Preserve compression method when instrumenting zip entries

org.jacoco.core.test/src/org/jacoco/core/instr/InstrumenterTest.java

@@ -26,6 +26,7 @@
 import java.io.OutputStream;
 import java.io.Serializable;
 import java.util.Arrays;
+import java.util.zip.CRC32;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 import java.util.zip.ZipEntry;
@@ -250,18 +251,38 @@ public void testInstrumentAll_Class() throws IOException {
 	public void testInstrumentAll_Zip() throws IOException {
 		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
 		ZipOutputStream zipout = new ZipOutputStream(buffer);
-		zipout.putNextEntry(new ZipEntry("Test.class"));
+
+		// Compressed Entry
+		ZipEntry entry = new ZipEntry("TestCompressed.class");
+		entry.setMethod(ZipEntry.DEFLATED);
+		zipout.putNextEntry(entry);
+		zipout.write(TargetLoader.getClassDataAsBytes(getClass()));
+
+		// Uncompressed Entry
+		entry = new ZipEntry("TestUncompressed.class");
+		entry.setMethod(ZipEntry.STORED);
+		entry.setSize(TargetLoader.getClassDataAsBytes(getClass()).length);
+		CRC32 crc = new CRC32();
+		crc.update(TargetLoader.getClassDataAsBytes(getClass()));
+		entry.setCrc(crc.getValue());
+		zipout.putNextEntry(entry);
 		zipout.write(TargetLoader.getClassDataAsBytes(getClass()));
+
 		zipout.finish();
 		ByteArrayOutputStream out = new ByteArrayOutputStream();
 
 		int count = instrumenter.instrumentAll(
 				new ByteArrayInputStream(buffer.toByteArray()), out, "Test");
 
-		assertEquals(1, count);
+		assertEquals(2, count);
 		ZipInputStream zipin = new ZipInputStream(
 				new ByteArrayInputStream(out.toByteArray()));
-		assertEquals("Test.class", zipin.getNextEntry().getName());
+		entry = zipin.getNextEntry();
+		assertEquals("TestCompressed.class", entry.getName());
+		assertEquals(ZipEntry.DEFLATED, entry.getMethod());
+		entry = zipin.getNextEntry();
+		assertEquals("TestUncompressed.class", entry.getName());
+		assertEquals(ZipEntry.STORED, entry.getMethod());
 		assertNull(zipin.getNextEntry());
 	}
 

org.jacoco.core/src/org/jacoco/core/instr/Instrumenter.java

@@ -16,6 +16,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.util.zip.CRC32;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 import java.util.zip.ZipEntry;
@@ -216,16 +217,46 @@ private int instrumentZip(final InputStream input,
 				continue;
 			}
 
-			zipout.putNextEntry(new ZipEntry(entryName));
-			if (!signatureRemover.filterEntry(entryName, zipin, zipout)) {
-				count += instrumentAll(zipin, zipout, name + "@" + entryName);
+			final ZipEntry newEntry = new ZipEntry(entryName);
+			switch (entry.getMethod()) {
+			case ZipEntry.DEFLATED:
+				newEntry.setMethod(ZipEntry.DEFLATED);
+				zipout.putNextEntry(newEntry);
+				count += filterOrInstrument(zipin, zipout, name, entryName);
+				break;
+			case ZipEntry.STORED:
+				// Uncompressed entries must be processed in-memory to calculate
+				// mandatory entry size and CRC
+				newEntry.setMethod(ZipEntry.STORED);
+				final ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+				count += filterOrInstrument(zipin, buffer, name, entryName);
+				final byte[] bytes = buffer.toByteArray();
+				newEntry.setSize(bytes.length);
+				newEntry.setCompressedSize(bytes.length);
+				final CRC32 crc = new CRC32();
+				crc.update(bytes);
+				newEntry.setCrc(crc.getValue());
+				zipout.putNextEntry(newEntry);
+				zipout.write(bytes);
+				break;
+			default:
+				throw new AssertionError(entry.getMethod());
 			}
 			zipout.closeEntry();
 		}
 		zipout.finish();
 		return count;
 	}
 
+	private int filterOrInstrument(final InputStream in, final OutputStream out,
+			final String name, final String entryName) throws IOException {
+		if (signatureRemover.filterEntry(entryName, in, out)) {
+			return 0;
+		} else {
+			return instrumentAll(in, out, name + "@" + entryName);
+		}
+	}
+
 	private ZipEntry nextEntry(final ZipInputStream input,
 			final String location) throws IOException {
 		try {

org.jacoco.doc/docroot/doc/changes.html

@@ -37,6 +37,13 @@ <h3>New Features</h3>
       (GitHub <a href="https://github.com/jacoco/jacoco/issues/1016">#1016</a>).</li>
 </ul>
 
+<h3>Fixed bugs</h3>
+<ul>
+  <li>Compression method of zip entries is now preserved when instrumenting archives.
+      This allows to use JaCoCo with frameworks that expect uncompressed entries
+      (GitHub <a href="https://github.com/jacoco/jacoco/issues/1004">#1004</a>).</li>
+</ul>
+
 <h3>Non-functional Changes</h3>
 <ul>
   <li>Support for Pack200 was removed in JDK 14. JaCoCo will now throw a detailed