Fix batching of mdm-clear tasks

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3295-fix-mdm-clear-batch-exceptions.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 3295
+title: "When $mdm-clear operation batch was split into multiple threads, ResourceVersionConflictExceptions were being
+   thrown. This issue has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

@@ -676,8 +676,8 @@ This operation takes two optional Parameters.
             <td>Integer</td>
             <td>0..1</td>
             <td>
-                The number of links that should be deleted at a time.  If ommitted, then the batch size will be determined by the value
-of [Expunge Batch Size](/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
+                The number of links that should be deleted at a time.  If omitted, then the batch size will be determined by the value
+of [Reindex Batch Size](/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getReindexBatchSize())
 property.
             </td>
         </tr>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmLinkDeleter.java

@@ -58,7 +58,7 @@ public class MdmLinkDeleter implements ItemProcessor<List<Long>, List<Long>> {
 	public List<Long> process(List<Long> thePidList) throws Exception {
 		ConcurrentLinkedQueue<Long> goldenPidAggregator = new ConcurrentLinkedQueue<>();
 		PartitionRunner partitionRunner = new PartitionRunner(PROCESS_NAME, THREAD_PREFIX, myDaoConfig.getReindexBatchSize(), myDaoConfig.getReindexThreadCount());
-		partitionRunner.runInPartitionedThreads(new SliceImpl<>(thePidList), pids -> removeLinks(thePidList, goldenPidAggregator));
+		partitionRunner.runInPartitionedThreads(new SliceImpl<>(thePidList), pids -> removeLinks(pids, goldenPidAggregator));
 		return new ArrayList<>(goldenPidAggregator);
 	}
 

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

@@ -95,7 +95,11 @@ public void runInPartitionedThreads(Slice<Long> theResourceIds, Consumer<List<Lo
 	private List<Callable<Void>> buildCallableTasks(Slice<Long> theResourceIds, Consumer<List<Long>> partitionConsumer) {
 		List<Callable<Void>> retval = new ArrayList<>();
 
-		ourLog.info("Splitting batch job of {} entries into chunks of {}", theResourceIds.getContent().size(), myBatchSize);
+		if (myBatchSize > theResourceIds.getContent().size()) {
+			ourLog.info("Splitting batch job of {} entries into chunks of {}", theResourceIds.getContent().size(), myBatchSize);
+		} else {
+			ourLog.info("Creating batch job of {} entries", theResourceIds.getContent().size());
+		}
 		List<List<Long>> partitions = Lists.partition(theResourceIds.getContent(), myBatchSize);
 
 		for (List<Long> nextPartition : partitions) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmLinkDeleterTest.java

@@ -0,0 +1,63 @@
+package ca.uhn.fhir.jpa.batch.mdm.job;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.transaction.PlatformTransactionManager;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.anyList;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.verifyNoMoreInteractions;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+public class MdmLinkDeleterTest {
+	@Mock
+	private DaoConfig myDaoConfig;
+	@Mock
+	private PlatformTransactionManager myPlatformTransactionManager;
+	@Mock
+	private IMdmLinkDao myMdmLinkDao;
+
+	@Captor
+	ArgumentCaptor<List<Long>> myPidListCaptor;
+
+	@InjectMocks
+	private MdmLinkDeleter myMdmLinkDeleter;
+
+	@Test
+	public void testMdmLinkDeleterSplitsPidList() throws Exception {
+		int threadCount = 4;
+		int batchSize = 5;
+		when(myDaoConfig.getReindexBatchSize()).thenReturn(batchSize);
+		when(myDaoConfig.getReindexThreadCount()).thenReturn(threadCount);
+
+		List<Long> allPidsList = new ArrayList<>();
+		int count = threadCount*batchSize;
+		for (long i = 0; i < count; ++i) {
+			allPidsList.add(i);
+		}
+		myMdmLinkDeleter.process(allPidsList);
+
+		verify(myMdmLinkDao, times(threadCount)).findAllById(myPidListCaptor.capture());
+		verify(myMdmLinkDao, times(threadCount)).deleteAll(anyList());
+		verifyNoMoreInteractions(myMdmLinkDao);
+		List<List<Long>> pidListList = myPidListCaptor.getAllValues();
+		assertEquals(threadCount, pidListList.size());
+		for (List<Long> pidList : pidListList) {
+			assertEquals(batchSize, pidList.size());
+		}
+	}
+
+}