GH-5148 Introduce "soft fail" for corrupt ValueStore (#5157)

.gitignore

@@ -52,3 +52,4 @@ org.eclipse.dash.licenses-1.0.2.jar
 e2e/node_modules
 e2e/playwright-report
 e2e/test-results
+.aider*

core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/NativeStatementIterator.java

@@ -10,6 +10,8 @@
  *******************************************************************************/
 package org.eclipse.rdf4j.sail.nativerdf;
 
+import static org.eclipse.rdf4j.sail.nativerdf.NativeStore.SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES;
+
 import java.io.IOException;
 
 import org.eclipse.rdf4j.common.io.ByteArrayUtil;
@@ -20,13 +22,20 @@
 import org.eclipse.rdf4j.model.Value;
 import org.eclipse.rdf4j.sail.SailException;
 import org.eclipse.rdf4j.sail.nativerdf.btree.RecordIterator;
+import org.eclipse.rdf4j.sail.nativerdf.model.CorruptIRI;
+import org.eclipse.rdf4j.sail.nativerdf.model.CorruptIRIOrBNode;
+import org.eclipse.rdf4j.sail.nativerdf.model.CorruptUnknownValue;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * A statement iterator that wraps a RecordIterator containing statement records and translates these records to
  * {@link Statement} objects.
  */
 class NativeStatementIterator extends LookAheadIteration<Statement> {
 
+	private static final Logger logger = LoggerFactory.getLogger(NativeStatementIterator.class);
+
 	/*-----------*
 	 * Variables *
 	 *-----------*/
@@ -54,25 +63,42 @@ public NativeStatementIterator(RecordIterator btreeIter, ValueStore valueStore)
 	@Override
 	public Statement getNextElement() throws SailException {
 		try {
-			byte[] nextValue = btreeIter.next();
+			byte[] nextValue;
+			try {
+				nextValue = btreeIter.next();
+			} catch (AssertionError | Exception e) {
+				logger.error("Error while reading next value from btree iterator for {}", btreeIter.toString(), e);
+				throw e;
+			}
 
 			if (nextValue == null) {
 				return null;
 			}
 
 			int subjID = ByteArrayUtil.getInt(nextValue, TripleStore.SUBJ_IDX);
-			Resource subj = (Resource) valueStore.getValue(subjID);
+			Resource subj = valueStore.getResource(subjID);
 
 			int predID = ByteArrayUtil.getInt(nextValue, TripleStore.PRED_IDX);
-			IRI pred = (IRI) valueStore.getValue(predID);
+			IRI pred = valueStore.getIRI(predID);
 
 			int objID = ByteArrayUtil.getInt(nextValue, TripleStore.OBJ_IDX);
 			Value obj = valueStore.getValue(objID);
 
 			Resource context = null;
 			int contextID = ByteArrayUtil.getInt(nextValue, TripleStore.CONTEXT_IDX);
 			if (contextID != 0) {
-				context = (Resource) valueStore.getValue(contextID);
+				context = valueStore.getResource(contextID);
+			}
+			if (SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES) {
+				if (subj == null) {
+					subj = new CorruptIRIOrBNode(valueStore.getRevision(), subjID, null);
+				}
+				if (pred == null) {
+					pred = new CorruptIRI(valueStore.getRevision(), predID, null, null);
+				}
+				if (obj == null) {
+					obj = new CorruptUnknownValue(valueStore.getRevision(), objID, null);
+				}
 			}
 
 			return valueStore.createStatement(subj, pred, obj, context);

core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/NativeStore.java

@@ -24,6 +24,7 @@
 import org.apache.commons.io.FileUtils;
 import org.eclipse.rdf4j.collection.factory.api.CollectionFactory;
 import org.eclipse.rdf4j.collection.factory.mapdb.MapDb3CollectionFactory;
+import org.eclipse.rdf4j.common.annotation.InternalUseOnly;
 import org.eclipse.rdf4j.common.concurrent.locks.Lock;
 import org.eclipse.rdf4j.common.concurrent.locks.LockManager;
 import org.eclipse.rdf4j.common.io.MavenUtil;
@@ -62,6 +63,17 @@ public class NativeStore extends AbstractNotifyingSail implements FederatedServi
 
 	private static final String VERSION = MavenUtil.loadVersion("org.eclipse.rdf4j", "rdf4j-sail-nativerdf", "devel");
 
+	/**
+	 * Do not throw an exception when corrupt data is detected. Instead, try to return as much data as possible.
+	 *
+	 * Variable can be set through the system property
+	 * org.eclipse.rdf4j.sail.nativerdf.softFailOnCorruptDataAndRepairIndexes.
+	 */
+	@InternalUseOnly
+	public static boolean SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES = "true"
+			.equalsIgnoreCase(
+					System.getProperty("org.eclipse.rdf4j.sail.nativerdf.softFailOnCorruptDataAndRepairIndexes"));;
+
 	private static final Cleaner REMOVE_STORES_USED_FOR_MEMORY_OVERFLOW = Cleaner.create();
 
 	/**

core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/TripleStore.java

@@ -287,9 +287,71 @@ private Set<String> parseIndexSpecList(String indexSpecStr) throws SailException
 	}
 
 	private void initIndexes(Set<String> indexSpecs) throws IOException {
+
+		HashSet<String> invalidIndexes = new HashSet<>();
+
 		for (String fieldSeq : indexSpecs) {
 			logger.trace("Initializing index '{}'...", fieldSeq);
-			indexes.add(new TripleIndex(fieldSeq));
+			try {
+				indexes.add(new TripleIndex(fieldSeq, false));
+			} catch (Exception e) {
+				if (NativeStore.SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES) {
+					invalidIndexes.add(fieldSeq);
+					logger.warn("Ignoring index because it failed to initialize index '{}'", fieldSeq, e);
+				} else {
+					logger.error(
+							"Failed to initialize index '{}', consider setting org.eclipse.rdf4j.sail.nativerdf.softFailOnCorruptDataAndRepairIndexes to true.",
+							fieldSeq, e);
+					throw e;
+				}
+
+			}
+
+		}
+
+		if (NativeStore.SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES) {
+			indexSpecs.removeAll(invalidIndexes);
+		}
+
+		List<TripleIndex> emptyIndexes = new ArrayList<>();
+		List<TripleIndex> nonEmptyIndexes = new ArrayList<>();
+
+		checkIfIndexesAreEmptyOrNot(nonEmptyIndexes, emptyIndexes);
+
+		if (!emptyIndexes.isEmpty() && !nonEmptyIndexes.isEmpty()) {
+			if (NativeStore.SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES) {
+				indexes.removeAll(emptyIndexes);
+			} else {
+				for (TripleIndex index : emptyIndexes) {
+					throw new IOException("Index '" + new String(index.getFieldSeq())
+							+ "' is unexpectedly empty while other indexes are not. Consider setting the system property org.eclipse.rdf4j.sail.nativerdf.softFailOnCorruptDataAndRepairIndexes to true. Index file: "
+							+ index.getBTree().getFile().getAbsolutePath());
+				}
+			}
+		}
+
+	}
+
+	private void checkIfIndexesAreEmptyOrNot(List<TripleIndex> nonEmptyIndexes, List<TripleIndex> emptyIndexes)
+			throws IOException {
+		for (TripleIndex index : indexes) {
+			try (RecordIterator recordIterator = index.getBTree().iterateAll()) {
+				try {
+					byte[] next = recordIterator.next();
+					if (next != null) {
+						next = recordIterator.next();
+						if (next != null) {
+							nonEmptyIndexes.add(index);
+						} else {
+							emptyIndexes.add(index);
+						}
+					} else {
+						emptyIndexes.add(index);
+					}
+				} catch (Throwable ignored) {
+					emptyIndexes.add(index);
+				}
+			}
 		}
 	}
 
@@ -355,7 +417,7 @@ private void reindex(Set<String> currentIndexSpecs, Set<String> newIndexSpecs) t
 			for (String fieldSeq : addedIndexSpecs) {
 				logger.debug("Initializing new index '{}'...", fieldSeq);
 
-				TripleIndex addedIndex = new TripleIndex(fieldSeq);
+				TripleIndex addedIndex = new TripleIndex(fieldSeq, true);
 				BTree addedBTree = null;
 				RecordIterator sourceIter = null;
 				try {
@@ -1122,7 +1184,17 @@ private class TripleIndex {
 
 		private final BTree btree;
 
-		public TripleIndex(String fieldSeq) throws IOException {
+		public TripleIndex(String fieldSeq, boolean deleteExistingIndexFile) throws IOException {
+			if (deleteExistingIndexFile) {
+				File indexFile = new File(dir, getFilenamePrefix(fieldSeq) + ".dat");
+				if (indexFile.exists()) {
+					indexFile.delete();
+				}
+				File alloxFile = new File(dir, getFilenamePrefix(fieldSeq) + ".alloc");
+				if (alloxFile.exists()) {
+					alloxFile.delete();
+				}
+			}
 			tripleComparator = new TripleComparator(fieldSeq);
 			btree = new BTree(dir, getFilenamePrefix(fieldSeq), 2048, RECORD_LENGTH, tripleComparator, forceSync);
 		}