Fix test, then fix code.

jar-infer/jar-infer-lib/src/main/java/com/uber/nullaway/jarinfer/BytecodeAnnotator.java

@@ -61,7 +61,7 @@ private static void LOG(boolean cond, String tag, String msg) {
   private static final String BASE64_PATTERN =
       "(?:[A-Za-z0-9+/]{4})*(?:[A-Za-z0-9+/]{2}==|[A-Za-z0-9+/]{3}=)?";
   private static final String DIGEST_ENTRY_PATTERN =
-      "Name: [A-Za-z0-9/\\$\\n\\s]+\\.class\\nSHA-256-Digest: " + BASE64_PATTERN;
+      "Name: [A-Za-z0-9/\\$\\n\\s\\-\\.]+[A-Za-z0-9]\\nSHA-256-Digest: " + BASE64_PATTERN;
 
   private static void addAnnotationIfNotPresent(
       List<AnnotationNode> annotationList, String annotation) {
@@ -154,17 +154,17 @@ private static void copyAndAnnotateJarEntry(
       MethodReturnAnnotations nullableReturns,
       boolean stripJarSignatures)
       throws IOException {
-    jarOS.putNextEntry(new ZipEntry(jarEntry.getName()));
     String entryName = jarEntry.getName();
     if (entryName.endsWith(".class")) {
+      jarOS.putNextEntry(new ZipEntry(jarEntry.getName()));
       annotateBytecode(is, jarOS, nonnullParams, nullableReturns);
-    } else if (entryName.equals("META-INF/MANIFEST.SF")) {
+    } else if (entryName.equals("META-INF/MANIFEST.MF")) {
       // Read full file
       StringBuilder stringBuilder = new StringBuilder();
       BufferedReader br = new BufferedReader(new InputStreamReader(is, "UTF-8"));
       String currentLine;
       while ((currentLine = br.readLine()) != null) {
-        stringBuilder.append(currentLine);
+        stringBuilder.append(currentLine + "\n");
       }
       String manifestText = stringBuilder.toString();
       // Check for evidence of jar signing, note that lines can be split if too long so regex
@@ -174,13 +174,17 @@ private static void copyAndAnnotateJarEntry(
       if (!manifestText.equals(manifestMinusDigests) && !stripJarSignatures) {
         throw new SignedJarException(SIGNED_JAR_ERROR_MESSAGE);
       }
+      jarOS.putNextEntry(new ZipEntry(jarEntry.getName()));
       jarOS.write(manifestMinusDigests.getBytes("UTF-8"));
     } else if (entryName.startsWith("META-INF/")
-        && (entryName.endsWith(".DSA") || entryName.endsWith(".RSA"))) {
+        && (entryName.endsWith(".DSA")
+            || entryName.endsWith(".RSA")
+            || entryName.endsWith(".SF"))) {
       if (!stripJarSignatures) {
         throw new SignedJarException(SIGNED_JAR_ERROR_MESSAGE);
       } // the case where stripJarSignatures==true is handled by default by skipping these files
     } else {
+      jarOS.putNextEntry(new ZipEntry(jarEntry.getName()));
       jarOS.write(IOUtils.toByteArray(is));
     }
     jarOS.closeEntry();

jar-infer/jar-infer-lib/src/test/java/com/uber/nullaway/jarinfer/EntriesComparator.java

@@ -109,9 +109,9 @@ public static boolean compareEntriesInAars(String aarFile1, String aarFile2) thr
 
   private static String readManifestFromJar(String jarfile) throws IOException {
     JarFile jar = new JarFile(jarfile);
-    ZipEntry manifestEntry = jar.getEntry("META-INF/MANIFEST.SF");
+    ZipEntry manifestEntry = jar.getEntry("META-INF/MANIFEST.MF");
     if (manifestEntry == null) {
-      return "";
+      throw new IllegalArgumentException("Jar does not contain a manifest at META-INF/MANIFEST.MF");
     }
     StringBuilder stringBuilder = new StringBuilder();
     BufferedReader bufferedReader =
@@ -120,19 +120,20 @@ private static String readManifestFromJar(String jarfile) throws IOException {
     while ((currentLine = bufferedReader.readLine()) != null) {
       // Ignore empty new lines
       if (currentLine.trim().length() > 0) {
-        stringBuilder.append(currentLine);
+        stringBuilder.append(currentLine + "\n");
       }
     }
     return stringBuilder.toString();
   }
 
   /**
-   * Compares the META-INF/MANIFEST.SF file in the given 2 jar files. We ignore empty newlines.
+   * Compares the META-INF/MANIFEST.MF file in the given 2 jar files. We ignore empty newlines.
    *
    * @param jarFile1 Path to the first jar file.
    * @param jarFile2 Path to the second jar file.
-   * @return True iff the MANIFEST.SF files in the two jar files exist and are the same.
+   * @return True iff the MANIFEST.MF files in the two jar files exist and are the same.
    * @throws IOException
+   * @throws IllegalArgumentException
    */
   public static boolean compareManifestContents(String jarFile1, String jarFile2)
       throws IOException {

jar-infer/jar-infer-lib/src/test/java/com/uber/nullaway/jarinfer/JarInferTest.java

@@ -486,11 +486,11 @@ public void testSignedJars() throws Exception {
     Assert.assertTrue(
         "Annotated jar after signature stripping does not have all the entries present in the input "
             + "jar (before signing), or contains extra (e.g. META-INF) entries!",
-        EntriesComparator.compareEntriesInJars(outputJarPath, inputJarPath));
+        EntriesComparator.compareEntriesInJars(outputJarPath, baseJarPath));
     // Check that META-INF/Manifest.MF is content-identical to the original unsigned jar
     Assert.assertTrue(
-        "Annotated jar after signature stripping does not preserve the info inside META-INF/MANIFEST.SF",
-        EntriesComparator.compareManifestContents(outputJarPath, inputJarPath));
+        "Annotated jar after signature stripping does not preserve the info inside META-INF/MANIFEST.MF",
+        EntriesComparator.compareManifestContents(outputJarPath, baseJarPath));
   }
 
   private byte[] sha1sum(String path) throws Exception {

jar-infer/test-java-lib-jarinfer/build.gradle

@@ -25,6 +25,17 @@ targetCompatibility = "1.8"
 
 def astubxPath = "META-INF/nullaway/jarinfer.astubx"
 
+jar {
+    manifest {
+        attributes(
+                'Build-Timestamp': new java.text.SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSZ").format(new Date()),
+                'Created-By'     : "Gradle ${gradle.gradleVersion}",
+                'Build-Jdk'      : "${System.properties['java.version']} (${System.properties['java.vendor']} ${System.properties['java.vm.version']})",
+                'Build-OS'       : "${System.properties['os.name']} ${System.properties['os.arch']} ${System.properties['os.version']}"
+        )
+    }
+}
+
 jar.doLast {
     javaexec {
         classpath = files("${rootProject.projectDir}/jar-infer/jar-infer-cli/build/libs/jar-infer-cli-${VERSION_NAME}.jar")