TS-35786 Use apache commons zip since it preserves flags

src/main/java/com/teamscale/upload/utils/FileSystemUtils.java

@@ -30,9 +30,6 @@
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-import java.util.zip.ZipInputStream;
 
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
@@ -94,22 +91,24 @@ public static String stripTarExtension(String fileName) {
 	 * Extract entries of a ZipFile to a directory when the ZipFile is created
 	 * externally. Note that this does not close the ZipFile, so the caller has to
 	 * take care of this.
+	 * <p>
+	 * We use the apache commons ZipArchiveEntry instead of the java standard library
+	 * ZipEntry since the apache commons variant preserves flags on files in the zip.
+	 * In particular executable flags on shell scripts.
 	 */
 	public static List<String> unzip(ZipFile zip, File targetDirectory) throws IOException {
-		Enumeration<? extends ZipEntry> entries = zip.entries();
+		Enumeration<? extends ZipArchiveEntry> entries = zip.getEntries();
 		List<String> extractedPaths = new ArrayList<>();
 
 		while (entries.hasMoreElements()) {
-			ZipEntry entry = entries.nextElement();
+			ZipArchiveEntry entry = entries.nextElement();
 			if (entry.isDirectory()) {
 				continue;
 			}
 			String fileName = entry.getName();
-
 			try (InputStream entryStream = zip.getInputStream(entry)) {
 				File file = new File(targetDirectory, fileName);
 				ensureDirectoryExists(file.getParentFile());
-
 				try (FileOutputStream outputStream = new FileOutputStream(file)) {
 					copy(entryStream, outputStream);
 				}

src/main/java/com/teamscale/upload/utils/ZipFile.java

@@ -0,0 +1,61 @@
+/*
+ * Copyright (c) CQSE GmbH
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.teamscale.upload.utils;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
+
+/** Wrapper around Apache Compress ZIP file that exposes the filename */
+public class ZipFile extends org.apache.commons.compress.archivers.zip.ZipFile {
+
+	/** The filename */
+	private String name;
+
+	public ZipFile(File f) throws IOException {
+		super(f);
+		this.name = f.getName();
+	}
+
+	public ZipFile(String name) throws IOException {
+		super(name);
+		this.name = name;
+	}
+
+	public ZipFile(String name, String encoding) throws IOException {
+		super(name, encoding);
+		this.name = name;
+	}
+
+	public ZipFile(File f, String encoding) throws IOException {
+		super(f, encoding);
+		this.name = f.getName();
+	}
+
+	public ZipFile(File f, String encoding, boolean useUnicodeExtraFields) throws IOException {
+		super(f, encoding, useUnicodeExtraFields);
+		this.name = f.getName();
+	}
+
+	public ZipFile(File f, Charset charset) throws IOException {
+		this(f, charset.toString());
+	}
+
+	public String getName() {
+		return name;
+	}
+}

src/test/java/com/teamscale/upload/JLinkIntegrationTest.java

@@ -3,9 +3,9 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.util.zip.ZipFile;
 
 import com.teamscale.upload.utils.FileSystemUtils;
+import com.teamscale.upload.utils.ZipFile;
 import org.apache.commons.lang3.SystemUtils;
 import org.assertj.core.api.SoftAssertions;
 import org.jetbrains.annotations.NotNull;