a little bit of refactoring

src/main/java/gov/loc/repository/bagit/reader/BagReader.java

@@ -34,7 +34,6 @@
 /**
  * Responsible for reading a bag from the filesystem.
  */
-@SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
 public class BagReader {
   private static final Logger logger = LoggerFactory.getLogger(PayloadFileExistsInManifestVistor.class);
 
@@ -265,6 +264,7 @@ public Bag readBagMetadata(final Path rootDir, final Bag bag) throws IOException
    * 
    * @throws IOException if there is a problem reading a file
    */
+  @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   public Bag readFetch(final Path fetchFile, final Bag bag) throws IOException{
     logger.info("Attempting to read [{}]", fetchFile);
     final Bag newBag = new Bag(bag);
@@ -289,6 +289,7 @@ public Bag readFetch(final Path fetchFile, final Bag bag) throws IOException{
     return newBag;
   }
 
+  @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   protected List<Pair<String, String>> readKeyValuesFromFile(final Path file, final String splitRegex) throws IOException, InvalidBagMetadataException{
     final List<Pair<String, String>> keyValues = new ArrayList<>();
     final BufferedReader br = Files.newBufferedReader(file);

src/main/java/gov/loc/repository/bagit/tasks/CheckIfFileExistsTask.java

@@ -2,29 +2,29 @@
 
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.List;
 import java.util.concurrent.CountDownLatch;
 
 /**
  * A simple task to check if a file exists on the filesystem. This is thread safe, so many can be called at once.
  */
-@SuppressWarnings(value = {"PMD.DoNotUseThreads", "PMD.AvoidStringBufferField"})
+@SuppressWarnings(value = {"PMD.DoNotUseThreads"})
 public class CheckIfFileExistsTask implements Runnable {
   private transient final Path file;
-  private transient final StringBuilder messageBuilder;
+  private transient final List<Path> missingFiles;
   private transient final CountDownLatch latch;
 
-  public CheckIfFileExistsTask(final Path file, final StringBuilder messageBuilder, final CountDownLatch latch) {
+  public CheckIfFileExistsTask(final Path file, final List<Path> missingFiles, final CountDownLatch latch) {
     this.file = file;
-    this.messageBuilder = messageBuilder;
     this.latch = latch;
+    this.missingFiles = missingFiles;
   }
 
   @Override
   public void run() {
     if(!Files.exists(file)){
-      messageBuilder.append("Manifest lists file [").append(file).append("] but it does not exist").append(System.lineSeparator());
+      missingFiles.add(file);
     }
     latch.countDown();
   }
-
 }

src/main/java/gov/loc/repository/bagit/verify/BagVerifier.java

@@ -44,7 +44,6 @@
 /**
  * Responsible for verifying if a bag is valid, complete
  */
-@SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
 public class BagVerifier {
   private static final Logger logger = LoggerFactory.getLogger(BagVerifier.class);
 
@@ -165,6 +164,7 @@ public void isValid(final Bag bag, final boolean ignoreHiddenFiles) throws IOExc
    * @throws InterruptedException if the thread is interrupted
    * @throws VerificationException if there is some other exception while checking the checksum(s)
    */
+  @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   protected void checkHashes(final Manifest manifest) throws CorruptChecksumException, InterruptedException, VerificationException{
     final ExecutorService executor = Executors.newCachedThreadPool();
     final CountDownLatch latch = new CountDownLatch( manifest.getFileToChecksumMap().size());
@@ -318,22 +318,22 @@ protected Set<Path> getAllFilesListedInManifests(final Bag bag) throws IOExcepti
     return filesListedInManifests;
   }
 
+  @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   protected void checkAllFilesListedInManifestExist(final Set<Path> files) throws FileNotInPayloadDirectoryException, InterruptedException{
     final ExecutorService executor = Executors.newCachedThreadPool();
     final CountDownLatch latch = new CountDownLatch(files.size());
-    final StringBuilder messageBuilder = new StringBuilder();
+    final List<Path> missingFiles = new ArrayList<>();
 
     logger.debug("Checking if all files listed in the manifest(s) exist");
     for(final Path file : files){
-      executor.execute(new CheckIfFileExistsTask(file, messageBuilder, latch));
+      executor.execute(new CheckIfFileExistsTask(file, missingFiles, latch));
     }
 
     latch.await();
     executor.shutdown();
 
-    final String missingFilesMessage = messageBuilder.toString();
-    if(!missingFilesMessage.isEmpty()){
-      throw new FileNotInPayloadDirectoryException(missingFilesMessage);
+    if(!missingFiles.isEmpty()){
+      throw new FileNotInPayloadDirectoryException("Manifest(s) contains file(s) " + missingFiles + " but they don't exist!");
     }
   }
 

src/main/java/gov/loc/repository/bagit/writer/BagWriter.java

@@ -28,7 +28,7 @@
 /**
  * responsible for writing out a bag.
  */
-@SuppressWarnings(value = {"PMD.TooManyMethods", "PMD.AvoidInstantiatingObjectsInLoops"}) //TODO refactor to remove methods?
+@SuppressWarnings("PMD.TooManyMethods")
 public final class BagWriter {
   private static final Logger logger = LoggerFactory.getLogger(BagWriter.class);
   private static final Version VERSION_0_98 = new Version(0, 98);
@@ -152,6 +152,7 @@ public static void writePayloadManifests(final Set<Manifest> manifests, final Pa
     writeManifests(manifests, outputDir, bagitRootDir, "manifest-", charsetName);
   }
 
+  @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   private static Set<Manifest> updateTagManifests(final Bag bag, final Path newBagRootDir) throws NoSuchAlgorithmException, IOException{
     final Set<Manifest> newManifests = new HashSet<>();