		for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
-			nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
-			nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
-		}
 		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
 		ourLog.info("Created {} resources", outcome.getEntry().size());
 
@@ -145,11 +138,7 @@ public class IpsGenerationR4Test extends BaseResourceProviderR4Test {
 		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
 
 		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/large-patient-everything-3.json.gz");
-		sourceData.setType(Bundle.BundleType.TRANSACTION);
+		sourceData = convertBundleIntoTransaction(myFhirContext, sourceData, null);
-		for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
-			nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
-			nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
-		}
 		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
 		ourLog.info("Created {} resources", outcome.getEntry().size());
 
@@ -166,16 +155,33 @@ public class IpsGenerationR4Test extends BaseResourceProviderR4Test {
 		assertEquals(80, output.getEntry().size());
 	}
 
+	@Test
+	public void testGenerateLargePatientSummary4() {
+		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/large-patient-everything-4.json.gz");
+		sourceData = convertBundleIntoTransaction(myFhirContext, sourceData, "EPD");
+
+		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
+		ourLog.info("Created {} resources", outcome.getEntry().size());
+
+		Bundle output = myClient
+			.operation()
+			.onInstance("Patient/EPD2223")
+			.named(JpaConstants.OPERATION_SUMMARY)
+			.withNoParameters(Parameters.class)
+			.returnResourceType(Bundle.class)
+			.execute();
+		ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
+
+		// Verify
+		assertEquals(55, output.getEntry().size());
+	}
+
 	@Test
 	public void testGenerateTinyPatientSummary() throws IOException {
 		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
 
 		Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/tiny-patient-everything.json.gz");
-		sourceData.setType(Bundle.BundleType.TRANSACTION);
+		sourceData = convertBundleIntoTransaction(myFhirContext, sourceData, null);
-		for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
-			nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
-			nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
-		}
 		Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
 		ourLog.info("Created {} resources", outcome.getEntry().size());
 

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/bundle/BundleUtilTest.java

@@ -680,6 +680,56 @@ public class BundleUtilTest {
 		assertNull(BundleUtil.getBundleTypeEnum(ourCtx, bundle));
 	}
 
+	@Test
+	public void testConvertBundleIntoTransaction() {
+		Bundle input = createBundleWithPatientAndObservation();
+
+		Bundle output = BundleUtil.convertBundleIntoTransaction(ourCtx, input, null);
+		assertEquals(Bundle.BundleType.TRANSACTION, output.getType());
+		assertEquals("Patient/123", output.getEntry().get(0).getFullUrl());
+		assertEquals("Patient/123", output.getEntry().get(0).getRequest().getUrl());
+		assertEquals(Bundle.HTTPVerb.PUT, output.getEntry().get(0).getRequest().getMethod());
+		assertTrue(((Patient) output.getEntry().get(0).getResource()).getActive());
+		assertEquals("Observation/456", output.getEntry().get(1).getFullUrl());
+		assertEquals("Observation/456", output.getEntry().get(1).getRequest().getUrl());
+		assertEquals(Bundle.HTTPVerb.PUT, output.getEntry().get(1).getRequest().getMethod());
+		assertEquals("Patient/123", ((Observation)output.getEntry().get(1).getResource()).getSubject().getReference());
+		assertEquals(Observation.ObservationStatus.AMENDED, ((Observation)output.getEntry().get(1).getResource()).getStatus());
+	}
+
+	@Test
+	public void testConvertBundleIntoTransaction_WithPrefix() {
+		Bundle input = createBundleWithPatientAndObservation();
+
+		Bundle output = BundleUtil.convertBundleIntoTransaction(ourCtx, input, "A");
+		assertEquals(Bundle.BundleType.TRANSACTION, output.getType());
+		assertEquals("Patient/A123", output.getEntry().get(0).getFullUrl());
+		assertEquals("Patient/A123", output.getEntry().get(0).getRequest().getUrl());
+		assertEquals(Bundle.HTTPVerb.PUT, output.getEntry().get(0).getRequest().getMethod());
+		assertTrue(((Patient) output.getEntry().get(0).getResource()).getActive());
+		assertEquals("Observation/A456", output.getEntry().get(1).getFullUrl());
+		assertEquals("Observation/A456", output.getEntry().get(1).getRequest().getUrl());
+		assertEquals(Bundle.HTTPVerb.PUT, output.getEntry().get(1).getRequest().getMethod());
+		assertEquals("Patient/A123", ((Observation)output.getEntry().get(1).getResource()).getSubject().getReference());
+		assertEquals(Observation.ObservationStatus.AMENDED, ((Observation)output.getEntry().get(1).getResource()).getStatus());
+	}
+
+	private static @Nonnull Bundle createBundleWithPatientAndObservation() {
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.COLLECTION);
+		Patient patient = new Patient();
+		patient.setActive(true);
+		patient.setId("123");
+		input.addEntry().setResource(patient);
+		Observation observation = new Observation();
+		observation.setId("456");
+		observation.setStatus(Observation.ObservationStatus.AMENDED);
+		observation.setSubject(new Reference("Patient/123"));
+		input.addEntry().setResource(observation);
+		return input;
+	}
+
+
 	@Nonnull
 	private static Bundle withBundle(Resource theResource) {
 		final Bundle bundle = new Bundle();