Merge main into develop

AGENTS.md

@@ -510,6 +510,7 @@ Do **not** modify existing headers’ years.
 
 ## Branch & PR Workflow (Agent)
 
+- Confirm issue number first (mandatory): before creating a branch, pause and request/confirm the GitHub issue number. Do not proceed to branch creation until the issue number is provided or confirmed.
 - Name branch: `GH-<issue>-<short-slug>` (kebab‑case slug).
 - Create branch: `git checkout -b GH-XXXX-your-slug`.
 - Stage changes: `git add -A` (ensure new Java files have the required header).

core/rio/turtle/src/main/java/org/eclipse/rdf4j/rio/turtle/TurtleParser.java

@@ -808,7 +808,11 @@ protected Literal parseNumber() throws IOException, RDFParseException {
 			// read optional fractional digits
 			if (c == '.') {
 
-				if (TurtleUtil.isWhitespace(peekCodePoint())) {
+				int next = peekCodePoint();
+				// Treat '.' as statement terminator at EOF only when we already parsed at least one digit
+				// (e.g., "30.") or when whitespace follows. Otherwise, attempt to parse as decimal
+				// which will surface a useful error for a stray '.' token.
+				if ((value.length() > 0 && next == -1) || TurtleUtil.isWhitespace(next)) {
 					// We're parsing an integer that did not have a space before
 					// the
 					// period to end the statement

core/rio/turtle/src/test/java/org/eclipse/rdf4j/rio/turtle/TurtleParserTest.java

@@ -89,6 +89,47 @@ public void testParseDots() throws IOException {
 
 	}
 
+	@Test
+	public void testIntegerFollowedByDotAtEOF() throws IOException {
+		// Reproduces bug: integer literal immediately followed by statement terminator '.' at EOF
+		String data = prefixes + ":alice :age 30."; // no trailing whitespace/newline
+
+		parser.parse(new StringReader(data), baseURI);
+
+		assertTrue(errorCollector.getWarnings().isEmpty());
+		assertTrue(errorCollector.getErrors().isEmpty());
+		assertTrue(errorCollector.getFatalErrors().isEmpty());
+
+		assertEquals(1, statementCollector.getStatements().size());
+		Statement st = statementCollector.getStatements().iterator().next();
+		assertEquals(vf.createIRI("http://example.org/alice"), st.getSubject());
+		assertEquals(vf.createIRI("http://example.org/age"), st.getPredicate());
+		assertTrue(st.getObject() instanceof Literal);
+		Literal lit = (Literal) st.getObject();
+		assertEquals("30", lit.getLabel());
+		assertEquals(XSD.INTEGER, lit.getDatatype());
+	}
+
+	@Test
+	public void testLetterFollowedByDotAtEOF() throws IOException {
+		String data = prefixes + ":alice :age \"a\"."; // no trailing whitespace/newline
+
+		parser.parse(new StringReader(data), baseURI);
+
+		assertTrue(errorCollector.getWarnings().isEmpty());
+		assertTrue(errorCollector.getErrors().isEmpty());
+		assertTrue(errorCollector.getFatalErrors().isEmpty());
+
+		assertEquals(1, statementCollector.getStatements().size());
+		Statement st = statementCollector.getStatements().iterator().next();
+		assertEquals(vf.createIRI("http://example.org/alice"), st.getSubject());
+		assertEquals(vf.createIRI("http://example.org/age"), st.getPredicate());
+		assertTrue(st.getObject() instanceof Literal);
+		Literal lit = (Literal) st.getObject();
+		assertEquals("a", lit.getLabel());
+		assertEquals(XSD.STRING, lit.getDatatype());
+	}
+
 	@Test
 	public void testParseIllegalURIFatal() throws IOException {
 		String data = " <urn:foo_bar\\r> <urn:foo> <urn:bar> ; <urn:foo2> <urn:bar2> . <urn:foobar> <urn:food> <urn:barf> . ";

core/sail/base/src/main/java/org/eclipse/rdf4j/sail/base/SailSourceBranch.java

@@ -27,6 +27,7 @@
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.model.ModelFactory;
 import org.eclipse.rdf4j.model.Resource;
+import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.Value;
 import org.eclipse.rdf4j.model.impl.DynamicModelFactory;
 import org.eclipse.rdf4j.sail.SailException;
@@ -70,7 +71,7 @@ class SailSourceBranch implements SailSource {
 
 	/**
 	 * The {@link Model} instances that should be used to store {@link SailSink#approve(Resource, IRI, Value, Resource)}
-	 * and {@link SailSink#deprecate(Resource, IRI, Value, Resource)} statements.
+	 * and {@link SailSink#deprecate(Statement)} statements.
 	 */
 	private final ModelFactory modelFactory;
 
@@ -306,7 +307,7 @@ public void flush() throws SailException {
 					prepared = null;
 				}
 			}
-		} catch (SailException e) {
+		} catch (Throwable e) {
 			// clear changes if flush fails
 			changes.clear();
 			prepared = null;

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

@@ -37,6 +37,7 @@
 import org.eclipse.rdf4j.model.Value;
 import org.eclipse.rdf4j.model.ValueFactory;
 import org.eclipse.rdf4j.query.algebra.evaluation.impl.EvaluationStatistics;
+import org.eclipse.rdf4j.sail.Sail;
 import org.eclipse.rdf4j.sail.SailException;
 import org.eclipse.rdf4j.sail.base.BackingSailSource;
 import org.eclipse.rdf4j.sail.base.Changeset;
@@ -389,7 +390,11 @@ public synchronized void flush() throws SailException {
 				throw new SailException(e);
 			} catch (RuntimeException e) {
 				logger.error("Encountered an unexpected problem while trying to commit", e);
-				throw e;
+				if (e instanceof SailException) {
+					throw e;
+				}
+				// Ensure upstream handles this as a SailException so branch flush clears pending changes
+				throw new SailException(e);
 			} finally {
 				sinkStoreAccessLock.unlock();
 			}
@@ -445,7 +450,15 @@ public void clear(Resource... contexts) throws SailException {
 
 		@Override
 		public void approve(Resource subj, IRI pred, Value obj, Resource ctx) throws SailException {
-			addStatement(subj, pred, obj, explicit, ctx);
+			try {
+				addStatement(subj, pred, obj, explicit, ctx);
+			} catch (RuntimeException e) {
+				if (e instanceof SailException) {
+					throw e;
+				}
+				// Ensure upstream handles this as a SailException so branch flush clears pending changes
+				throw new SailException(e);
+			}
 		}
 
 		@Override
@@ -478,8 +491,11 @@ public void approveAll(Set<Statement> approved, Set<Resource> approvedContexts)
 			} catch (IOException e) {
 				throw new SailException(e);
 			} catch (RuntimeException e) {
+				if (e instanceof SailException) {
+					throw e;
+				}
 				logger.error("Encountered an unexpected problem while trying to add a statement", e);
-				throw e;
+				throw new SailException(e);
 			} finally {
 				sinkStoreAccessLock.unlock();
 			}
@@ -540,8 +556,11 @@ private boolean addStatement(Resource subj, IRI pred, Value obj, boolean explici
 			} catch (IOException e) {
 				throw new SailException(e);
 			} catch (RuntimeException e) {
+				if (e instanceof SailException) {
+					throw e;
+				}
 				logger.error("Encountered an unexpected problem while trying to add a statement", e);
-				throw e;
+				throw new SailException(e);
 			} finally {
 				sinkStoreAccessLock.unlock();
 			}
@@ -614,7 +633,11 @@ private long removeStatements(Resource subj, IRI pred, Value obj, boolean explic
 				throw new SailException(e);
 			} catch (RuntimeException e) {
 				logger.error("Encountered an unexpected problem while trying to remove statements", e);
-				throw e;
+				if (e instanceof SailException) {
+					throw e;
+				}
+				// Ensure upstream handles this as a SailException so branch flush clears pending changes
+				throw new SailException(e);
 			} finally {
 				sinkStoreAccessLock.unlock();
 			}

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

@@ -76,8 +76,10 @@ protected void commitInternal() throws SailException {
 		try {
 			super.commitInternal();
 		} finally {
-			txnLock.release();
-			txnLock = null;
+			if (txnLock != null) {
+				txnLock.release();
+				txnLock = null;
+			}
 		}
 
 		nativeStore.notifySailChanged(sailChangedEvent);
@@ -91,8 +93,10 @@ protected void rollbackInternal() throws SailException {
 		try {
 			super.rollbackInternal();
 		} finally {
-			txnLock.release();
-			txnLock = null;
+			if (txnLock != null) {
+				txnLock.release();
+				txnLock = null;
+			}
 		}
 		// create a fresh event object.
 		sailChangedEvent = new DefaultSailChangedEvent(nativeStore);

core/sail/nativerdf/src/test/java/org/eclipse/rdf4j/sail/nativerdf/NativeSailStoreRuntimeWrappingIT.java

@@ -0,0 +1,113 @@
+/*
+ * Copyright (c) 2025 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
+ */
+package org.eclipse.rdf4j.sail.nativerdf;
+
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
+
+import java.io.File;
+import java.lang.reflect.Field;
+import java.nio.file.Files;
+import java.util.Map;
+
+import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.Resource;
+import org.eclipse.rdf4j.model.ValueFactory;
+import org.eclipse.rdf4j.sail.SailException;
+import org.eclipse.rdf4j.sail.base.SailSink;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Verifies that NativeSailStore wraps unexpected RuntimeExceptions in SailException so upstream callers can reliably
+ * handle failures (e.g., branch flush clearing pending changes).
+ */
+public class NativeSailStoreRuntimeWrappingIT {
+
+	private File dataDir;
+	private NativeSailStore store;
+
+	@BeforeEach
+	public void setUp() throws Exception {
+		dataDir = Files.createTempDirectory("nativestore-wrap-test").toFile();
+		store = new NativeSailStore(dataDir, "spoc");
+	}
+
+	@AfterEach
+	public void tearDown() throws Exception {
+		if (store != null) {
+			store.close();
+		}
+	}
+
+	@Test
+	public void testFlushWrapsRuntimeIntoSailException() throws Exception {
+		// Replace TripleStore with a stub that throws at commit()
+		replaceTripleStore(new ThrowOnCommitTripleStore(dataDir, "spoc"));
+
+		// Add a statement to ensure a triplestore transaction is started
+		SailSink sink = store.getExplicitSailSource().sink(null);
+		ValueFactory vf = store.getValueFactory();
+		IRI s = vf.createIRI("urn:s");
+		IRI p = vf.createIRI("urn:p");
+		IRI o = vf.createIRI("urn:o");
+		sink.approve(s, p, o, (Resource) null);
+
+		// Now flush, expecting a SailException (wrapping the runtime)
+		assertThatThrownBy(() -> sink.flush())
+				.isInstanceOf(SailException.class);
+	}
+
+	@Test
+	public void testRemoveStatementsWrapsRuntimeIntoSailException() throws Exception {
+		// Replace TripleStore with a stub that throws at removeTriplesByContext()
+		replaceTripleStore(new ThrowOnRemoveTripleStore(dataDir, "spoc"));
+
+		SailSink sink = store.getExplicitSailSource().sink(null);
+		// Expect SailException when attempting to remove (deprecateByQuery delegates)
+		assertThatThrownBy(() -> sink.deprecateByQuery(null, null, null, new Resource[] { null }))
+				.isInstanceOf(SailException.class);
+	}
+
+	private void replaceTripleStore(TripleStore newTripleStore) throws Exception {
+		Field f = NativeSailStore.class.getDeclaredField("tripleStore");
+		f.setAccessible(true);
+		f.set(store, newTripleStore);
+	}
+
+	private static class ThrowOnCommitTripleStore extends TripleStore {
+		public ThrowOnCommitTripleStore(File dir, String indexSpecStr) throws Exception {
+			super(dir, indexSpecStr, false);
+		}
+
+		@Override
+		public void commit() {
+			throw new RuntimeException("simulated failure during commit");
+		}
+	}
+
+	private static class ThrowOnRemoveTripleStore extends TripleStore {
+		public ThrowOnRemoveTripleStore(File dir, String indexSpecStr) throws Exception {
+			super(dir, indexSpecStr, false);
+		}
+
+		@Override
+		public Map<Integer, Long> removeTriplesByContext(int subjID, int predID, int objID, int contextId,
+				boolean explicit) {
+			throw new RuntimeException("simulated failure during removeTriplesByContext");
+		}
+
+		@Override
+		public void startTransaction() {
+			// no-op; we're only interested in remove path throwing
+		}
+	}
+}