6486 implement patient merge

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

@@ -265,30 +265,48 @@ public static IBase addIssueWithMessageId(
 	}
 
 	public static void addDetailsToIssue(FhirContext theFhirContext, IBase theIssue, String theSystem, String theCode) {
+		addDetailsToIssue(theFhirContext, theIssue, theSystem, theCode, null);
+	}
+
+	public static void addDetailsToIssue(
+			FhirContext theFhirContext, IBase theIssue, String theSystem, String theCode, String theText) {
 		BaseRuntimeElementCompositeDefinition<?> issueElement =
 				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition(theIssue.getClass());
 		BaseRuntimeChildDefinition detailsChildDef = issueElement.getChildByName("details");
-
-		BaseRuntimeElementCompositeDefinition<?> codingDef =
-				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("Coding");
-		ICompositeType coding = (ICompositeType) codingDef.newInstance();
-
-		// System
-		IPrimitiveType<?> system =
-				(IPrimitiveType<?>) theFhirContext.getElementDefinition("uri").newInstance();
-		system.setValueAsString(theSystem);
-		codingDef.getChildByName("system").getMutator().addValue(coding, system);
-
-		// Code
-		IPrimitiveType<?> code =
-				(IPrimitiveType<?>) theFhirContext.getElementDefinition("code").newInstance();
-		code.setValueAsString(theCode);
-		codingDef.getChildByName("code").getMutator().addValue(coding, code);
 		BaseRuntimeElementCompositeDefinition<?> ccDef =
 				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("CodeableConcept");
-
 		ICompositeType codeableConcept = (ICompositeType) ccDef.newInstance();
-		ccDef.getChildByName("coding").getMutator().addValue(codeableConcept, coding);
+
+		if (isNotBlank(theSystem) || isNotBlank(theCode)) {
+			BaseRuntimeElementCompositeDefinition<?> codingDef =
+					(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("Coding");
+			ICompositeType coding = (ICompositeType) codingDef.newInstance();
+
+			// System
+			if (isNotBlank(theSystem)) {
+				IPrimitiveType<?> system = (IPrimitiveType<?>)
+						theFhirContext.getElementDefinition("uri").newInstance();
+				system.setValueAsString(theSystem);
+				codingDef.getChildByName("system").getMutator().addValue(coding, system);
+			}
+
+			// Code
+			if (isNotBlank(theCode)) {
+				IPrimitiveType<?> code = (IPrimitiveType<?>)
+						theFhirContext.getElementDefinition("code").newInstance();
+				code.setValueAsString(theCode);
+				codingDef.getChildByName("code").getMutator().addValue(coding, code);
+			}
+
+			ccDef.getChildByName("coding").getMutator().addValue(codeableConcept, coding);
+		}
+
+		if (isNotBlank(theText)) {
+			IPrimitiveType<?> textElem = (IPrimitiveType<?>)
+					ccDef.getChildByName("text").getChildByName("text").newInstance(theText);
+			ccDef.getChildByName("text").getMutator().addValue(codeableConcept, textElem);
+		}
+
 		detailsChildDef.getMutator().addValue(theIssue, codeableConcept);
 	}
 

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

@@ -0,0 +1,69 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package ca.uhn.fhir.util;
+
+import jakarta.annotation.Nonnull;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.stream.Stream;
+
+/**
+ * This class collects items from a stream to a given limit and know whether there are
+ * still more items beyond that limit.
+ *
+ * @param <T> the type of object being streamed
+ */
+public class StopLimitAccumulator<T> {
+	private final boolean isTruncated;
+	private final List<T> myList;
+
+	private StopLimitAccumulator(List<T> theList, boolean theIsTruncated) {
+		myList = Collections.unmodifiableList(theList);
+		isTruncated = theIsTruncated;
+	}
+
+	public static <T> StopLimitAccumulator<T> fromStreamAndLimit(@Nonnull Stream<T> theItemStream, long theLimit) {
+		assert theLimit > 0;
+		AtomicBoolean isBeyondLimit = new AtomicBoolean(false);
+		List<T> accumulator = new ArrayList<>();
+
+		theItemStream
+				.limit(theLimit + 1) // Fetch one extra item to see if there are any more items past our limit
+				.forEach(item -> {
+					if (accumulator.size() < theLimit) {
+						accumulator.add(item);
+					} else {
+						isBeyondLimit.set(true);
+					}
+				});
+		return new StopLimitAccumulator<>(accumulator, isBeyondLimit.get());
+	}
+
+	public boolean isTruncated() {
+		return isTruncated;
+	}
+
+	public List<T> getItemList() {
+		return myList;
+	}
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopLimitAccumulatorTest.java

@@ -0,0 +1,69 @@
+package ca.uhn.fhir.util;
+
+import org.junit.jupiter.api.Test;
+
+import java.util.List;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+class StopLimitAccumulatorTest {
+
+	@Test
+	void testFromStreamAndLimit_withNoTruncation() {
+		// setup
+		Stream<Integer> stream = Stream.of(1, 2, 3, 4, 5);
+		int limit = 5;
+
+		// execute
+		StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit);
+
+		// verify
+		assertFalse(accumulator.isTruncated(), "The result should not be truncated");
+		assertEquals(List.of(1, 2, 3, 4, 5), accumulator.getItemList(), "The list should contain all items within the limit");
+	}
+
+	@Test
+	void testFromStreamAndLimit_withTruncation() {
+		// setup
+		Stream<Integer> stream = Stream.of(1, 2, 3, 4, 5, 6, 7);
+		int limit = 5;
+
+		// execute
+		StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit);
+
+		// verify
+		assertTrue(accumulator.isTruncated(), "The result should be truncated");
+		assertEquals(List.of(1, 2, 3, 4, 5), accumulator.getItemList(), "The list should contain only the items within the limit");
+	}
+
+	@Test
+	void testFromStreamAndLimit_withEmptyStream() {
+		// setup
+		Stream<Integer> stream = Stream.empty();
+		int limit = 5;
+
+		// execute
+		StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit);
+
+		// verify
+		assertFalse(accumulator.isTruncated(), "The result should not be truncated for an empty stream");
+		assertTrue(accumulator.getItemList().isEmpty(), "The list should be empty");
+	}
+
+	@Test
+	void testImmutabilityOfItemList() {
+		// setup
+		Stream<Integer> stream = Stream.of(1, 2, 3);
+		int limit = 3;
+
+		StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit);
+
+		// execute and Assert
+		List<Integer> itemList = accumulator.getItemList();
+		assertThrows(UnsupportedOperationException.class, () -> itemList.add(4), "The list should be immutable");
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/Batch2DaoSvcImpl.java

@@ -31,11 +31,13 @@
 import ca.uhn.fhir.jpa.api.pid.TypedResourcePid;
 import ca.uhn.fhir.jpa.api.pid.TypedResourceStream;
 import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
+import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
@@ -46,6 +48,7 @@
 import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IIdType;
 
 import java.util.Date;
 import java.util.function.Supplier;
@@ -56,6 +59,8 @@ public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
 
 	private final IResourceTableDao myResourceTableDao;
 
+	private final IResourceLinkDao myResourceLinkDao;
+
 	private final MatchUrlService myMatchUrlService;
 
 	private final DaoRegistry myDaoRegistry;
@@ -71,11 +76,13 @@ public boolean isAllResourceTypeSupported() {
 
 	public Batch2DaoSvcImpl(
 			IResourceTableDao theResourceTableDao,
+			IResourceLinkDao theResourceLinkDao,
 			MatchUrlService theMatchUrlService,
 			DaoRegistry theDaoRegistry,
 			FhirContext theFhirContext,
 			IHapiTransactionService theTransactionService) {
 		myResourceTableDao = theResourceTableDao;
+		myResourceLinkDao = theResourceLinkDao;
 		myMatchUrlService = theMatchUrlService;
 		myDaoRegistry = theDaoRegistry;
 		myFhirContext = theFhirContext;
@@ -95,6 +102,11 @@ public IResourcePidStream fetchResourceIdStream(
 		}
 	}
 
+	@Override
+	public Stream<IdDt> streamSourceIdsThatReferenceTargetId(IIdType theTargetId) {
+		return myResourceLinkDao.streamSourceIdsForTargetFhirId(theTargetId.getResourceType(), theTargetId.getIdPart());
+	}
+
 	private Stream<TypedResourcePid> streamResourceIdsWithUrl(
 			Date theStart, Date theEnd, String theUrl, RequestPartitionId theRequestPartitionId) {
 		validateUrl(theUrl);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/Batch2SupportConfig.java

@@ -44,12 +44,18 @@ public class Batch2SupportConfig {
 	@Bean
 	public IBatch2DaoSvc batch2DaoSvc(
 			IResourceTableDao theResourceTableDao,
+			IResourceLinkDao theResourceLinkDao,
 			MatchUrlService theMatchUrlService,
 			DaoRegistry theDaoRegistry,
 			FhirContext theFhirContext,
 			IHapiTransactionService theTransactionService) {
 		return new Batch2DaoSvcImpl(
-				theResourceTableDao, theMatchUrlService, theDaoRegistry, theFhirContext, theTransactionService);
+				theResourceTableDao,
+				theResourceLinkDao,
+				theMatchUrlService,
+				theDaoRegistry,
+				theFhirContext,
+				theTransactionService);
 	}
 
 	@Bean

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java

@@ -19,9 +19,11 @@
  */
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobPersistence;
 import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeJobSubmitterImpl;
+import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
@@ -55,6 +57,7 @@
 import ca.uhn.fhir.jpa.dao.ResourceHistoryCalculator;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceModifiedDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceSearchUrlDao;
 import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
@@ -175,6 +178,7 @@
 import ca.uhn.fhir.jpa.validation.ResourceLoaderImpl;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
+import ca.uhn.fhir.replacereferences.ReplaceReferencesPatchBundleSvc;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
@@ -930,7 +934,31 @@ public CacheTagDefinitionDao tagDefinitionDao(
 	}
 
 	@Bean
-	public IReplaceReferencesSvc replaceReferencesSvc(FhirContext theFhirContext, DaoRegistry theDaoRegistry) {
-		return new ReplaceReferencesSvcImpl(theFhirContext, theDaoRegistry);
+	public Batch2TaskHelper batch2TaskHelper() {
+		return new Batch2TaskHelper();
+	}
+
+	@Bean
+	public IReplaceReferencesSvc replaceReferencesSvc(
+			DaoRegistry theDaoRegistry,
+			HapiTransactionService theHapiTransactionService,
+			IResourceLinkDao theResourceLinkDao,
+			IJobCoordinator theJobCoordinator,
+			ReplaceReferencesPatchBundleSvc theReplaceReferencesPatchBundle,
+			Batch2TaskHelper theBatch2TaskHelper,
+			JpaStorageSettings theStorageSettings) {
+		return new ReplaceReferencesSvcImpl(
+				theDaoRegistry,
+				theHapiTransactionService,
+				theResourceLinkDao,
+				theJobCoordinator,
+				theReplaceReferencesPatchBundle,
+				theBatch2TaskHelper,
+				theStorageSettings);
+	}
+
+	@Bean
+	public ReplaceReferencesPatchBundleSvc replaceReferencesPatchBundleSvc(DaoRegistry theDaoRegistry) {
+		return new ReplaceReferencesPatchBundleSvc(theDaoRegistry);
 	}
 }