various attempts at fixing issue

Author: hmottestad

core/sail/api/src/main/java/org/eclipse/rdf4j/common/concurrent/locks/ExclusiveReentrantLockManager.java

@@ -34,7 +34,7 @@ public class ExclusiveReentrantLockManager {
 
 	private final int waitToCollect;
 
-	LockMonitoring<ExclusiveReentrantLock> lockMonitoring;
+	LockMonitoring<Lock> lockMonitoring;
 
 	public ExclusiveReentrantLockManager() {
 		this(false);
@@ -50,18 +50,18 @@ public ExclusiveReentrantLockManager(boolean trackLocks, int collectionFrequency
 
 		if (trackLocks || Properties.lockTrackingEnabled()) {
 
-			lockMonitoring = new LockTracking(
+			lockMonitoring = new LockTracking<>(
 					true,
-					"ExclusiveReentrantLockManager",
+					"ExclusiveReentrantLockManager-Tracking",
 					LoggerFactory.getLogger(this.getClass()),
 					waitToCollect,
 					Lock.ExtendedSupplier.wrap(this::getExclusiveLockInner, this::tryExclusiveLockInner)
 			);
 
 		} else {
-			lockMonitoring = new LockCleaner(
+			lockMonitoring = new LockCleaner<>(
 					false,
-					"ExclusiveReentrantLockManager",
+					"ExclusiveReentrantLockManager-Cleaner",
 					LoggerFactory.getLogger(this.getClass()),
 					Lock.ExtendedSupplier.wrap(this::getExclusiveLockInner, this::tryExclusiveLockInner)
 			);
@@ -87,6 +87,8 @@ private Lock tryExclusiveLockInner() {
 
 	}
 
+	private final AtomicLong ownerIsDead = new AtomicLong();
+
 	private Lock getExclusiveLockInner() throws InterruptedException {
 
 		synchronized (owner) {
@@ -100,6 +102,14 @@ private Lock getExclusiveLockInner() throws InterruptedException {
 					if (lock != null) {
 						return lock;
 					} else {
+						if (!owner.get().isAlive()) {
+							long l = ownerIsDead.incrementAndGet();
+							if (l > 10) {
+								ownerIsDead.set(0);
+								continue;
+							}
+
+						}
 						lockMonitoring.runCleanup();
 						owner.wait(waitToCollect);
 					}
@@ -113,6 +123,12 @@ private Lock getExclusiveLockInner() throws InterruptedException {
 					if (lock != null) {
 						return lock;
 					} else {
+						if (!owner.get().isAlive()) {
+							System.out.println("Owner thread is dead");
+//							activeLocks.set(0);
+//							owner.set(null);
+//							continue;
+						}
 						owner.wait(waitToCollect);
 					}
 				}

core/sail/api/src/main/java/org/eclipse/rdf4j/sail/helpers/AbstractSail.java

@@ -18,6 +18,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
+import java.util.WeakHashMap;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import org.eclipse.rdf4j.common.transaction.IsolationLevel;
@@ -119,6 +120,7 @@ protected static boolean debugEnabled() {
 	 * debugging was disable at the time the connection was acquired.
 	 */
 	private final Map<SailConnection, Throwable> activeConnections = new IdentityHashMap<>();
+//	private final Map<SailConnection, Throwable> activeConnections = new WeakHashMap<>();
 
 	/*
 	 * constructors

core/sail/api/src/main/java/org/eclipse/rdf4j/sail/helpers/AbstractSailConnection.java

@@ -22,9 +22,9 @@
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.concurrent.atomic.LongAdder;
 import java.util.concurrent.locks.LockSupport;
-import java.util.concurrent.locks.ReentrantLock;
 
 import org.eclipse.rdf4j.common.annotation.InternalUseOnly;
+import org.eclipse.rdf4j.common.concurrent.locks.ExclusiveReentrantLockManager;
 import org.eclipse.rdf4j.common.concurrent.locks.Lock;
 import org.eclipse.rdf4j.common.concurrent.locks.diagnostics.ConcurrentCleaner;
 import org.eclipse.rdf4j.common.iteration.CloseableIteration;
@@ -98,17 +98,16 @@ public abstract class AbstractSailConnection implements SailConnection {
 	private final AtomicReference<Thread> activeThread = new AtomicReference<>();
 
 	@SuppressWarnings("FieldMayBeFinal")
-	private boolean isOpen = true;
+	private volatile boolean isOpen = true;
 	private static final VarHandle IS_OPEN;
 
 	private Thread owner;
 
 	/**
 	 * Lock used to prevent concurrent calls to update methods like addStatement, clear, commit, etc. within a
 	 * transaction.
-	 *
 	 */
-	private final ReentrantLock updateLock = new ReentrantLock();
+	private final ExclusiveReentrantLockManager updateLock = new ExclusiveReentrantLockManager();
 	private final LongAdder iterationsOpened = new LongAdder();
 	private final LongAdder iterationsClosed = new LongAdder();
 
@@ -200,8 +199,7 @@ public void begin(IsolationLevel isolationLevel) throws SailException {
 			activeThread.setRelease(Thread.currentThread());
 
 			verifyIsOpen();
-
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
 			try {
 				if (isActive()) {
 					throw new SailException("a transaction is already active on this connection.");
@@ -210,8 +208,11 @@ public void begin(IsolationLevel isolationLevel) throws SailException {
 				startTransactionInternal();
 				txnActive = true;
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -505,15 +506,19 @@ public final void prepare() throws SailException {
 			activeThread.setRelease(Thread.currentThread());
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				if (txnActive) {
 					prepareInternal();
 					txnPrepared = true;
 				}
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -535,7 +540,8 @@ public final void commit() throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				if (txnActive) {
 					if (!txnPrepared) {
@@ -546,8 +552,11 @@ public final void commit() throws SailException {
 					txnPrepared = false;
 				}
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -572,7 +581,8 @@ public final void rollback() throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				if (txnActive) {
 					try {
@@ -586,8 +596,11 @@ public final void rollback() throws SailException {
 							debugEnabled ? new Throwable() : null);
 				}
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -694,13 +707,17 @@ public final void endUpdate(UpdateContext op) throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				verifyIsActive();
 				endUpdateInternal(op);
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -750,14 +767,18 @@ public final void clear(Resource... contexts) throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				verifyIsActive();
 				clearInternal(contexts);
 				statementsRemoved = true;
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -820,13 +841,17 @@ public final void setNamespace(String prefix, String name) throws SailException
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				verifyIsActive();
 				setNamespaceInternal(prefix, name);
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -848,13 +873,17 @@ public final void removeNamespace(String prefix) throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				verifyIsActive();
 				removeNamespaceInternal(prefix);
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);
@@ -873,13 +902,17 @@ public final void clearNamespaces() throws SailException {
 
 			verifyIsOpen();
 
-			updateLock.lock();
+			Lock exclusiveLock = updateLock.getExclusiveLock();
+
 			try {
 				verifyIsActive();
 				clearNamespacesInternal();
 			} finally {
-				updateLock.unlock();
+				exclusiveLock.release();
 			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new SailException(e);
 		} finally {
 			try {
 				activeThread.setRelease(null);

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ShaclSailConnection.java

@@ -734,56 +734,59 @@ synchronized public void close() throws SailException {
 		if (closed) {
 			return;
 		}
-
-		if (getWrappedConnection() instanceof AbstractSailConnection) {
-			AbstractSailConnection abstractSailConnection = (AbstractSailConnection) getWrappedConnection();
-
-			abstractSailConnection.waitForOtherOperations(true);
-		}
-
 		try {
-			if (isActive()) {
-				rollback();
+			if (getWrappedConnection() instanceof AbstractSailConnection) {
+				AbstractSailConnection abstractSailConnection = (AbstractSailConnection) getWrappedConnection();
+
+				abstractSailConnection.waitForOtherOperations(true);
 			}
 		} finally {
-			try {
-				shapesRepoConnection.close();
 
+			try {
+				if (isActive()) {
+					rollback();
+				}
 			} finally {
 				try {
-					if (previousStateConnection != null) {
-						previousStateConnection.close();
-					}
+					shapesRepoConnection.close();
 
 				} finally {
 					try {
-						if (serializableConnection != null) {
-							serializableConnection.close();
+						if (previousStateConnection != null) {
+							previousStateConnection.close();
 						}
-					} finally {
 
+					} finally {
 						try {
-							super.close();
+							if (serializableConnection != null) {
+								serializableConnection.close();
+							}
 						} finally {
+
 							try {
-								sail.closeConnection();
+								super.close();
 							} finally {
 								try {
-									cleanupShapesReadWriteLock();
+									sail.closeConnection();
 								} finally {
 									try {
-										cleanupReadWriteLock();
+										cleanupShapesReadWriteLock();
 									} finally {
-										closed = true;
-									}
+										try {
+											cleanupReadWriteLock();
+										} finally {
+											closed = true;
+										}
 
+									}
 								}
 							}
 						}
 					}
 				}
 			}
 		}
+
 	}
 
 	@Override