increase code coverage

Author: johnscancella

src/main/java/gov/loc/repository/bagit/creator/AbstractCreateManifestsVistor.java

@@ -25,8 +25,8 @@ public abstract class AbstractCreateManifestsVistor extends SimpleFileVisitor<Pa
   private static final Logger logger = LoggerFactory.getLogger(AbstractCreateManifestsVistor.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
-  protected final Map<Manifest, MessageDigest> manifestToMessageDigestMap;
-  protected final boolean includeHiddenFiles;
+  protected transient final Map<Manifest, MessageDigest> manifestToMessageDigestMap;
+  protected transient final boolean includeHiddenFiles;
 
   public AbstractCreateManifestsVistor(final Map<Manifest, MessageDigest> manifestToMessageDigestMap, final boolean includeHiddenFiles){
     this.manifestToMessageDigestMap = manifestToMessageDigestMap;
@@ -57,12 +57,4 @@ public FileVisitResult visitFile(final Path path, final BasicFileAttributes attr
 
     return FileVisitResult.CONTINUE;
   }
-
-  public Map<Manifest, MessageDigest> getManifestToMessageDigestMap() {
-    return manifestToMessageDigestMap;
-  }
-
-  public boolean isIncludeHiddenFiles() {
-    return includeHiddenFiles;
-  }
 }

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

@@ -19,7 +19,7 @@
 abstract public class AbstractPayloadFileExistsInManifestsVistor extends SimpleFileVisitor<Path> {
   protected static final Logger logger = LoggerFactory.getLogger(AbstractPayloadFileExistsInManifestsVistor.class);
   protected static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
-  protected final boolean ignoreHiddenFiles;
+  protected transient final boolean ignoreHiddenFiles;
 
   public AbstractPayloadFileExistsInManifestsVistor(final boolean ignoreHiddenFiles) {
     this.ignoreHiddenFiles = ignoreHiddenFiles;
@@ -34,8 +34,4 @@ public FileVisitResult preVisitDirectory(final Path dir, final BasicFileAttribut
 
     return FileVisitResult.CONTINUE;
   }
-
-  public boolean isIgnoreHiddenFiles() {
-    return ignoreHiddenFiles;
-  }
 }

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

@@ -19,10 +19,9 @@
 public class CheckIfFileExistsTask implements Runnable {
   private static final Logger logger = LoggerFactory.getLogger(CheckIfFileExistsTask.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
-  private final Path file;
-  //TODO if performance is an issue look at concurrentHashMap - it will take up more space but insertion is O(1) vs O(n)
-  private final Set<Path> missingFiles;
-  private final CountDownLatch latch;
+  private transient final Path file;
+  private transient final Set<Path> missingFiles;
+  private transient final CountDownLatch latch;
 
   public CheckIfFileExistsTask(final Path file, final Set<Path> missingFiles, final CountDownLatch latch) {
     this.file = file;
@@ -72,16 +71,4 @@ private boolean existsNormalized(){
 
     return false;
   }
-
-  public Path getFile() {
-    return file;
-  }
-
-  public Set<Path> getMissingFiles() {
-    return missingFiles;
-  }
-
-  public CountDownLatch getLatch() {
-    return latch;
-  }
 }

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

@@ -25,10 +25,10 @@ public class CheckManifestHashesTask implements Runnable {
   private static final Logger logger = LoggerFactory.getLogger(CheckManifestHashesTask.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
-  private final Entry<Path, String> entry;
-  private final CountDownLatch latch;
-  private final Collection<Exception> exceptions;
-  private final String algorithm;
+  private transient final Entry<Path, String> entry;
+  private transient final CountDownLatch latch;
+  private transient final Collection<Exception> exceptions;
+  private transient final String algorithm;
 
   public CheckManifestHashesTask(final Entry<Path, String> entry, final String algorithm, final CountDownLatch latch, final Collection<Exception> exceptions) {
     this.entry = entry;
@@ -59,21 +59,4 @@ protected static void checkManifestEntry(final Entry<Path, String> entry, final
     }
     //if the file doesn't exist it will be caught by checkAllFilesListedInManifestExist method
   }
-
-  public Entry<Path, String> getEntry() {
-    return entry;
-  }
-
-  public CountDownLatch getLatch() {
-    return latch;
-  }
-
-  public Collection<Exception> getExceptions() {
-    return exceptions;
-  }
-
-  public String getAlgorithm() {
-    return algorithm;
-  }
-
 }

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

@@ -19,8 +19,8 @@ public class FileCountAndTotalSizeVistor extends SimpleFileVisitor<Path> {
   private static final Logger logger = LoggerFactory.getLogger(FileCountAndTotalSizeVistor.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
-  private long totalSize;
-  private long count;
+  private transient long totalSize;
+  private transient long count;
 
   @Override
   public FileVisitResult preVisitDirectory(final Path dir, final BasicFileAttributes attrs) throws IOException {
@@ -49,12 +49,4 @@ public long getCount() {
   public long getTotalSize() {
     return totalSize;
   }
-
-  public void setTotalSize(final long totalSize) {
-    this.totalSize = totalSize;
-  }
-
-  public void setCount(final long count) {
-    this.count = count;
-  }
 }

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

@@ -35,8 +35,8 @@ public class PayloadVerifier implements AutoCloseable{
   private static final Logger logger = LoggerFactory.getLogger(PayloadVerifier.class);
   private static final ResourceBundle messages = ResourceBundle.getBundle("MessageBundle");
 
-  private final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping;
-  private final ExecutorService executor;
+  private transient final BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping;
+  private transient final ExecutorService executor;
 
   /**
    * Create a PayloadVerifier using a cached thread pool and the 
@@ -176,12 +176,4 @@ private static void CheckAllFilesInPayloadDirAreListedInAllManifests(final Set<M
       Files.walkFileTree(payloadDir, new PayloadFileExistsInAllManifestsVistor(payLoadManifests, ignoreHiddenFiles));
     }
   }
-
-  public BagitAlgorithmNameToSupportedAlgorithmMapping getNameMapping() {
-    return nameMapping;
-  }
-
-  public ExecutorService getExecutor() {
-    return executor;
-  }
 }

src/test/java/gov/loc/repository/bagit/reader/TagFileReaderTest.java

@@ -25,6 +25,14 @@ public void testCreateFileFromManifestWithAsterisk() throws Exception{
     Assertions.assertEquals(bagRootDir.resolve("data/bar/ham.txt"), path);
   }
 
+  @Test
+  public void testCreateFileFromManifestWithURISyntax() throws Exception{
+    Path bagRootDir = Paths.get("/foo");
+    String uri = "file:///foo/data/bar/ham.txt";
+    Path path = TagFileReader.createFileFromManifest(bagRootDir, uri);
+    Assertions.assertEquals(bagRootDir.resolve("data/bar/ham.txt"), path);
+  }
+  
   @Test
   public void testBackslashThrowsException() throws Exception{
     Path bagRootDir = Paths.get("foo");

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

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.concurrent.Executors;
 
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
@@ -25,6 +26,18 @@ public class PayloadVerifierTest {
   public void setup(){
     sut = new PayloadVerifier(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 PayloadVerifier(Executors.newCachedThreadPool());
+    sut.verifyPayload(bag, true);
+  }
 
   @Test
   public void testErrorWhenManifestListFileThatDoesntExist() throws Exception{