Use commons-compression for the default code path

The JVM code has too much exception throwing and hardcoded behavior
given what the migration tool does, as seen in issue #20. The
commons-compression code does not seem to have the same check in that
case, as seen when using -zipInMemory (it does not do anything special
yet does not complain about duplicate entries since there's no check for
that in the code).
In some cases, this seems faster. In others not so much. This needs more
investigation to verify there's no regression in that area (or anywhere
else).

CHANGES.md

@@ -2,6 +2,8 @@
 
 ## 1.0.1 (in progress)
 
+- Fix [#20] by using commons-compression instead of the Java zip code (remm)
+
 ## 1.0.0
 
 - Fix [#14](https://github.com/apache/tomcat-jakartaee-migration/issues/14). Do not migrate `javax.xml.(registry|rpc)` namespaces. (mgrigorov)

src/main/java/org/apache/tomcat/jakartaee/Migration.java

@@ -30,21 +30,16 @@
 import java.util.List;
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
-import java.util.jar.JarEntry;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import java.util.zip.ZipEntry;
 import java.util.zip.ZipException;
-import java.util.zip.ZipInputStream;
-import java.util.zip.ZipOutputStream;
 
 import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
+import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
 import org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream;
 import org.apache.commons.compress.archivers.zip.ZipFile;
 import org.apache.commons.compress.utils.SeekableInMemoryByteChannel;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.io.input.CloseShieldInputStream;
-import org.apache.commons.io.output.CloseShieldOutputStream;
 
 public class Migration {
 
@@ -214,23 +209,22 @@ private void migrateFile(File src, File dest) throws IOException {
 
 
     private void migrateArchiveStreaming(String name, InputStream src, OutputStream dest) throws IOException {
-        try (ZipInputStream zipIs = new ZipInputStream(new CloseShieldInputStream(src));
-                ZipOutputStream zipOs = new ZipOutputStream(new CloseShieldOutputStream(dest))) {
-            ZipEntry zipEntry;
-            while ((zipEntry = zipIs.getNextEntry()) != null) {
-                String sourceName = zipEntry.getName();
-                if (isSignatureFile(sourceName)) {
-                    logger.log(Level.WARNING, sm.getString("migration.skipSignatureFile", sourceName));
+        try (ZipArchiveInputStream srcZipStream = new ZipArchiveInputStream(src);
+                ZipArchiveOutputStream destZipStream = new ZipArchiveOutputStream(dest)) {
+            ZipArchiveEntry srcZipEntry;
+            while ((srcZipEntry = srcZipStream.getNextZipEntry()) != null) {
+                String srcName = srcZipEntry.getName();
+                if (isSignatureFile(srcName)) {
+                    logger.log(Level.WARNING, sm.getString("migration.skipSignatureFile", srcName));
                     continue;
                 }
-                String destName = profile.convert(sourceName);
-                JarEntry destEntry = new JarEntry(destName);
-                zipOs.putNextEntry(destEntry);
-                migrateStream(sourceName, zipIs, zipOs);
+                String destName = profile.convert(srcName);
+                RenamableZipArchiveEntry destZipEntry = new RenamableZipArchiveEntry(srcZipEntry);
+                destZipEntry.setName(destName);
+                destZipStream.putArchiveEntry(destZipEntry);
+                migrateStream(srcName, srcZipStream, destZipStream);
+                destZipStream.closeArchiveEntry();
             }
-        } catch (ZipException ze) {
-            logger.log(Level.SEVERE, sm.getString("migration.archiveFailed", name), ze);
-            throw ze;
         }
     }
 

src/main/resources/org/apache/tomcat/jakartaee/LocalStrings.properties

@@ -21,7 +21,6 @@ migration.archive.complete=Migration finished for archive [{0}]
 migration.archive.memory=Migration starting for archive [{0}] using in memory copy
 migration.skip=Migration skipped for archive [{0}] because it is excluded (the archive was copied unchanged)
 migration.archive.stream=Migration starting for archive [{0}] using streaming
-migration.archiveFailed=Failed to migrate archive [{0}]. Using the "-zipInMemory" option may help. 
 migration.cannotReadSource=Cannot read source location [{0}]
 migration.done=Migration completed successfully in [{0}] milliseconds
 migration.error=Error performing migration