Fix parent reference conflicts in SPARQL aggregation query parsing

core/queryalgebra/evaluation/src/test/java/org/eclipse/rdf4j/query/algebra/evaluation/impl/AggregationParentReferenceTest.java

@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * 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.query.algebra.evaluation.impl;
+
+import org.eclipse.rdf4j.query.algebra.TupleExpr;
+import org.eclipse.rdf4j.query.algebra.evaluation.optimizer.ParentReferenceChecker;
+import org.eclipse.rdf4j.query.impl.EmptyBindingSet;
+import org.eclipse.rdf4j.query.impl.SimpleDataset;
+import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test to reproduce and fix the parent reference issue with aggregation queries.
+ */
+public class AggregationParentReferenceTest {
+
+	@Test
+	public void testAggregationParentReferences() {
+		String query = "SELECT (COUNT(?s) AS ?count) WHERE { ?s ?p ?o  }";
+
+		TupleExpr expr = new SPARQLParser().parseQuery(query, null).getTupleExpr();
+
+		// This should not throw an AssertionError about parent references
+		new ParentReferenceChecker(null).optimize(expr, new SimpleDataset(), new EmptyBindingSet());
+	}
+
+	@Test
+	public void testComplexAggregationParentReferences() {
+		String query = "SELECT (COUNT(?s)/30 AS ?count) WHERE { ?s ?p ?o  }";
+
+		TupleExpr expr = new SPARQLParser().parseQuery(query, null).getTupleExpr();
+
+		// This should not throw an AssertionError about parent references
+		new ParentReferenceChecker(null).optimize(expr, new SimpleDataset(), new EmptyBindingSet());
+	}
+}

core/queryparser/sparql/src/main/java/org/eclipse/rdf4j/query/parser/sparql/TupleExprBuilder.java

@@ -568,20 +568,27 @@ public TupleExpr visit(ASTSelect node, Object data) throws VisitorException {
 						}
 
 						if (operator.equals(valueExpr)) {
-							group.addGroupElement(new GroupElem(alias, operator));
+							// For simple aggregations like COUNT(?s), clone the operator to avoid
+							// parent reference conflicts when it's added to both GroupElem and ExtensionElem
+							group.addGroupElement(new GroupElem(alias, operator.clone()));
 							extension.setArg(group);
 						} else {
 							ValueExpr expr = (ValueExpr) operator.getParentNode();
 
 							Extension anonymousExtension = new Extension();
 							Var anonVar = createAnonVar();
 							expr.replaceChildNode(operator, anonVar);
-							anonymousExtension.addElement(new ExtensionElem(operator, anonVar.getName()));
+							// Clone the operator for the ExtensionElem to avoid parent reference conflicts
+							anonymousExtension.addElement(new ExtensionElem(operator.clone(), anonVar.getName()));
 
 							anonymousExtension.setArg(result);
 							result = anonymousExtension;
 							group.addGroupElement(new GroupElem(anonVar.getName(), operator));
 
+							// Update the group's argument to point to the new result structure
+							if (!isExistingGroup) {
+								group.setArg(result);
+							}
 						}
 
 						if (!isExistingGroup) {
@@ -593,7 +600,9 @@ public TupleExpr visit(ASTSelect node, Object data) throws VisitorException {
 				// SELECT expressions need to be captured as an extension, so that original and alias are
 				// available for the ORDER BY clause (which gets applied _before_ projection). See GH-4066
 				// and https://www.w3.org/TR/sparql11-query/#sparqlSolMod .
-				ExtensionElem extElem = new ExtensionElem(valueExpr, alias);
+				// Clone valueExpr if it contains aggregates to avoid parent reference conflicts
+				ValueExpr extValueExpr = !collector.getOperators().isEmpty() ? valueExpr.clone() : valueExpr;
+				ExtensionElem extElem = new ExtensionElem(extValueExpr, alias);
 				extension.addElement(extElem);
 				elem.setSourceExpression(extElem);
 			} else if (child instanceof ASTVar) {