various fixes

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/hash/StandardSupportedAlgorithms.java

@@ -6,9 +6,9 @@
 public enum StandardSupportedAlgorithms implements SupportedAlgorithm{
   MD5("MD5"),
   SHA1("SHA-1"),
-  SHA224("SHA-224"),
-  SHA256("SHA-256"),
-  SHA512("SHA-512");
+  SHA224("SHA224"),
+  SHA256("SHA256"),
+  SHA512("SHA512");
 
   private final String messageDigestName;
 

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

@@ -37,7 +37,7 @@ 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;
 
   /**
@@ -74,7 +74,7 @@ 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;
   }
 
@@ -209,14 +209,14 @@ 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;
@@ -42,7 +42,7 @@ public class PayloadVerifier implements AutoCloseable{
    * Create a PayloadVerifier using a cached thread pool and the 
    * {@link StandardBagitAlgorithmNameToSupportedAlgorithmMapping} mapping
    */
-  public PayloadVerifier(){
+  public ManifestVerifier(){
     this(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping(), Executors.newCachedThreadPool());
   }
 
@@ -51,7 +51,7 @@ public PayloadVerifier(){
    * 
    * @param nameMapping the mapping between BagIt algorithm name and the java supported algorithm
    */
-  public PayloadVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping) {
+  public ManifestVerifier(final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping) {
     this(nameMapping, Executors.newCachedThreadPool());
   }
 
@@ -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/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<>();

src/test/java/gov/loc/repository/bagit/verify/PayloadVerifierTest.java

@@ -20,23 +20,23 @@ public class PayloadVerifierTest {
   private Path rootDir = Paths.get(new File("src/test/resources/bags/v0_97/bag").toURI());
   private BagReader reader = new BagReader();
 
-  private PayloadVerifier sut;
+  private ManifestVerifier sut;
 
   @BeforeEach
   public void setup(){
-    sut = new PayloadVerifier(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping());
+    sut = new ManifestVerifier(new StandardBagitAlgorithmNameToSupportedAlgorithmMapping());
   }
 
   @Test
   public void testOtherConstructors() throws Exception {
     rootDir = Paths.get(new File("src/test/resources/bags/v0_96/bag-with-tagfiles-in-payload-manifest").toURI());
     Bag bag = reader.read(rootDir);
 
-    sut = new PayloadVerifier();
-    sut.verifyPayload(bag, true);
+    sut = new ManifestVerifier();
+    sut.verifyManifests(bag, true);
 
-    sut = new PayloadVerifier(Executors.newCachedThreadPool());
-    sut.verifyPayload(bag, true);
+    sut = new ManifestVerifier(Executors.newCachedThreadPool());
+    sut.verifyManifests(bag, true);
   }
 
   @Test
@@ -45,7 +45,7 @@ public void testErrorWhenManifestListFileThatDoesntExist() throws Exception{
     Bag bag = reader.read(rootDir);
 
     Assertions.assertThrows(FileNotInPayloadDirectoryException.class, 
-        () -> { sut.verifyPayload(bag, true); });
+        () -> { sut.verifyManifests(bag, true); });
   }
 
   @Test
@@ -54,22 +54,22 @@ public void testErrorWhenFileIsntInManifest() throws Exception{
     Bag bag = reader.read(rootDir);
 
     Assertions.assertThrows(FileNotInManifestException.class, 
-        () -> { sut.verifyPayload(bag, true); });
+        () -> { sut.verifyManifests(bag, true); });
   }
 
   @Test
   public void testBagWithTagFilesInPayloadIsValid() throws Exception{
     rootDir = Paths.get(new File("src/test/resources/bags/v0_96/bag-with-tagfiles-in-payload-manifest").toURI());
     Bag bag = reader.read(rootDir);
 
-    sut.verifyPayload(bag, true);
+    sut.verifyManifests(bag, true);
   }
 
   @Test
   public void testNotALlFilesListedInAllManifestsThrowsException() throws Exception{
     Path bagDir = Paths.get(new File("src/test/resources/notAllFilesListedInAllManifestsBag").toURI());
     Bag bag = reader.read(bagDir);
     Assertions.assertThrows(FileNotInManifestException.class, 
-        () -> { sut.verifyPayload(bag, true); });
+        () -> { sut.verifyManifests(bag, true); });
   }
 }

src/test/resources/bags/v1_0/bag/bag-info.txt

@@ -0,0 +1,3 @@
+Bag-Software-Agent: bagit.py v1.7.0 <https://github.com/LibraryOfCongress/bagit-python>
+Bagging-Date: 2018-07-22
+Payload-Oxum: 6.1

src/test/resources/bags/v1_0/bag/bagit.txt

@@ -0,0 +1,2 @@
+BagIt-Version: 1.0
+Tag-File-Character-Encoding: UTF-8

src/test/resources/bags/v1_0/bag/data/foo.txt

@@ -0,0 +1 @@
+hello

src/test/resources/bags/v1_0/bag/manifest-sha512.txt

@@ -0,0 +1 @@
+e7c22b994c59d9cf2b48e549b1e24666636045930d3da7c1acb299d1c3b7f931f94aae41edda2c2b207a36e10f8bcb8d45223e54878f5b316e7ce3b6bc019629  data/foo.txt

src/test/resources/bags/v1_0/bag/tagmanifest-sha512.txt

@@ -0,0 +1,3 @@
+f5bdbc7f273dd8b95d30b77b3d6f727d999ecbe9be06a7656388e7a3a46d963881563d779a2a99265b0c2785de2a7b72ac05fa7bc5b66b471d3f4e80fe9bb370 bag-info.txt
+1d73ae108d4109b61f56698a5e19ee1f8947bdf8940bbce6adbe5e0940c2363caace6a547b4f1b3ec6a4fd2b7fa845e9cb9d28823bc72c59971718bb26f2fbd8 bagit.txt
+35d40e38f5e2eb7261a1cc0c0ccf9c6c50d2e07e39a9460ec4f99046048f939d82647c68d8f744c653c7a37c05cc9d71153c8028786dfeba4322a3be5fe81af0 manifest-sha512.txt