Ignore metadata of deleted indices at start (#48918)

Today in 6.x it is possible to add an index tombstone to the graveyard without
deleting the corresponding index metadata, because the deletion is slightly
deferred. If you shut down the node and upgrade to 7.x when in this state then
the node will fail to apply any cluster states, reporting

    java.lang.IllegalStateException: Cannot delete index [...], it is still part of the cluster state.

This commit addresses this situation by skipping over any index metadata with a
corresponding tombstone, allowing this metadata to be cleaned up by the 7.x
node.

server/src/main/java/org/elasticsearch/gateway/MetaStateService.java

@@ -21,6 +21,7 @@ package org.elasticsearch.gateway;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.elasticsearch.cluster.metadata.IndexGraveyard;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
 import org.elasticsearch.cluster.metadata.Manifest;
 import org.elasticsearch.cluster.metadata.MetaData;
@@ -115,12 +116,15 @@ public class MetaStateService {
         MetaData globalMetaData = metaDataAndGeneration.v1();
         long globalStateGeneration = metaDataAndGeneration.v2();
 
+        final IndexGraveyard indexGraveyard;
         if (globalMetaData != null) {
             metaDataBuilder = MetaData.builder(globalMetaData);
+            indexGraveyard = globalMetaData.custom(IndexGraveyard.TYPE);
             // TODO https://github.com/elastic/elasticsearch/issues/38556
             // assert Version.CURRENT.major < 8 : "failed to find manifest file, which is mandatory staring with Elasticsearch version 8.0";
         } else {
             metaDataBuilder = MetaData.builder();
+            indexGraveyard = IndexGraveyard.builder().build();
         }
 
         for (String indexFolderName : nodeEnv.availableIndexFolders()) {
@@ -132,8 +136,13 @@ public class MetaStateService {
             IndexMetaData indexMetaData = indexMetaDataAndGeneration.v1();
             long generation = indexMetaDataAndGeneration.v2();
             if (indexMetaData != null) {
-                indices.put(indexMetaData.getIndex(), generation);
-                metaDataBuilder.put(indexMetaData, false);
+                if (indexGraveyard.containsIndex(indexMetaData.getIndex())) {
+                    logger.debug("[{}] found metadata for deleted index [{}]", indexFolderName, indexMetaData.getIndex());
+                    // this index folder is cleared up when state is recovered
+                } else {
+                    indices.put(indexMetaData.getIndex(), generation);
+                    metaDataBuilder.put(indexMetaData, false);
+                }
             } else {
                 logger.debug("[{}] failed to find metadata for existing index location", indexFolderName);
             }

server/src/test/java/org/elasticsearch/gateway/GatewayIndexStateIT.java

@@ -30,8 +30,10 @@ import org.elasticsearch.action.support.ActiveShardCount;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.Requests;
 import org.elasticsearch.cluster.ClusterState;
+import org.elasticsearch.cluster.coordination.CoordinationMetaData;
 import org.elasticsearch.cluster.metadata.IndexGraveyard;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
+import org.elasticsearch.cluster.metadata.Manifest;
 import org.elasticsearch.cluster.metadata.MappingMetaData;
 import org.elasticsearch.cluster.metadata.MetaData;
 import org.elasticsearch.cluster.routing.IndexRoutingTable;
@@ -39,11 +41,13 @@ import org.elasticsearch.cluster.routing.IndexShardRoutingTable;
 import org.elasticsearch.cluster.routing.RoutingTable;
 import org.elasticsearch.cluster.routing.ShardRoutingState;
 import org.elasticsearch.cluster.routing.UnassignedInfo;
+import org.elasticsearch.cluster.service.ClusterService;
 import org.elasticsearch.common.CheckedConsumer;
 import org.elasticsearch.common.Priority;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.xcontent.XContentFactory;
 import org.elasticsearch.common.xcontent.XContentType;
+import org.elasticsearch.core.internal.io.IOUtils;
 import org.elasticsearch.env.NodeEnvironment;
 import org.elasticsearch.index.mapper.MapperParsingException;
 import org.elasticsearch.indices.IndexClosedException;
@@ -54,6 +58,8 @@ import org.elasticsearch.test.ESIntegTestCase.Scope;
 import org.elasticsearch.test.InternalTestCluster.RestartCallback;
 
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.TimeUnit;
@@ -66,6 +72,7 @@ import static org.elasticsearch.index.query.QueryBuilders.matchAllQuery;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAcked;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertHitCount;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.notNullValue;
@@ -508,6 +515,42 @@ public class GatewayIndexStateIT extends ESIntegTestCase {
         assertHitCount(client().prepareSearch().setQuery(matchAllQuery()).get(), 1L);
     }
 
+    public void testHalfDeletedIndexImport() throws Exception {
+        // It's possible for a 6.x node to add a tombstone for an index but not actually delete the index metadata from disk since that
+        // deletion is slightly deferred and may race against the node being shut down; if you upgrade to 7.x when in this state then the
+        // node won't start.
+
+        internalCluster().startNode();
+        createIndex("test", Settings.builder()
+            .put(IndexMetaData.SETTING_NUMBER_OF_SHARDS, 1)
+            .put(IndexMetaData.SETTING_NUMBER_OF_REPLICAS, 0)
+            .build());
+        ensureGreen("test");
+
+        final MetaData metaData = internalCluster().getInstance(ClusterService.class).state().metaData();
+        final Path[] paths = internalCluster().getInstance(NodeEnvironment.class).nodeDataPaths();
+        writeBrokenMeta(metaStateService -> {
+            metaStateService.writeGlobalState("test", MetaData.builder(metaData)
+                // we remove the manifest file, resetting the term and making this look like an upgrade from 6.x, so must also reset the
+                // term in the coordination metadata
+                .coordinationMetaData(CoordinationMetaData.builder(metaData.coordinationMetaData()).term(0L).build())
+                // add a tombstone but do not delete the index metadata from disk
+                .putCustom(IndexGraveyard.TYPE, IndexGraveyard.builder().addTombstone(metaData.index("test").getIndex()).build()).build());
+            for (final Path path : paths) {
+                try (Stream<Path> stateFiles = Files.list(path.resolve(MetaDataStateFormat.STATE_DIR_NAME))) {
+                    for (final Path manifestPath : stateFiles
+                        .filter(p -> p.getFileName().toString().startsWith(Manifest.FORMAT.getPrefix())).collect(Collectors.toList())) {
+                        IOUtils.rm(manifestPath);
+                    }
+                }
+            }
+        });
+
+        ensureGreen();
+
+        assertBusy(() -> assertThat(internalCluster().getInstance(NodeEnvironment.class).availableIndexFolders(), empty()));
+    }
+
     private void writeBrokenMeta(CheckedConsumer<MetaStateService, IOException> writer) throws Exception {
         Map<String, MetaStateService> metaStateServices = Stream.of(internalCluster().getNodeNames())
             .collect(Collectors.toMap(Function.identity(), nodeName -> internalCluster().getInstance(MetaStateService.class, nodeName)));