drop index.shard.check_on_startup: fix

docs/reference/index-modules.asciidoc

@@ -65,9 +65,7 @@ corruption is detected, it will prevent the shard from being opened. Accepts:
 
 `fix`::
 
-    Check for both physical and logical corruption.  Segments that were reported
-    as corrupted will be automatically removed. This option *may result in data loss*.
-    Use with extreme caution!
+    The same as `false`. This option is deprecated and will be completely removed in 7.0.
 
 WARNING: Expert only. Checking shards may take a lot of time on large indices.
 --

server/src/main/java/org/elasticsearch/index/shard/IndexShard.java

@@ -1323,7 +1323,7 @@ private void innerOpenEngineAndTranslog() throws IOException {
         }
         recoveryState.setStage(RecoveryState.Stage.VERIFY_INDEX);
         // also check here, before we apply the translog
-        if (Booleans.isTrue(checkIndexOnStartup)) {
+        if (Booleans.isTrue(checkIndexOnStartup) || "checksum".equals(checkIndexOnStartup)) {
             try {
                 checkIndex();
             } catch (IOException ex) {
@@ -1923,6 +1923,9 @@ void checkIndex() throws IOException {
         if (store.tryIncRef()) {
             try {
                 doCheckIndex();
+            } catch (IOException e) {
+                store.markStoreCorrupted(e);
+                throw e;
             } finally {
                 store.decRef();
             }
@@ -1966,18 +1969,7 @@ private void doCheckIndex() throws IOException {
                     return;
                 }
                 logger.warn("check index [failure]\n{}", os.bytes().utf8ToString());
-                if ("fix".equals(checkIndexOnStartup)) {
-                    if (logger.isDebugEnabled()) {
-                        logger.debug("fixing index, writing new segments file ...");
-                    }
-                    store.exorciseIndex(status);
-                    if (logger.isDebugEnabled()) {
-                        logger.debug("index fixed, wrote new segments file \"{}\"", status.segmentsFileName);
-                    }
-                } else {
-                    // only throw a failure if we are not going to fix the index
-                    throw new IllegalStateException("index check failure but can't fix it");
-                }
+                throw new IOException("index check failure");
             }
         }
 

server/src/main/java/org/elasticsearch/index/store/Store.java

@@ -134,7 +134,8 @@ public class Store extends AbstractIndexShardComponent implements Closeable, Ref
     static final int VERSION_STACK_TRACE = 1; // we write the stack trace too since 1.4.0
     static final int VERSION_START = 0;
     static final int VERSION = VERSION_WRITE_THROWABLE;
-    static final String CORRUPTED = "corrupted_";
+    // public is for test purposes
+    public static final String CORRUPTED = "corrupted_";
     public static final Setting<TimeValue> INDEX_STORE_STATS_REFRESH_INTERVAL_SETTING =
         Setting.timeSetting("index.store.stats_refresh_interval", TimeValue.timeValueSeconds(10), Property.IndexScope);
 
@@ -360,18 +361,6 @@ public CheckIndex.Status checkIndex(PrintStream out) throws IOException {
         }
     }
 
-    /**
-     * Repairs the index using the previous returned status from {@link #checkIndex(PrintStream)}.
-     */
-    public void exorciseIndex(CheckIndex.Status status) throws IOException {
-        metadataLock.writeLock().lock();
-        try (CheckIndex checkIndex = new CheckIndex(directory)) {
-            checkIndex.exorciseIndex(status);
-        } finally {
-            metadataLock.writeLock().unlock();
-        }
-    }
-
     public StoreStats stats() throws IOException {
         ensureOpen();
         return new StoreStats(directory.estimateSize());

server/src/test/java/org/elasticsearch/index/shard/IndexShardTests.java

@@ -22,6 +22,7 @@
 import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.IndexCommit;
+import org.apache.lucene.index.IndexWriter;
 import org.apache.lucene.index.Term;
 import org.apache.lucene.search.IndexSearcher;
 import org.apache.lucene.search.TermQuery;
@@ -111,6 +112,7 @@
 import org.elasticsearch.snapshots.SnapshotId;
 import org.elasticsearch.snapshots.SnapshotInfo;
 import org.elasticsearch.snapshots.SnapshotShardFailure;
+import org.elasticsearch.test.CorruptionUtils;
 import org.elasticsearch.test.DummyShardLock;
 import org.elasticsearch.test.FieldMaskingReader;
 import org.elasticsearch.test.VersionUtils;
@@ -119,7 +121,11 @@
 
 import java.io.IOException;
 import java.nio.charset.Charset;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -1230,7 +1236,7 @@ public String[] listAll() throws IOException {
         };
 
         try (Store store = createStore(shardId, new IndexSettings(metaData, Settings.EMPTY), directory)) {
-            IndexShard shard = newShard(shardRouting, shardPath, metaData, store,
+            IndexShard shard = newShard(shardRouting, shardPath, metaData, i -> store,
                     null, new InternalEngineFactory(), () -> {
                     }, EMPTY_EVENT_LISTENER);
             AtomicBoolean failureCallbackTriggered = new AtomicBoolean(false);
@@ -2571,6 +2577,142 @@ public void testReadSnapshotConcurrently() throws IOException, InterruptedExcept
         closeShards(newShard);
     }
 
+    public void testIndexCheckOnStartup() throws Exception {
+        final IndexShard indexShard = newStartedShard(true);
+
+        final long numDocs = between(10, 100);
+        for (long i = 0; i < numDocs; i++) {
+            indexDoc(indexShard, "_doc", Long.toString(i), "{}");
+        }
+        indexShard.flush(new FlushRequest());
+        closeShards(indexShard);
+
+        final ShardPath shardPath = indexShard.shardPath();
+
+        final Path indexPath = corruptIndexFile(shardPath);
+
+        final AtomicInteger corruptedMarkerCount = new AtomicInteger();
+        final SimpleFileVisitor<Path> corruptedVisitor = new SimpleFileVisitor<Path>() {
+            @Override
+            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+                if (Files.isRegularFile(file) && file.getFileName().toString().startsWith(Store.CORRUPTED)) {
+                    corruptedMarkerCount.incrementAndGet();
+                }
+                return FileVisitResult.CONTINUE;
+            }
+        };
+        Files.walkFileTree(indexPath, corruptedVisitor);
+
+        assertThat("corruption marker should not be there", corruptedMarkerCount.get(), equalTo(0));
+
+        final ShardRouting shardRouting = ShardRoutingHelper.initWithSameId(indexShard.routingEntry(),
+            RecoverySource.StoreRecoverySource.EXISTING_STORE_INSTANCE
+        );
+        // start shard and perform index check on startup. It enforce shard to fail due to corrupted index files
+        final IndexMetaData indexMetaData = IndexMetaData.builder(indexShard.indexSettings().getIndexMetaData())
+            .settings(Settings.builder()
+                .put(indexShard.indexSettings.getSettings())
+                .put(IndexSettings.INDEX_CHECK_ON_STARTUP.getKey(), randomFrom("true", "checksum")))
+            .build();
+
+        IndexShard corruptedShard = newShard(shardRouting, shardPath, indexMetaData,
+            null, null, indexShard.engineFactory,
+            indexShard.getGlobalCheckpointSyncer(), EMPTY_EVENT_LISTENER);
+
+        final IndexShardRecoveryException indexShardRecoveryException =
+            expectThrows(IndexShardRecoveryException.class, () -> newStartedShard(p -> corruptedShard, true));
+        assertThat(indexShardRecoveryException.getMessage(), equalTo("failed recovery"));
+
+        // check that corrupt marker is there
+        Files.walkFileTree(indexPath, corruptedVisitor);
+        assertThat("store has to be marked as corrupted", corruptedMarkerCount.get(), equalTo(1));
+
+        try {
+            closeShards(corruptedShard);
+        } catch (RuntimeException e) {
+            assertThat(e.getMessage(), equalTo("CheckIndex failed"));
+        }
+    }
+
+    public void testShardDoesNotStartIfCorruptedMarkerIsPresent() throws Exception {
+        final IndexShard indexShard = newStartedShard(true);
+
+        final long numDocs = between(10, 100);
+        for (long i = 0; i < numDocs; i++) {
+            indexDoc(indexShard, "_doc", Long.toString(i), "{}");
+        }
+        indexShard.flush(new FlushRequest());
+        closeShards(indexShard);
+
+        final ShardPath shardPath = indexShard.shardPath();
+
+        final ShardRouting shardRouting = ShardRoutingHelper.initWithSameId(indexShard.routingEntry(),
+            RecoverySource.StoreRecoverySource.EXISTING_STORE_INSTANCE
+        );
+        final IndexMetaData indexMetaData = indexShard.indexSettings().getIndexMetaData();
+
+        final Path indexPath = shardPath.getDataPath().resolve(ShardPath.INDEX_FOLDER_NAME);
+
+        // create corrupted marker
+        final String corruptionMessage = "fake ioexception";
+        try(Store store = createStore(indexShard.indexSettings(), shardPath)) {
+            store.markStoreCorrupted(new IOException(corruptionMessage));
+        }
+
+        // try to start shard on corrupted files
+        final IndexShard corruptedShard = newShard(shardRouting, shardPath, indexMetaData,
+            null, null, indexShard.engineFactory,
+            indexShard.getGlobalCheckpointSyncer(), EMPTY_EVENT_LISTENER);
+
+        final IndexShardRecoveryException exception1 = expectThrows(IndexShardRecoveryException.class,
+            () -> newStartedShard(p -> corruptedShard, true));
+        assertThat(exception1.getCause().getMessage(), equalTo(corruptionMessage + " (resource=preexisting_corruption)"));
+        closeShards(corruptedShard);
+
+        final AtomicInteger corruptedMarkerCount = new AtomicInteger();
+        final SimpleFileVisitor<Path> corruptedVisitor = new SimpleFileVisitor<Path>() {
+            @Override
+            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+                if (Files.isRegularFile(file) && file.getFileName().toString().startsWith(Store.CORRUPTED)) {
+                    corruptedMarkerCount.incrementAndGet();
+                }
+                return FileVisitResult.CONTINUE;
+            }
+        };
+        Files.walkFileTree(indexPath, corruptedVisitor);
+        assertThat("store has to be marked as corrupted", corruptedMarkerCount.get(), equalTo(1));
+
+        // try to start another time shard on corrupted files
+        final IndexShard corruptedShard2 = newShard(shardRouting, shardPath, indexMetaData,
+            null, null, indexShard.engineFactory,
+            indexShard.getGlobalCheckpointSyncer(), EMPTY_EVENT_LISTENER);
+
+        final IndexShardRecoveryException exception2 = expectThrows(IndexShardRecoveryException.class,
+            () -> newStartedShard(p -> corruptedShard2, true));
+        assertThat(exception2.getCause().getMessage(), equalTo(corruptionMessage + " (resource=preexisting_corruption)"));
+        closeShards(corruptedShard2);
+
+        // check that corrupt marker is there
+        corruptedMarkerCount.set(0);
+        Files.walkFileTree(indexPath, corruptedVisitor);
+        assertThat("store still has a single corrupt marker", corruptedMarkerCount.get(), equalTo(1));
+    }
+
+    private Path corruptIndexFile(ShardPath shardPath) throws IOException {
+        final Path indexPath = shardPath.getDataPath().resolve(ShardPath.INDEX_FOLDER_NAME);
+        final Path[] filesToCorrupt =
+            Files.walk(indexPath)
+                .filter(p -> {
+                    final String name = p.getFileName().toString();
+                    return Files.isRegularFile(p)
+                        && IndexWriter.WRITE_LOCK_NAME.equals(name) == false
+                        && name.startsWith("segments_") == false && name.endsWith(".si") == false;
+                })
+                .toArray(Path[]::new);
+        CorruptionUtils.corruptFile(random(), filesToCorrupt);
+        return indexPath;
+    }
+
     /**
      * Simulates a scenario that happens when we are async fetching snapshot metadata from GatewayService
      * and checking index concurrently. This should always be possible without any exception.

test/framework/src/main/java/org/elasticsearch/index/shard/IndexShardTestCase.java

@@ -37,6 +37,7 @@
 import org.elasticsearch.cluster.routing.ShardRoutingHelper;
 import org.elasticsearch.cluster.routing.ShardRoutingState;
 import org.elasticsearch.cluster.routing.TestShardRouting;
+import org.elasticsearch.common.CheckedFunction;
 import org.elasticsearch.common.Nullable;
 import org.elasticsearch.common.bytes.BytesArray;
 import org.elasticsearch.common.lucene.uid.Versions;
@@ -163,7 +164,6 @@ public Settings threadPoolSettings() {
         return Settings.EMPTY;
     }
 
-
     protected Store createStore(IndexSettings indexSettings, ShardPath shardPath) throws IOException {
         return createStore(shardPath.getShardId(), indexSettings, newFSDirectory(shardPath.resolveIndex()));
     }
@@ -176,20 +176,30 @@ public Directory newDirectory() throws IOException {
             }
         };
         return new Store(shardId, indexSettings, directoryService, new DummyShardLock(shardId));
-
     }
 
     /**
      * creates a new initializing shard. The shard will have its own unique data path.
      *
      * @param primary indicates whether to a primary shard (ready to recover from an empty store) or a replica
      *                (ready to recover from another shard)
+     * @param indexSettings the {@link Settings} to use for this index
      */
-    protected IndexShard newShard(boolean primary) throws IOException {
+    protected IndexShard newShard(boolean primary, Settings indexSettings) throws IOException {
         ShardRouting shardRouting = TestShardRouting.newShardRouting(new ShardId("index", "_na_", 0), randomAlphaOfLength(10), primary,
             ShardRoutingState.INITIALIZING,
             primary ? RecoverySource.StoreRecoverySource.EMPTY_STORE_INSTANCE : RecoverySource.PeerRecoverySource.INSTANCE);
-        return newShard(shardRouting);
+        return newShard(shardRouting, indexSettings);
+    }
+
+    /**
+     * creates a new initializing shard. The shard will have its own unique data path.
+     *
+     * @param primary indicates whether to a primary shard (ready to recover from an empty store) or a replica
+     *                (ready to recover from another shard)
+     */
+    protected IndexShard newShard(boolean primary) throws IOException {
+        return newShard(primary, Settings.EMPTY);
     }
 
     /**
@@ -198,13 +208,29 @@ protected IndexShard newShard(boolean primary) throws IOException {
      * @param shardRouting the {@link ShardRouting} to use for this shard
      * @param listeners    an optional set of listeners to add to the shard
      */
+    protected IndexShard newShard(
+        final ShardRouting shardRouting,
+        final IndexingOperationListener... listeners) throws IOException {
+        return newShard(shardRouting, Settings.EMPTY, listeners);
+    }
+
+    /**
+     * creates a new initializing shard. The shard will have its own unique data path.
+     *
+     * @param shardRouting  the {@link ShardRouting} to use for this shard
+     * @param indexSettings the {@link Settings} to use for this index
+     * @param listeners     an optional set of listeners to add to the shard
+     */
     protected IndexShard newShard(
             final ShardRouting shardRouting,
+            final Settings indexSettings,
             final IndexingOperationListener... listeners) throws IOException {
         assert shardRouting.initializing() : shardRouting;
-        Settings settings = Settings.builder().put(IndexMetaData.SETTING_VERSION_CREATED, Version.CURRENT)
+        Settings settings = Settings.builder()
+            .put(IndexMetaData.SETTING_VERSION_CREATED, Version.CURRENT)
             .put(IndexMetaData.SETTING_NUMBER_OF_REPLICAS, 0)
             .put(IndexMetaData.SETTING_NUMBER_OF_SHARDS, 1)
+            .put(indexSettings)
             .build();
         IndexMetaData.Builder metaData = IndexMetaData.builder(shardRouting.getIndexName())
             .settings(settings)
@@ -298,23 +324,25 @@ protected IndexShard newShard(ShardRouting routing, IndexMetaData indexMetaData,
      * @param routing                       shard routing to use
      * @param shardPath                     path to use for shard data
      * @param indexMetaData                 indexMetaData for the shard, including any mapping
-     * @param store                         an optional custom store to use. If null a default file based store will be created
+     * @param storeProvider                 an optional custom store provider to use. If null a default file based store will be created
      * @param indexSearcherWrapper          an optional wrapper to be used during searchers
      * @param globalCheckpointSyncer        callback for syncing global checkpoints
      * @param indexEventListener            index event listener
      * @param listeners                     an optional set of listeners to add to the shard
      */
     protected IndexShard newShard(ShardRouting routing, ShardPath shardPath, IndexMetaData indexMetaData,
-                                  @Nullable Store store, @Nullable IndexSearcherWrapper indexSearcherWrapper,
+                                  @Nullable CheckedFunction<IndexSettings, Store, IOException> storeProvider,
+                                  @Nullable IndexSearcherWrapper indexSearcherWrapper,
                                   @Nullable EngineFactory engineFactory,
                                   Runnable globalCheckpointSyncer,
                                   IndexEventListener indexEventListener, IndexingOperationListener... listeners) throws IOException {
         final Settings nodeSettings = Settings.builder().put("node.name", routing.currentNodeId()).build();
         final IndexSettings indexSettings = new IndexSettings(indexMetaData, nodeSettings);
         final IndexShard indexShard;
-        if (store == null) {
-            store = createStore(indexSettings, shardPath);
+        if (storeProvider == null) {
+            storeProvider = is -> createStore(is, shardPath);
         }
+        final Store store = storeProvider.apply(indexSettings);
         boolean success = false;
         try {
             IndexCache indexCache = new IndexCache(indexSettings, new DisabledQueryCache(indexSettings), null);
@@ -384,7 +412,18 @@ protected IndexShard newStartedShard() throws IOException {
      * @param primary controls whether the shard will be a primary or a replica.
      */
     protected IndexShard newStartedShard(boolean primary) throws IOException {
-        IndexShard shard = newShard(primary);
+        return newStartedShard(p -> newShard(p), primary);
+    }
+
+    /**
+     * creates a new empty shard and starts it.
+     *
+     * @param shardFunction shard factory function
+     * @param primary controls whether the shard will be a primary or a replica.
+     */
+    protected IndexShard newStartedShard(CheckedFunction<Boolean, IndexShard, IOException> shardFunction,
+                                         boolean primary) throws IOException {
+        IndexShard shard = shardFunction.apply(primary);
         if (primary) {
             recoverShardFromStore(shard);
         } else {