fixes after review

Author: hmottestad

core/sail/lmdb/src/main/java/org/eclipse/rdf4j/sail/lmdb/LmdbSailStore.java

@@ -416,6 +416,7 @@ public void close() throws SailException {
 			try {
 				cancelAndDrainScheduledBackgroundSampling();
 				cancelAndDrainScheduledEstimatorPersist();
+				shutdownAndAwaitEstimatorPersistExecutor();
 				if (sketchBasedJoinEstimator != null) {
 					sketchBasedJoinEstimator.close();
 				}
@@ -447,15 +448,7 @@ public void close() throws SailException {
 										throw new InterruptedSailException(e);
 									}
 								} finally {
-									estimatorPersistExec.shutdown();
-									try {
-										while (!estimatorPersistExec.awaitTermination(1, TimeUnit.SECONDS)) {
-											logger.warn("Waiting for join estimator persist executor to terminate");
-										}
-									} catch (InterruptedException e) {
-										Thread.currentThread().interrupt();
-										throw new InterruptedSailException(e);
-									}
+									shutdownAndAwaitEstimatorPersistExecutor();
 									tripleStore.close();
 								}
 							}
@@ -474,6 +467,18 @@ public void close() throws SailException {
 		}
 	}
 
+	private void shutdownAndAwaitEstimatorPersistExecutor() {
+		estimatorPersistExec.shutdown();
+		try {
+			while (!estimatorPersistExec.awaitTermination(1, TimeUnit.SECONDS)) {
+				logger.warn("Waiting for join estimator persist executor to terminate");
+			}
+		} catch (InterruptedException e) {
+			Thread.currentThread().interrupt();
+			throw new InterruptedSailException(e);
+		}
+	}
+
 	private void cancelAndDrainScheduledBackgroundSampling() {
 		ScheduledFuture<?> future = backgroundSamplingFuture;
 		if (future == null) {

core/sail/lmdb/src/test/java/org/eclipse/rdf4j/sail/lmdb/LmdbSailStoreCloseTest.java

@@ -0,0 +1,122 @@
+/*******************************************************************************
+ * Copyright (c) 2026 Eclipse RDF4J contributors.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Distribution License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ *******************************************************************************/
+// Some portions generated by Codex
+
+package org.eclipse.rdf4j.sail.lmdb;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.Mockito.doAnswer;
+import static org.mockito.Mockito.spy;
+
+import java.io.File;
+import java.lang.reflect.Field;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.ScheduledFuture;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicReference;
+
+import org.eclipse.rdf4j.sail.lmdb.config.LmdbStoreConfig;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+class LmdbSailStoreCloseTest {
+
+	@Test
+	void closeDrainsRunningScheduledPersistBeforeClosingEstimator(@TempDir File dataDir) throws Exception {
+		LmdbStoreConfig config = new LmdbStoreConfig("spoc").setBackgroundRawSamplingMaxMillisPerCycle(0L);
+		LmdbStore store = new LmdbStore(dataDir, config);
+		store.init();
+
+		LmdbSailStore backingStore = store.getBackingStore();
+		LmdbFilterSelectivityStats filterStats = (LmdbFilterSelectivityStats) getField(backingStore,
+				"filterSelectivityStats");
+		LmdbFilterSelectivityStats filterStatsSpy = spy(filterStats);
+		CountDownLatch filterPersistStarted = new CountDownLatch(1);
+		doAnswer(invocation -> {
+			filterPersistStarted.countDown();
+			return invocation.callRealMethod();
+		}).when(filterStatsSpy).persistIfDirty();
+		setField(backingStore, "filterSelectivityStats", filterStatsSpy);
+
+		ScheduledExecutorService executor = (ScheduledExecutorService) getField(backingStore, "estimatorPersistExec");
+		CountDownLatch taskStarted = new CountDownLatch(1);
+		CountDownLatch releaseTask = new CountDownLatch(1);
+		CountDownLatch taskFinished = new CountDownLatch(1);
+		AtomicReference<Throwable> closeFailure = new AtomicReference<>();
+
+		ScheduledFuture<?> runningPersist = executor.schedule(() -> {
+			taskStarted.countDown();
+			try {
+				assertTrue(releaseTask.await(5, TimeUnit.SECONDS),
+						"Test timed out before releasing the scheduled persist task");
+			} catch (InterruptedException e) {
+				Thread.currentThread().interrupt();
+			} finally {
+				taskFinished.countDown();
+			}
+		}, 0L, TimeUnit.MILLISECONDS);
+		setField(backingStore, "persistFuture", runningPersist);
+
+		assertTrue(taskStarted.await(5, TimeUnit.SECONDS), "Scheduled persist task should be running before close");
+
+		Thread closeThread = new Thread(() -> {
+			try {
+				store.shutDown();
+			} catch (Throwable e) {
+				closeFailure.set(e);
+			}
+		}, "LmdbSailStore-close-test");
+		closeThread.start();
+		try {
+			awaitExecutorShutdown(executor);
+
+			assertFalse(isCountedDown(filterPersistStarted),
+					"Filter stats must not persist while a scheduled persist task is still running");
+			assertFalse(isCountedDown(taskFinished), "Scheduled persist task should still be blocked by the test");
+		} finally {
+			releaseTask.countDown();
+			closeThread.join(TimeUnit.SECONDS.toMillis(5));
+		}
+
+		assertFalse(closeThread.isAlive(), "Store shutdown should finish after releasing the scheduled task");
+		assertEquals(0, taskFinished.getCount(), "Scheduled persist task should have finished");
+		assertEquals(0, filterPersistStarted.getCount(), "Filter stats should persist after scheduled task drain");
+		assertNull(closeFailure.get(), "Store shutdown should not fail");
+	}
+
+	private static void awaitExecutorShutdown(ScheduledExecutorService executor) throws InterruptedException {
+		long deadline = System.nanoTime() + TimeUnit.SECONDS.toNanos(5);
+		while (!executor.isShutdown() && System.nanoTime() < deadline) {
+			Thread.sleep(10L);
+		}
+		assertTrue(executor.isShutdown(), "Store close should begin draining the estimator scheduler");
+	}
+
+	private static boolean isCountedDown(CountDownLatch latch) {
+		return latch.getCount() == 0;
+	}
+
+	private static Object getField(Object target, String name) throws ReflectiveOperationException {
+		Field field = target.getClass().getDeclaredField(name);
+		field.setAccessible(true);
+		return field.get(target);
+	}
+
+	private static void setField(Object target, String name, Object value) throws ReflectiveOperationException {
+		Field field = target.getClass().getDeclaredField(name);
+		field.setAccessible(true);
+		field.set(target, value);
+	}
+}