Merge main into develop (#5388)

Author: hmottestad

core/repository/manager/src/main/java/org/eclipse/rdf4j/repository/manager/LocalRepositoryManager.java

@@ -261,8 +261,12 @@ public synchronized RepositoryConfig getRepositoryConfig(String id) {
 		File dataDir = getRepositoryDir(id);
 		if (new File(dataDir, CFG_FILE).exists()) {
 			File configFile = new File(dataDir, CFG_FILE);
-			try (InputStream input = new FileInputStream(configFile)) {
-				Model model = Rio.parse(input, configFile.toURI().toString(), CONFIG_FORMAT);
+			try {
+				Model model;
+				// We read the input and close it so that it may be reopend by the migration process
+				try (InputStream input = new FileInputStream(configFile)) {
+					model = Rio.parse(input, configFile.toURI().toString(), CONFIG_FORMAT);
+				}
 
 				Set<String> repositoryIDs = RepositoryConfigUtil.getRepositoryIDs(model);
 				if (repositoryIDs.isEmpty()) {

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

@@ -11,7 +11,7 @@
 package org.eclipse.rdf4j.console.command;
 
 import java.io.BufferedInputStream;
-import java.io.BufferedWriter;
+import java.io.BufferedOutputStream;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -132,7 +132,7 @@ private void convert(String fileFrom, String fileTo) {
 		String baseURI = pathFrom.toUri().toString();
 
 		try (BufferedInputStream r = new BufferedInputStream(Files.newInputStream(pathFrom));
-				BufferedWriter w = Files.newBufferedWriter(pathTo)) {
+				BufferedOutputStream w = new BufferedOutputStream(Files.newOutputStream(pathTo))) {
 			RDFWriter writer = Rio.createWriter(fmtTo.get(), w);
 			parser.setRDFHandler(writer);
 
@@ -141,6 +141,8 @@ private void convert(String fileFrom, String fileTo) {
 
 			parser.parse(r, baseURI);
 
+			w.flush();
+
 			long diff = (System.nanoTime() - startTime) / 1_000_000;
 			writeln("Data has been written to file (" + diff + " ms)");
 		} catch (IOException | RDFParseException | RDFHandlerException e) {

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

@@ -10,9 +10,7 @@
  *******************************************************************************/
 package org.eclipse.rdf4j.console.command;
 
-import java.io.IOException;
-import java.io.Writer;
-import java.nio.charset.StandardCharsets;
+import java.io.*;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
@@ -127,8 +125,8 @@ private void export(Repository repository, String fileName, Resource... contexts
 		}
 
 		try (RepositoryConnection conn = repository.getConnection();
-				Writer w = Files.newBufferedWriter(path, StandardCharsets.UTF_8, StandardOpenOption.CREATE,
-						StandardOpenOption.TRUNCATE_EXISTING)) {
+				BufferedOutputStream w = new BufferedOutputStream(Files.newOutputStream(path, StandardOpenOption.CREATE,
+						StandardOpenOption.TRUNCATE_EXISTING))) {
 
 			RDFFormat fmt = Rio.getWriterFormatForFileName(fileName)
 					.orElseThrow(() -> new UnsupportedRDFormatException("No RDF parser for " + fileName));
@@ -139,6 +137,8 @@ private void export(Repository repository, String fileName, Resource... contexts
 
 			conn.export(writer, contexts);
 
+			w.flush();
+
 			long diff = (System.nanoTime() - startTime) / 1_000_000;
 			writeln("Data has been written to file (" + diff + " ms)");
 		} catch (IOException | UnsupportedRDFormatException e) {

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

@@ -10,9 +10,9 @@
  *******************************************************************************/
 package org.eclipse.rdf4j.console.command;
 
+import java.io.BufferedOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.Writer;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.nio.file.Files;
@@ -186,7 +186,7 @@ private void shacl(String dataPath, String shaclPath, String reportFile) {
 				writeln("Loading shapes from " + shaclPath);
 
 				URL shaclURL = new URL(shaclPath);
-				RDFFormat format = Rio.getParserFormatForFileName(reportFile).orElse(RDFFormat.TURTLE);
+				RDFFormat format = Rio.getParserFormatForFileName(shaclPath).orElse(RDFFormat.TURTLE);
 
 				try (SailRepositoryConnection conn = repo.getConnection()) {
 					conn.begin(IsolationLevels.NONE, ShaclSail.TransactionSettings.ValidationApproach.Disabled);
@@ -279,8 +279,9 @@ private void writeReport(Model model, String reportFile) {
 
 		RDFFormat format = Rio.getParserFormatForFileName(reportFile).orElse(RDFFormat.TURTLE);
 
-		try (Writer w = Files.newBufferedWriter(Paths.get(reportFile))) {
+		try (BufferedOutputStream w = new BufferedOutputStream(Files.newOutputStream(Paths.get(reportFile)))) {
 			Rio.write(model, w, format, cfg);
+			w.flush();
 		} catch (IOException ex) {
 			writeError("Could not write report to " + reportFile, ex);
 		}

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

@@ -66,6 +66,14 @@ public final void testConvert() {
 		assertTrue(o != null, "Invalid JSON");
 	}
 
+	@Test
+	public final void testConvertToBinary() {
+		File binary = new File(locationFile, "alien.brf");
+		cmd.execute("convert", from.getAbsolutePath(), binary.getAbsolutePath());
+
+		assertTrue(binary.length() > 0, "File is empty");
+	}
+
 	@Test
 	public final void testConvertWorkDir() {
 		setWorkingDir(cmd);

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

@@ -68,6 +68,15 @@ public final void testExportAll() throws RepositoryException, IOException {
 		nq.delete();
 	}
 
+	@Test
+	public final void testExportAllToBinary() throws RepositoryException {
+		File binary = new File(locationFile, "all.brf");
+		cmd.execute("export", binary.getAbsolutePath());
+		assertTrue(binary.length() > 0, "File is empty");
+
+		binary.delete();
+	}
+
 	@Test
 	public final void testExportWorkDir() throws RepositoryException, IOException {
 		setWorkingDir(cmd);

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

@@ -127,6 +127,44 @@ public final void testShaclValid() throws IOException {
 		assertFalse(io.wasErrorWritten());
 	}
 
+	@Test
+	public final void testShaclInvalidFormat() throws IOException {
+		File report = new File(locationFile, "testShaclInvalid.nt");
+		cmd.execute("verify", copyFromRes("ok.ttl"), copyFromRes("shacl_invalid.ttl"), report.toString());
+		assertTrue(io.wasErrorWritten());
+		assertTrue(Files.size(report.toPath()) > 0);
+	}
+
+	@Test
+	public final void testShaclValidFormat() throws IOException {
+		File report = new File(locationFile, "testShaclValid.nt");
+		assertTrue(report.createNewFile());
+		cmd.execute("verify", copyFromRes("ok.ttl"), copyFromRes("shacl_valid.ttl"), report.toString());
+
+		verify(mockConsoleIO, never()).writeError(anyString());
+		assertFalse(Files.size(report.toPath()) > 0);
+		assertFalse(io.wasErrorWritten());
+	}
+
+	@Test
+	public final void testShaclInvalidToBinary() throws IOException {
+		File report = new File(locationFile, "testShaclInvalid.brf");
+		cmd.execute("verify", copyFromRes("ok.ttl"), copyFromRes("shacl_invalid.ttl"), report.toString());
+		assertTrue(io.wasErrorWritten());
+		assertTrue(Files.size(report.toPath()) > 0);
+	}
+
+	@Test
+	public final void testShaclValidToBinary() throws IOException {
+		File report = new File(locationFile, "testShaclValid.brf");
+		assertTrue(report.createNewFile());
+		cmd.execute("verify", copyFromRes("ok.ttl"), copyFromRes("shacl_valid.ttl"), report.toString());
+
+		verify(mockConsoleIO, never()).writeError(anyString());
+		assertFalse(Files.size(report.toPath()) > 0);
+		assertFalse(io.wasErrorWritten());
+	}
+
 	@Test
 	public final void testShaclValidWorkDir() throws IOException {
 		setWorkingDir(cmd);