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core/src/main/java/org/elasticsearch/action/bulk/TransportShardBulkAction.java

@@ -50,6 +50,7 @@
 import org.elasticsearch.index.engine.EngineClosedException;
 import org.elasticsearch.index.engine.VersionConflictEngineException;
 import org.elasticsearch.index.mapper.MapperParsingException;
+import org.elasticsearch.index.seqno.GlobalCheckpointSyncAction;
 import org.elasticsearch.index.seqno.SequenceNumbersService;
 import org.elasticsearch.index.shard.IndexShard;
 import org.elasticsearch.index.shard.IndexShardClosedException;
@@ -184,6 +185,7 @@ private Translog.Location executeBulkItemRequest(IndexMetaData metaData, IndexSh
                     break;
                 default: throw new IllegalStateException("unexpected opType [" + itemRequest.opType() + "] found");
             }
+
             // update the bulk item request because update request execution can mutate the bulk item request
             request.items()[requestIndex] = replicaRequest;
             if (operationResult == null) { // in case of noop update operation
@@ -346,6 +348,10 @@ private UpdateResultHolder executeUpdateRequest(UpdateRequest updateRequest, Ind
                         replicaRequest = new BulkItemRequest(request.items()[requestIndex].id(), updateDeleteRequest);
                         break;
                 }
+                assert (replicaRequest.request() instanceof IndexRequest
+                    && ((IndexRequest) replicaRequest.request()).seqNo() != SequenceNumbersService.UNASSIGNED_SEQ_NO) ||
+                    (replicaRequest.request() instanceof DeleteRequest
+                        && ((DeleteRequest) replicaRequest.request()).seqNo() != SequenceNumbersService.UNASSIGNED_SEQ_NO);
                 // successful operation
                 break; // out of retry loop
             } else if (updateOperationResult.getFailure() instanceof VersionConflictEngineException == false) {
@@ -368,10 +374,10 @@ protected WriteReplicaResult shardOperationOnReplica(BulkShardRequest request, I
                     switch (docWriteRequest.opType()) {
                         case CREATE:
                         case INDEX:
-                            operationResult = executeIndexRequestOnReplica(((IndexRequest) docWriteRequest), replica);
+                            operationResult = executeIndexRequestOnReplica((IndexRequest) docWriteRequest, replica);
                             break;
                         case DELETE:
-                            operationResult = executeDeleteRequestOnReplica(((DeleteRequest) docWriteRequest), replica);
+                            operationResult = executeDeleteRequestOnReplica((DeleteRequest) docWriteRequest, replica);
                             break;
                         default:
                             throw new IllegalStateException("Unexpected request operation type on replica: "

core/src/main/java/org/elasticsearch/index/engine/InternalEngine.java

@@ -178,9 +178,9 @@ public InternalEngine(EngineConfig engineConfig) throws EngineException {
                 seqNoService = sequenceNumberService(shardId, engineConfig.getIndexSettings(), seqNoStats);
                 // norelease
                 /*
-                 * We have no guarantees that all operations above the local checkpoint are in the Lucene commit. These means that we there
-                 * might be operations greater than the local checkpoint that will not be replayed. Here we force the local checkpoint to
-                 * the maximum sequence number in the commit (at the potential expense of correctness).
+                 * We have no guarantees that all operations above the local checkpoint are in the Lucene commit or the translog. This means
+                 * that we there might be operations greater than the local checkpoint that will not be replayed. Here we force the local
+                 * checkpoint to the maximum sequence number in the commit (at the potential expense of correctness).
                  */
                 while (seqNoService.getLocalCheckpoint() < seqNoService.getMaxSeqNo()) {
                     final long next = seqNoService.getLocalCheckpoint() + 1;
@@ -795,7 +795,7 @@ private DeleteResult innerDelete(Delete delete) throws IOException {
                 seqNo = delete.seqNo();
             }
 
-            if (checkVersionConflict(delete, currentVersion, expectedVersion, deleted)) {
+            if (conflict) {
                 // skip executing delete because of version conflict on recovery
                 deleteResult = new DeleteResult(expectedVersion, seqNo, true);
             } else {

core/src/main/java/org/elasticsearch/index/seqno/GlobalCheckpointService.java

@@ -149,6 +149,11 @@ public synchronized long getCheckpoint() {
      * updates the global checkpoint on a replica shard (after it has been updated by the primary).
      */
     synchronized void updateCheckpointOnReplica(long globalCheckpoint) {
+        /*
+         * The global checkpoint here is a local knowledge which is updated under the mandate of the primary. It can happen that the primary
+         * information is lagging compared to a replica (e.g., if a replica is promoted to primary but has stale info relative to other
+         * replica shards). In these cases, the local knowledge of the global checkpoint could be higher than sync from the lagging primary.
+         */
         if (this.globalCheckpoint <= globalCheckpoint) {
             this.globalCheckpoint = globalCheckpoint;
             logger.trace("global checkpoint updated from primary to [{}]", globalCheckpoint);

core/src/main/java/org/elasticsearch/indices/recovery/RecoverySourceHandler.java

@@ -391,8 +391,8 @@ public void finalizeRecovery() {
         StopWatch stopWatch = new StopWatch().start();
         logger.trace("[{}][{}] finalizing recovery to {}", indexName, shardId, request.targetNode());
         cancellableThreads.execute(() -> {
-            recoveryTarget.finalizeRecovery(shard.getGlobalCheckpoint());
             shard.markAllocationIdAsInSync(recoveryTarget.getTargetAllocationId());
+            recoveryTarget.finalizeRecovery(shard.getGlobalCheckpoint());
         });
 
         if (request.isPrimaryRelocation()) {

core/src/main/java/org/elasticsearch/indices/recovery/RecoveryTargetHandler.java

@@ -39,8 +39,8 @@ public interface RecoveryTargetHandler {
     void prepareForTranslogOperations(int totalTranslogOps, long maxUnsafeAutoIdTimestamp) throws IOException;
 
     /**
-     * The finalize request clears unreferenced translog files, refreshes the engine now that new segments are available, enables garbage
-     * collection of tombstone files, and updates the global checkpoint.
+     * The finalize request refreshes the engine now that new segments are available, enables garbage collection of tombstone files, and
+     * updates the global checkpoint.
      *
      * @param globalCheckpoint the global checkpoint on the recovery source
      */

core/src/test/java/org/elasticsearch/index/engine/InternalEngineTests.java

@@ -2990,6 +2990,7 @@ public void testOutOfOrderSequenceNumbersWithVersionConflict() {
             }
         }
 
+        final boolean exists = operations.get(operations.size() - 1) instanceof Engine.Index;
         Randomness.shuffle(operations);
 
         for (final Engine.Operation operation : operations) {
@@ -3001,6 +3002,8 @@ public void testOutOfOrderSequenceNumbersWithVersionConflict() {
         }
 
         assertThat(engine.seqNoService().getLocalCheckpoint(), equalTo((long) (numberOfOperations - 1)));
+        final Engine.GetResult result = engine.get(new Engine.Get(true, uid));
+        assertThat(result.exists(), equalTo(exists));
     }
 
     private Engine.Index indexOperation(final Term uid, final ParsedDocument doc, final int seqNo, final int version) {
@@ -3010,7 +3013,7 @@ private Engine.Index indexOperation(final Term uid, final ParsedDocument doc, fi
             seqNo,
             1,
             version,
-            VersionType.INTERNAL,
+            VersionType.EXTERNAL,
             Engine.Operation.Origin.PEER_RECOVERY,
             System.nanoTime(),
             IndexRequest.UNSET_AUTO_GENERATED_TIMESTAMP,
@@ -3025,7 +3028,7 @@ private Engine.Delete deleteOperation(final String type, final String id, final
             seqNo,
             1,
             version,
-            VersionType.INTERNAL,
+            VersionType.EXTERNAL,
             Engine.Operation.Origin.PEER_RECOVERY,
             System.nanoTime());
     }