various fixes

code-quality.gradle

@@ -22,7 +22,12 @@ task integrationTest(type: Test, dependsOn: "cloneConformanceSuite") {
   description "Runs the integration tests."
   testClassesDirs = sourceSets.integrationTest.output.classesDirs
   classpath = sourceSets.integrationTest.runtimeClasspath
-  testLogging.showStandardStreams = true
+  //testLogging.showStandardStreams = true
+  useJUnitPlatform()
+
+  testLogging {
+    events "passed", "skipped", "failed"
+  }
 }
 
 jacocoTestReport.dependsOn integrationTest //include the integration tests in the code coverage reports

src/integration/java/gov/loc/repository/bagit/BagitSuiteComplanceTest.java

@@ -147,6 +147,7 @@ public void testReadWriteProducesSameBag() throws Exception{
       testTagFileContents(bag, newBagDir);
 
       testBagsStructureAreEqual(bagDir, newBagDir);
+      delete(newBagDir);
     }
   }
 

src/main/java/gov/loc/repository/bagit/conformance/ManifestChecker.java

@@ -123,9 +123,10 @@ private static void checkManifestPayload(final Path manifestFile, final Charset
         String path = parsePath(line);
 
         path = checkForManifestCreatedWithMD5SumTools(path, warnings, warningsToIgnore);
-        paths.add(path.toLowerCase());
 
         checkForDifferentCase(path, paths, manifestFile, warnings, warningsToIgnore);
+        paths.add(path.toLowerCase());
+
         if(encoding.name().startsWith("UTF")){
           checkNormalization(path, manifestFile.getParent(), warnings, warningsToIgnore);
         }
@@ -256,7 +257,7 @@ static void checkAlgorthm(final String algorithm, final Set<BagitWarning> warnin
       warnings.add(BagitWarning.WEAK_CHECKSUM_ALGORITHM);
     }
 
-    else if(!warningsToIgnore.contains(BagitWarning.NON_STANDARD_ALGORITHM) && !"SHA-512".equals(upperCaseAlg)){
+    else if(!warningsToIgnore.contains(BagitWarning.NON_STANDARD_ALGORITHM) && !"SHA512".equals(upperCaseAlg)){
       logger.warn(messages.getString("non_standard_algorithm_warning"), algorithm);
       warnings.add(BagitWarning.NON_STANDARD_ALGORITHM);
     }

src/main/java/gov/loc/repository/bagit/exceptions/MissingPayloadDirectoryException.java

@@ -1,12 +1,16 @@
 package gov.loc.repository.bagit.exceptions;
 
+import java.nio.file.Path;
+
+import org.slf4j.helpers.MessageFormatter;
+
 /**
  * The payload directory is a required file. This class represents the error if it is not found.
  */
 public class MissingPayloadDirectoryException extends Exception {
   private static final long serialVersionUID = 1L;
 
-  public MissingPayloadDirectoryException(final String message){
-    super(message);
+  public MissingPayloadDirectoryException(final String message, final Path path){
+    super(MessageFormatter.format(message, path).getMessage());
   }
 }

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

@@ -17,6 +17,7 @@
 import gov.loc.repository.bagit.domain.Bag;
 import gov.loc.repository.bagit.domain.Manifest;
 import gov.loc.repository.bagit.exceptions.CorruptChecksumException;
+import gov.loc.repository.bagit.exceptions.FileNotInManifestException;
 import gov.loc.repository.bagit.exceptions.FileNotInPayloadDirectoryException;
 import gov.loc.repository.bagit.exceptions.InvalidBagitFileFormatException;
 import gov.loc.repository.bagit.exceptions.InvalidPayloadOxumException;
@@ -37,15 +38,15 @@ public final class BagVerifier implements AutoCloseable{
   private static final Logger logger = LoggerFactory.getLogger(BagVerifier.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
-  private final PayloadVerifier manifestVerifier;
+  private final ManifestVerifier manifestVerifier;
   private final ExecutorService executor;
 
   /**
    * Create a BagVerifier with a cached thread pool and a 
    * {@link StandardBagitAlgorithmNameToSupportedAlgorithmMapping}
    */
   public BagVerifier(){
-    this(Executors.newCachedThreadPool(), new StandardBagitAlgorithmNameToSupportedAlgorithmMapping());
+    this(Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()), new StandardBagitAlgorithmNameToSupportedAlgorithmMapping());
   }
 
   /**
@@ -54,7 +55,7 @@ public BagVerifier(){
    * @param nameMapping the mapping between BagIt algorithm name and the java supported algorithm
    */
   public BagVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping){
-    this(Executors.newCachedThreadPool(), nameMapping);
+    this(Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()), nameMapping);
   }
 
   /**
@@ -74,7 +75,7 @@ public BagVerifier(final ExecutorService executor){
    * @param executor the thread pool to use when doing work
    */
   public BagVerifier(final ExecutorService executor, final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping){
-    manifestVerifier = new PayloadVerifier(nameMapping, executor);
+    manifestVerifier = new ManifestVerifier(nameMapping, executor);
     this.executor = executor;
   }
 
@@ -120,6 +121,7 @@ public static void quicklyVerify(final Bag bag) throws IOException, InvalidPaylo
    * 
    * @throws CorruptChecksumException when the computed hash doesn't match given hash
    * @throws IOException if there was an error with the file
+   * @throws FileNotInManifestException if a file is found in the payload directory but not in manifest(s)
    * @throws MissingPayloadManifestException if there is not at least one payload manifest
    * @throws MissingBagitFileException  if there is no bagit.txt file
    * @throws MissingPayloadDirectoryException if there is no /data directory
@@ -130,7 +132,7 @@ public static void quicklyVerify(final Bag bag) throws IOException, InvalidPaylo
    * @throws UnsupportedAlgorithmException if the manifest uses a algorithm that isn't supported
    * @throws InvalidBagitFileFormatException if the manifest is not formatted properly
    */
-  public void isValid(final Bag bag, final boolean ignoreHiddenFiles) throws IOException, MissingPayloadManifestException, MissingBagitFileException, MissingPayloadDirectoryException, FileNotInPayloadDirectoryException, InterruptedException, MaliciousPathException, CorruptChecksumException, VerificationException, UnsupportedAlgorithmException, InvalidBagitFileFormatException{
+  public void isValid(final Bag bag, final boolean ignoreHiddenFiles) throws IOException, FileNotInManifestException, MissingPayloadManifestException, MissingBagitFileException, MissingPayloadDirectoryException, FileNotInPayloadDirectoryException, InterruptedException, MaliciousPathException, CorruptChecksumException, VerificationException, UnsupportedAlgorithmException, InvalidBagitFileFormatException{
     logger.info(messages.getString("checking_bag_is_valid"), bag.getRootDir());
     isComplete(bag, ignoreHiddenFiles);
 
@@ -209,14 +211,14 @@ public void isComplete(final Bag bag, final boolean ignoreHiddenFiles) throws
 
     MandatoryVerifier.checkIfAtLeastOnePayloadManifestsExist(bag.getRootDir(), bag.getVersion());
 
-    manifestVerifier.verifyPayload(bag, ignoreHiddenFiles);
+    manifestVerifier.verifyManifests(bag, ignoreHiddenFiles);
   }
 
   public ExecutorService getExecutor() {
     return executor;
   }
 
-  public PayloadVerifier getManifestVerifier() {
+  public ManifestVerifier getManifestVerifier() {
     return manifestVerifier;
   }
 }

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

@@ -84,7 +84,7 @@ public static void checkPayloadDirectoryExists(final Bag bag) throws MissingPayl
     final Path dataDir = PathUtils.getDataDir(bag);
 
     if(!Files.exists(dataDir)){
-      throw new MissingPayloadDirectoryException(messages.getString("file_should_exist_error"));
+      throw new MissingPayloadDirectoryException(messages.getString("file_should_exist_error"), dataDir);
     }
   }
 

src/main/java/gov/loc/repository/bagit/verify/PayloadVerifier.java → src/main/java/gov/loc/repository/bagit/verify/ManifestVerifier.java

@@ -31,8 +31,8 @@
 /**
  * Responsible for all things related to the manifest during verification.
  */
-public class PayloadVerifier implements AutoCloseable{
-  private static final Logger logger = LoggerFactory.getLogger(PayloadVerifier.class);
+public class ManifestVerifier implements AutoCloseable{
+  private static final Logger logger = LoggerFactory.getLogger(ManifestVerifier.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
   private transient final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping;
@@ -42,17 +42,17 @@ public class PayloadVerifier implements AutoCloseable{
    * Create a PayloadVerifier using a cached thread pool and the 
    * {@link StandardBagitAlgorithmNameToSupportedAlgorithmMapping} mapping
    */
-  public PayloadVerifier(){
-    this(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping(), Executors.newCachedThreadPool());
+  public ManifestVerifier(){
+    this(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping(), Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()));
   }
 
   /**
    * Create a PayloadVerifier using a cached thread pool and a custom mapping
    * 
    * @param nameMapping the mapping between BagIt algorithm name and the java supported algorithm
    */
-  public PayloadVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping) {
-    this(nameMapping, Executors.newCachedThreadPool());
+  public ManifestVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping) {
+    this(nameMapping, Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()));
   }
 
   /**
@@ -61,7 +61,7 @@ public PayloadVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameM
    * 
    * @param executor the thread pool to use when doing work
    */
-  public PayloadVerifier(final ExecutorService executor) {
+  public ManifestVerifier(final ExecutorService executor) {
     this(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping(), executor);
   }
 
@@ -71,7 +71,7 @@ public PayloadVerifier(final ExecutorService executor) {
    * @param nameMapping the mapping between BagIt algorithm name and the java supported algorithm
    * @param executor the thread pool to use when doing work
    */
-  public PayloadVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping, final ExecutorService executor) {
+  public ManifestVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping, final ExecutorService executor) {
     this.nameMapping = nameMapping;
     this.executor = executor;
   }
@@ -83,19 +83,20 @@ public void close() throws SecurityException{
   }
 
   /**
-   * Verify that all the files in the payload directory are listed in the manifest and 
-   * all files listed in the manifests exist.
+   * Verify that all the files in the payload directory are listed in the payload manifest and 
+   * all files listed in all manifests exist.
    * 
    * @param bag the bag to check to check
    * @param ignoreHiddenFiles to ignore hidden files unless they are specifically listed in a manifest
+   * 
    * @throws IOException if there is a problem reading a file
    * @throws MaliciousPathException the path in the manifest was specifically crafted to cause harm
    * @throws UnsupportedAlgorithmException if the algorithm used for the manifest is unsupported
    * @throws InvalidBagitFileFormatException if any of the manifests don't conform to the bagit specification
    * @throws FileNotInPayloadDirectoryException if a file is listed in a manifest but doesn't exist in the payload directory
    * @throws InterruptedException if a thread is interrupted while doing work
    */
-  public void verifyPayload(final Bag bag, final boolean ignoreHiddenFiles)
+  public void verifyManifests(final Bag bag, final boolean ignoreHiddenFiles)
       throws IOException, MaliciousPathException, UnsupportedAlgorithmException, 
       InvalidBagitFileFormatException, FileNotInPayloadDirectoryException, InterruptedException {
 

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

@@ -1,10 +1,12 @@
 package gov.loc.repository.bagit.verify;
 
+import java.io.IOException;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
+import java.util.ResourceBundle;
 import java.util.Set;
 
 import org.slf4j.helpers.MessageFormatter;
@@ -15,6 +17,7 @@
  * Implements {@link SimpleFileVisitor} to ensure that the encountered file is in one of the manifests.
  */
 public class PayloadFileExistsInAtLeastOneManifestVistor extends AbstractPayloadFileExistsInManifestsVistor {
+  private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
   private transient final Set<Path> filesListedInManifests;
 
   public PayloadFileExistsInAtLeastOneManifestVistor(final Set<Path> filesListedInManifests, final boolean ignoreHiddenFiles) {
@@ -23,12 +26,18 @@ public PayloadFileExistsInAtLeastOneManifestVistor(final Set<Path> filesListedIn
   }
 
   @Override
-  public FileVisitResult visitFile(final Path path, final BasicFileAttributes attrs)throws FileNotInManifestException{
-    if(Files.isRegularFile(path) && !filesListedInManifests.contains(path.normalize())){
+  public FileVisitResult visitFile(final Path path, final BasicFileAttributes attrs)throws IOException, FileNotInManifestException{
+	if(Files.isHidden(path) && ignoreHiddenFiles){
+	  logger.debug(messages.getString("skipping_hidden_file"), path);
+  }
+	else {
+	  if(Files.isRegularFile(path) && !filesListedInManifests.contains(path.normalize())){
       final String formattedMessage = messages.getString("file_not_in_any_manifest_error");
       throw new FileNotInManifestException(MessageFormatter.format(formattedMessage, path).getMessage());
     }
-    logger.debug("[{}] is in at least one manifest", path);
-    return FileVisitResult.CONTINUE;
+    logger.debug(messages.getString("file_in_at_least_one_manifest"), path);
+	}
+	return FileVisitResult.CONTINUE;
   }
+
 }

src/main/resources/MessageBundle.properties

@@ -182,6 +182,9 @@ file_not_in_manifest_error=File [{}] is in the payload directory but isn't liste
 file_in_all_manifests=[{}] is in all manifests.
 file_not_in_any_manifest_error=File [{}] is in the payload directory but isn't listed in any manifest!
 
+#for PayloadFileExistsInAtLeastOneManifestVistor.java
+file_in_at_least_one_manifest="[{}] is in at least one manifest"
+
 #for PayloadVerifier.java
 all_files_in_manifests=Getting all files listed in the manifest(s).
 get_listing_in_manifest=Getting files and checksums listed in [{}].

src/test/java/gov/loc/repository/bagit/TempFolderTest.java

@@ -8,6 +8,7 @@
 import java.nio.file.attribute.BasicFileAttributes;
 
 import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 
 abstract public class TempFolderTest {
@@ -21,6 +22,8 @@ public void setupTempFolder() throws IOException{
   @AfterEach
   public void teardownTempFolder() throws IOException{
     delete(folder);
+    Assertions.assertFalse(Files.exists(folder));
+    //Assertions.assertEquals(0, Files.list(folder).count());
   }
 
   public Path createDirectory(String name) throws IOException {
@@ -33,7 +36,25 @@ public Path createFile(String name) throws IOException {
     return Files.createFile(newFile);
   }
 
-  private void delete(Path tempDirectory) throws IOException {
+  public Path copyBagToTempFolder(Path bagFolder) throws IOException{
+	  Path bagCopyDir = createDirectory(bagFolder.getFileName() + "_copy");
+	  Files.walkFileTree(bagFolder, new SimpleFileVisitor<Path>() {
+
+	      @Override
+	      public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+	    	Path relative = bagFolder.relativize(file);
+	    	if(relative.getParent() != null) {
+	    	  Files.createDirectories(bagCopyDir.resolve(relative.getParent()));
+	    	}
+	    	Files.copy(file, bagCopyDir.resolve(relative));
+	        return FileVisitResult.CONTINUE;
+	      }
+	    });
+
+	  return bagCopyDir;
+  }
+
+  protected void delete(Path tempDirectory) throws IOException {
     Files.walkFileTree(tempDirectory, new SimpleFileVisitor<Path>() {
 
       @Override

src/test/java/gov/loc/repository/bagit/TestUtils.java

@@ -12,6 +12,12 @@ public static boolean isExecutingOnWindows(){
     return System.getProperty("os.name").contains("Windows");
   }
 
+  /**
+   * walk a directory and make sure that files/folders are hidden if they start with a . on windows.
+   * 
+   * @param startingDir the directory to start walking
+   * @throws IOException if there is a problem setting the file/folder to be hidden
+   */
   public static void makeFilesHiddenOnWindows(Path startingDir) throws IOException {
     if (isExecutingOnWindows()) {
       Files.walkFileTree(startingDir, new SimpleFileVisitor<Path>() {

src/test/java/gov/loc/repository/bagit/conformance/BagLinterTest.java

@@ -28,6 +28,13 @@ public void testClassIsWellDefined() throws NoSuchMethodException, InvocationTar
     assertUtilityClassWellDefined(BagLinter.class);
   }
 
+  @Test
+  public void testConformantBag() throws Exception{
+	  Path goodBag = Paths.get("src", "test", "resources", "bags", "v1_0", "bag");
+	  Set<BagitWarning> warnings = BagLinter.lintBag(goodBag);
+	  Assertions.assertTrue(warnings.size() == 0);
+  }
+
   @Test
   public void testLintBag() throws Exception{
     Set<BagitWarning> expectedWarnings = new HashSet<>();