merge main into develop

core/queryalgebra/model/src/main/java/org/eclipse/rdf4j/query/algebra/helpers/collectors/StatementPatternCollector.java

@@ -15,8 +15,10 @@
 import java.util.List;
 
 import org.eclipse.rdf4j.query.algebra.Filter;
+import org.eclipse.rdf4j.query.algebra.Join;
 import org.eclipse.rdf4j.query.algebra.QueryModelNode;
 import org.eclipse.rdf4j.query.algebra.StatementPattern;
+import org.eclipse.rdf4j.query.algebra.TupleExpr;
 import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
 
 /**
@@ -46,6 +48,37 @@ public void meet(Filter node) {
 		node.getArg().visit(this);
 	}
 
+	@Override
+	public void meet(Join node) throws RuntimeException {
+		TupleExpr leftArg = node.getLeftArg();
+		TupleExpr rightArg = node.getRightArg();
+
+		// INSERT clause is often a deeply nested join. Recursive approach may cause stack overflow. Attempt
+		// non-recursive (or at least less-recursive) approach first.
+		while (true) {
+			if (leftArg instanceof Join && !(rightArg instanceof Join)) {
+				rightArg.visit(this);
+
+				Join join = (Join) leftArg;
+				leftArg = join.getLeftArg();
+				rightArg = join.getRightArg();
+
+			} else if (rightArg instanceof Join && !(leftArg instanceof Join)) {
+				leftArg.visit(this);
+
+				Join join = (Join) rightArg;
+				leftArg = join.getLeftArg();
+				rightArg = join.getRightArg();
+
+			} else {
+				leftArg.visit(this);
+				rightArg.visit(this);
+				return;
+			}
+		}
+
+	}
+
 	@Override
 	public void meet(StatementPattern node) {
 		statementPatterns.add(node);

core/sail/memory/src/test/java/org/eclipse/rdf4j/sail/memory/MemoryStoreConnectionTest.java

@@ -10,15 +10,47 @@
  *******************************************************************************/
 package org.eclipse.rdf4j.sail.memory;
 
+import static org.assertj.core.api.Assertions.assertThat;
+
 import java.io.File;
 
+import org.eclipse.rdf4j.common.transaction.IsolationLevels;
+import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.vocabulary.RDF;
 import org.eclipse.rdf4j.repository.Repository;
 import org.eclipse.rdf4j.repository.sail.SailRepository;
 import org.eclipse.rdf4j.testsuite.repository.RepositoryConnectionTest;
+import org.junit.jupiter.api.Test;
 
 public class MemoryStoreConnectionTest extends RepositoryConnectionTest {
 	@Override
 	protected Repository createRepository(File dataDir) {
 		return new SailRepository(new MemoryStore());
 	}
+
+	@Test
+	public void reallyBigUpdateToTriggerPotentialStackOverflowTest() {
+		setupTest(IsolationLevels.NONE);
+
+		IRI g1 = vf.createIRI("urn:test:g1");
+		testCon.begin();
+		testCon.add(vf.createBNode(), RDF.TYPE, g1);
+		testCon.commit();
+
+		testCon.begin();
+
+		StringBuilder bigUpdate = new StringBuilder();
+		bigUpdate.append("DELETE { ?s ?p ?o } INSERT{\n");
+
+		for (int i = 0; i < 20000; i++) {
+			bigUpdate.append(" [] <urn:test:prop> \"").append(i).append("\".\n");
+		}
+		bigUpdate.append("\n} WHERE { ?s ?p ?o }");
+
+		testCon.prepareUpdate(bigUpdate.toString()).execute();
+
+		long size = testCon.size();
+		assertThat(size).isEqualTo(20000);
+		testCon.commit();
+	}
 }

tools/console/src/main/java/org/eclipse/rdf4j/console/command/Create.java

@@ -28,6 +28,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -40,6 +41,7 @@
 import org.eclipse.rdf4j.model.impl.LinkedHashModel;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.model.util.Models;
+import org.eclipse.rdf4j.model.vocabulary.CONFIG;
 import org.eclipse.rdf4j.model.vocabulary.RDF;
 import org.eclipse.rdf4j.repository.RepositoryReadOnlyException;
 import org.eclipse.rdf4j.repository.config.ConfigTemplate;
@@ -143,12 +145,12 @@ private String getUserTemplates() {
 	 */
 	private String getBuiltinTemplates() {
 		// assume the templates are all located in the same jar "directory" as the RepositoryConfig class
-		Class cl = RepositoryConfig.class;
+		Class<RepositoryConfig> cl = RepositoryConfig.class;
 
 		try {
 			URI dir = cl.getResource(cl.getSimpleName() + ".class").toURI();
 			if (dir.getScheme().equals("jar")) {
-				try (FileSystem fs = FileSystems.newFileSystem(dir, Collections.EMPTY_MAP, null)) {
+				try (FileSystem fs = FileSystems.newFileSystem(dir, Collections.emptyMap(), null)) {
 					// turn package structure into directory structure
 					String pkg = cl.getPackage().getName().replaceAll("\\.", "/");
 					return getOrderedTemplates(fs.getPath(pkg));
@@ -187,15 +189,9 @@ private void createRepository(final String templateName) {
 				boolean eof = inputParameters(valueMap, variableMap, configTemplate.getMultilineMap());
 				if (!eof) {
 					final String configString = configTemplate.render(valueMap);
-					final Model graph = new LinkedHashModel();
+					final Model graph = parseConfigIntoModel(configString);
 
-					final RDFParser rdfParser = Rio.createParser(RDFFormat.TURTLE, SimpleValueFactory.getInstance());
-					rdfParser.setRDFHandler(new StatementCollector(graph));
-					rdfParser.parse(new StringReader(configString), RepositoryConfigSchema.NAMESPACE);
-
-					final Resource repositoryNode = Models
-							.subject(graph.getStatements(null, RDF.TYPE, RepositoryConfigSchema.REPOSITORY))
-							.orElseThrow(() -> new RepositoryConfigException("missing repository node"));
+					final Resource repositoryNode = findRepositoryNode(graph);
 
 					final RepositoryConfig repConfig = RepositoryConfig.create(graph, repositoryNode);
 					repConfig.validate();
@@ -232,6 +228,25 @@ private void createRepository(final String templateName) {
 		}
 	}
 
+	private Resource findRepositoryNode(final Model graph) {
+		Optional<Resource> modern = Models
+				.subject(graph.getStatements(null, RDF.TYPE, CONFIG.Rep.Repository));
+		Resource repositoryNode = modern
+				.orElseGet(() -> Models
+						.subject(graph.getStatements(null, RDF.TYPE, RepositoryConfigSchema.REPOSITORY))
+						.orElseThrow(() -> new RepositoryConfigException("missing repository node")));
+		return repositoryNode;
+	}
+
+	private Model parseConfigIntoModel(final String configString) throws IOException {
+		final Model graph = new LinkedHashModel();
+
+		final RDFParser rdfParser = Rio.createParser(RDFFormat.TURTLE, SimpleValueFactory.getInstance());
+		rdfParser.setRDFHandler(new StatementCollector(graph));
+		rdfParser.parse(new StringReader(configString), CONFIG.NAMESPACE);
+		return graph;
+	}
+
 	/**
 	 * Ask user to specify values for the template variables
 	 *
@@ -251,23 +266,7 @@ private boolean inputParameters(final Map<String, String> valueMap, final Map<St
 			final String var = entry.getKey();
 			final List<String> values = entry.getValue();
 
-			StringBuilder sb = new StringBuilder();
-			sb.append(var);
-
-			if (values.size() > 1) {
-				sb.append(" (");
-				for (int i = 0; i < values.size(); i++) {
-					if (i > 0) {
-						sb.append("|");
-					}
-					sb.append(values.get(i));
-				}
-				sb.append(")");
-			}
-			if (!values.isEmpty()) {
-				sb.append(" [" + values.get(0) + "]");
-			}
-			String prompt = sb.append(": ").toString();
+			String prompt = buildPromptString(values, var);
 			String value = multilineInput.containsKey(var) ? consoleIO.readMultiLineInput(prompt)
 					: consoleIO.readln(prompt);
 			eof = (value == null);
@@ -284,6 +283,25 @@ private boolean inputParameters(final Map<String, String> valueMap, final Map<St
 		return eof;
 	}
 
+	private String buildPromptString(final List<String> values, String var) {
+		StringBuilder sb = new StringBuilder();
+		sb.append(var);
+		if (values.size() > 1) {
+			sb.append(" (");
+			for (int i = 0; i < values.size(); i++) {
+				if (i > 0) {
+					sb.append("|");
+				}
+				sb.append(values.get(i));
+			}
+			sb.append(")");
+		}
+		if (!values.isEmpty()) {
+			sb.append(" [" + values.get(0) + "]");
+		}
+		return sb.append(": ").toString();
+	}
+
 	/**
 	 * Create input stream from a template file in the specified file directory. If the file cannot be found, try to
 	 * read it from the embedded java resources instead.

tools/console/src/test/java/org/eclipse/rdf4j/console/command/CreateTest.java

@@ -0,0 +1,93 @@
+/*******************************************************************************
+ * Copyright (c) 2018 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.console.command;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.eclipse.rdf4j.common.exception.RDF4JException;
+import org.eclipse.rdf4j.console.ConsoleIO;
+import org.eclipse.rdf4j.repository.manager.LocalRepositoryManager;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test verify command
+ *
+ * @author Bart Hanssens
+ */
+public class CreateTest extends AbstractCommandTest {
+	private Create cmd;
+	private ConsoleIO io;
+
+	@BeforeEach
+	public void setUp() throws IOException, RDF4JException {
+		InputStream input = mock(InputStream.class);
+		OutputStream out = mock(OutputStream.class);
+		when(mockConsoleState.getDataDirectory()).thenReturn(locationFile);
+		when(mockConsoleState.getManager()).thenReturn(new LocalRepositoryManager(locationFile));
+
+		io = new ConsoleIO(input, out, mockConsoleState) {
+
+			@Override
+			public String readMultiLineInput(String promt) {
+				switch (promt) {
+				default:
+					return null;
+				}
+			}
+
+			@Override
+			public String readMultiLineInput() {
+				return null;
+			}
+
+			@Override
+			public String readln(String... message) {
+				switch (message[0]) {
+				case "Repository ID [memory]: ":
+					return "Y";
+				case "Repository title [Memory store]: ":
+					return "Create-Test-Memory-Store";
+				case "Query Iteration Cache sync threshold [10000]: ":
+					return "10";
+				case "Persist (true|false) [true]: ":
+					return "false";
+				case "Sync delay [0]: ":
+					return "0";
+				case "Query Evaluation Mode (STRICT|STANDARD) [STRICT]: ":
+					return "STANDARD";
+				}
+				return null;
+			}
+
+			@Override
+			public boolean askProceed(String msg, boolean defaultValue) {
+				return true;
+			}
+
+		};
+
+		cmd = new Create(io, mockConsoleState);
+	}
+
+	@Test
+	public final void startCreate() {
+		cmd.execute("create", "memory");
+		assertFalse(io.wasErrorWritten());
+	}
+
+}