refs #38 replace File with Path

Author: jscancella

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

@@ -56,7 +56,7 @@ public FileVisitResult visitFile(Path path, BasicFileAttributes attrs)throws IOE
       InputStream inputStream = Files.newInputStream(path, StandardOpenOption.READ);
       String hash = Hasher.hash(inputStream, messageDigest);
       logger.debug("Adding [{}] to manifest with hash [{}]", path, hash);
-      manifest.getFileToChecksumMap().put(path.toFile(), hash); 
+      manifest.getFileToChecksumMap().put(path, hash); 
     }
 
     return FileVisitResult.CONTINUE;

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

@@ -1,10 +1,9 @@
 package gov.loc.repository.bagit.creator;
 
-import java.io.File;
 import java.io.IOException;
+import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 
@@ -37,24 +36,26 @@ public class BagCreator {
    * @throws IOException if there is a problem writing or moving file(s)
    * @return a {@link Bag} object representing the newly created bagit bag
    */
-  public static Bag bagInPlace(File root, SupportedAlgorithm algorithm, boolean includeHidden) throws NoSuchAlgorithmException, IOException{
+  public static Bag bagInPlace(Path root, SupportedAlgorithm algorithm, boolean includeHidden) throws NoSuchAlgorithmException, IOException{
     Bag bag = new Bag(new Version(0, 97));
     bag.setRootDir(root);
     logger.info("Creating a bag with version: [{}] in directory: [{}]", bag.getVersion(), root);
 
-    File[] files = root.listFiles();
-    File dataDir = new File(root, "data");
-    if(!dataDir.exists() && !dataDir.mkdir()){
-      throw new IOException("Unable to make " + dataDir);
-    }
 
-    moveFilesToDataDir(files, dataDir);
+    Path dataDir = root.resolve("data");
+    Files.createDirectory(dataDir);
+    DirectoryStream<Path> directoryStream = Files.newDirectoryStream(root);
+    for(Path path : directoryStream){
+      if(!path.equals(dataDir) && !Files.isHidden(path) || includeHidden){
+        Files.move(path, dataDir.resolve(path.getFileName()));
+      }
+    }
 
     logger.info("Creating payload manifest");
     Manifest manifest = new Manifest(algorithm);
     MessageDigest messageDigest = MessageDigest.getInstance(algorithm.getMessageDigestName());
     AddPayloadToBagManifestVistor visitor = new AddPayloadToBagManifestVistor(manifest, messageDigest, includeHidden);
-    Files.walkFileTree(Paths.get(dataDir.toURI()), visitor);
+    Files.walkFileTree(dataDir, visitor);
 
     bag.getPayLoadManifests().add(manifest);
     BagWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), root);
@@ -64,17 +65,6 @@ public static Bag bagInPlace(File root, SupportedAlgorithm algorithm, boolean in
     return bag;
   }
 
-  protected static void moveFilesToDataDir(File[] files, File dataDir) throws IOException{
-    if(files != null){
-      logger.info("Moving files to [{}]", dataDir);
-      for(File file : files){
-        Path dest = Paths.get(dataDir.getPath(), file.getName());
-        logger.debug("Moving [{}] to [{}]", file, dest);
-        Files.move(Paths.get(file.toURI()), dest);
-      }
-    }
-  }
-  
   /**
    * Creates a basic(only required elements) .bagit bag in place.
    * This creates files and directories, thus if an error is thrown during operation it may leave the filesystem 
@@ -87,21 +77,19 @@ protected static void moveFilesToDataDir(File[] files, File dataDir) throws IOEx
    * @throws IOException if there is a problem writing files or .bagit directory
    */
   @Incubating
-  public static Bag createDotBagit(File root, SupportedAlgorithm algorithm, boolean includeHidden) throws NoSuchAlgorithmException, IOException{
+  public static Bag createDotBagit(Path root, SupportedAlgorithm algorithm, boolean includeHidden) throws NoSuchAlgorithmException, IOException{
     Bag bag = new Bag(new Version(0, 98));
     bag.setRootDir(root);
     logger.info("Creating a bag with version: [{}] in directory: [{}]", bag.getVersion(), root);
 
-    File dotbagitDir = new File(root, ".bagit");
-    if(!dotbagitDir.mkdir()){
-      throw new IOException("Was unable to create " + dotbagitDir);
-    }
+    Path dotbagitDir = root.resolve(".bagit");
+    Files.createDirectories(dotbagitDir);
 
     logger.info("Creating payload manifest");
     Manifest manifest = new Manifest(algorithm);
     MessageDigest messageDigest = MessageDigest.getInstance(algorithm.getMessageDigestName());
     AddPayloadToBagManifestVistor visitor = new AddPayloadToBagManifestVistor(manifest, messageDigest, includeHidden);
-    Files.walkFileTree(Paths.get(root.toURI()), visitor);
+    Files.walkFileTree(root, visitor);
 
     bag.getPayLoadManifests().add(manifest);
     BagWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), dotbagitDir);

src/main/java/gov/loc/repository/bagit/domain/Bag.java

@@ -1,7 +1,7 @@
 package gov.loc.repository.bagit.domain;
 
-import java.io.File;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -33,7 +33,7 @@ public class Bag {
   private List<Pair<String, String>> metadata = new ArrayList<>();
 
   //the current location of the bag on the filesystem
-  private File rootDir;
+  private Path rootDir;
 
   public Bag(){
   }
@@ -142,11 +142,11 @@ public boolean equals(Object obj) {
         Objects.equals(this.metadata, other.getMetadata());
   }
 
-  public File getRootDir() {
+  public Path getRootDir() {
     return rootDir;
   }
 
-  public void setRootDir(File rootDir) {
+  public void setRootDir(Path rootDir) {
     this.rootDir = rootDir;
   }
 

src/main/java/gov/loc/repository/bagit/domain/Manifest.java

@@ -1,7 +1,7 @@
 
 package gov.loc.repository.bagit.domain;
 
-import java.io.File;
+import java.nio.file.Path;
 import java.util.HashMap;
 
 import gov.loc.repository.bagit.hash.SupportedAlgorithm;
@@ -11,17 +11,17 @@
  */
 public class Manifest {
   private final SupportedAlgorithm algorithm;
-  private HashMap<File, String> fileToChecksumMap = new HashMap<>();
+  private HashMap<Path, String> fileToChecksumMap = new HashMap<>();
 
   public Manifest(SupportedAlgorithm algorithm){
     this.algorithm = algorithm;
   }
 
-  public HashMap<File, String> getFileToChecksumMap() {
+  public HashMap<Path, String> getFileToChecksumMap() {
     return fileToChecksumMap;
   }
 
-  public void setFileToChecksumMap(HashMap<File, String> fileToChecksumMap) {
+  public void setFileToChecksumMap(HashMap<Path, String> fileToChecksumMap) {
     this.fileToChecksumMap = fileToChecksumMap;
   }
 

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

@@ -1,12 +1,11 @@
 package gov.loc.repository.bagit.reader;
 
 import java.io.BufferedReader;
-import java.io.File;
-import java.io.FilenameFilter;
 import java.io.IOException;
 import java.net.URL;
+import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
-import java.nio.file.Paths;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -48,22 +47,22 @@ public BagReader(BagitAlgorithmNameToSupportedAlgorithmMapping nameMapping){
    * @return a {@link Bag} object representing a bag on the filesystem
    * @throws UnparsableVersionException If there is a problem parsing the bagit version
    */
-  public Bag read(File rootDir) throws IOException, UnparsableVersionException{
-    File bagitDir = new File(rootDir, ".bagit");
-    if(!bagitDir.exists()){
+  public Bag read(Path rootDir) throws IOException, UnparsableVersionException{
+    Path bagitDir = rootDir.resolve(".bagit");
+    if(!Files.exists(bagitDir)){
       bagitDir = rootDir;
     }
 
-    File bagitFile = new File(bagitDir, "bagit.txt");
+    Path bagitFile = bagitDir.resolve("bagit.txt");
     Bag bag = readBagitTextFile(bagitFile, new Bag());
     bag.setRootDir(rootDir);
 
     bag = readAllManifests(bagitDir, bag);
 
     bag = readBagMetadata(bagitDir, bag);
 
-    File fetchFile = new File(bagitDir, "fetch.txt");
-    if(fetchFile.exists()){
+    Path fetchFile = bagitDir.resolve("fetch.txt");
+    if(Files.exists(fetchFile)){
       bag = readFetch(fetchFile, bag);
     }
 
@@ -79,7 +78,7 @@ public Bag read(File rootDir) throws IOException, UnparsableVersionException{
    * @throws IOException if there is a problem reading a file
    * @throws UnparsableVersionException if there is a problem parsing the bagit version number
    */
-  public Bag readBagitTextFile(File bagitFile, Bag bag) throws IOException, UnparsableVersionException{
+  public Bag readBagitTextFile(Path bagitFile, Bag bag) throws IOException, UnparsableVersionException{
     logger.debug("Reading bagit.txt file");
     List<Pair<String, String>> pairs = readKeyValuesFromFile(bagitFile, ":");
 
@@ -123,34 +122,33 @@ protected Version parseVersion(String version) throws UnparsableVersionException
    * @return a new bag that contains all the manifest(s) information
    * @throws IOException if there is a problem reading a file
    */
-  public Bag readAllManifests(File rootDir, Bag bag) throws IOException{
+  public Bag readAllManifests(Path rootDir, Bag bag) throws IOException{
     logger.info("Attempting to find and read manifests");
     Bag newBag = new Bag(bag);
-    File[] files = getAllManifestFiles(rootDir);
+    DirectoryStream<Path> manifests = getAllManifestFiles(rootDir);
 
-    for(File file : files){
-      if(file.getName().startsWith("tag")){
-        logger.debug("Found tag manifest [{}]", file);
-        newBag.getTagManifests().add(readManifest(file, bag.getRootDir()));
+    for (Path path : manifests){
+      if(path.getFileName().toString().startsWith("tagmanifest-")){
+        logger.debug("Found tag manifest [{}]", path);
+        newBag.getTagManifests().add(readManifest(path, bag.getRootDir()));
       }
-      else if(file.getName().startsWith("manifest")){
-        logger.debug("Found payload manifest [{}]", file);
-        newBag.getPayLoadManifests().add(readManifest(file, bag.getRootDir()));
+      else if(path.getFileName().toString().startsWith("manifest-")){
+        logger.debug("Found payload manifest [{}]", path);
+        newBag.getPayLoadManifests().add(readManifest(path, bag.getRootDir()));
       }
     }
 
     return newBag;
   }
 
-  protected File[] getAllManifestFiles(File rootDir){
-    File[] files = rootDir.listFiles(new FilenameFilter() {
-      @Override
-      public boolean accept(File dir, String name) {
-        return name.matches("(tag)?manifest\\-.*\\.txt");
+  protected DirectoryStream<Path> getAllManifestFiles(Path rootDir) throws IOException{
+    DirectoryStream.Filter<Path> filter = new DirectoryStream.Filter<Path>() {
+      public boolean accept(Path file) throws IOException {
+        return file.getFileName().toString().startsWith("tagmanifest-") || file.getFileName().toString().startsWith("manifest-");
       }
-    });
+    };
 
-    return files == null? new File[]{} : files;
+    return Files.newDirectoryStream(rootDir, filter);
   }
 
   /**
@@ -160,27 +158,27 @@ public boolean accept(File dir, String name) {
    * @return the converted manifest object from the file
    * @throws IOException if there is a problem reading a file
    */
-  public Manifest readManifest(File manifestFile, File bagRootDir) throws IOException{
+  public Manifest readManifest(Path manifestFile, Path bagRootDir) throws IOException{
     logger.debug("Reading manifest [{}]", manifestFile);
-    String alg = manifestFile.getName().split("[-\\.]")[1];
+    String alg = manifestFile.getFileName().toString().split("[-\\.]")[1];
     SupportedAlgorithm algorithm = nameMapping.getMessageDigestName(alg);
 
     Manifest manifest = new Manifest(algorithm);
 
-    HashMap<File, String> filetToChecksumMap = readChecksumFileMap(manifestFile, bagRootDir);
+    HashMap<Path, String> filetToChecksumMap = readChecksumFileMap(manifestFile, bagRootDir);
     manifest.setFileToChecksumMap(filetToChecksumMap);
 
     return manifest;
   }
 
-  protected HashMap<File, String> readChecksumFileMap(File manifestFile, File bagRootDir) throws IOException{
-    HashMap<File, String> map = new HashMap<>();
-    BufferedReader br = Files.newBufferedReader(Paths.get(manifestFile.toURI()));
+  protected HashMap<Path, String> readChecksumFileMap(Path manifestFile, Path bagRootDir) throws IOException{
+    HashMap<Path, String> map = new HashMap<>();
+    BufferedReader br = Files.newBufferedReader(manifestFile);
 
     String line = br.readLine();
     while(line != null){
       String[] parts = line.split("\\s+", 2);
-      File file = new File(bagRootDir, parts[1]);
+      Path file = bagRootDir.resolve(parts[1]);
       logger.debug("Read checksum [{}] and file [{}] from manifest [{}]", parts[0], file, manifestFile);
       map.put(file, parts[0]);
       line = br.readLine();
@@ -197,18 +195,18 @@ protected HashMap<File, String> readChecksumFileMap(File manifestFile, File bagR
    * @return a new bag that contains the bag-info.txt (metadata) information
    * @throws IOException if there is a problem reading a file
    */
-  public Bag readBagMetadata(File rootDir, Bag bag) throws IOException{
+  public Bag readBagMetadata(Path rootDir, Bag bag) throws IOException{
     logger.info("Attempting to read bag metadata file");
     Bag newBag = new Bag(bag);
     List<Pair<String, String>> metadata = new ArrayList<>();
 
-    File bagInfoFile = new File(rootDir, "bag-info.txt");
-    if(bagInfoFile.exists()){
+    Path bagInfoFile = rootDir.resolve("bag-info.txt");
+    if(Files.exists(bagInfoFile)){
       logger.debug("Found [{}] file", bagInfoFile);
       metadata = readKeyValuesFromFile(bagInfoFile, ":");
     }
-    File packageInfoFile = new File(rootDir, "package-info.txt"); //onlu exists in versions 0.93 - 0.95
-    if(packageInfoFile.exists()){
+    Path packageInfoFile = rootDir.resolve("package-info.txt"); //onlu exists in versions 0.93 - 0.95
+    if(Files.exists(packageInfoFile)){
       logger.debug("Found [{}] file", packageInfoFile);
       metadata = readKeyValuesFromFile(packageInfoFile, ":");
     }
@@ -226,10 +224,10 @@ public Bag readBagMetadata(File rootDir, Bag bag) throws IOException{
    * @return a new bag that contains a list of items to fetch
    * @throws IOException if there is a problem reading a file
    */
-  public Bag readFetch(File fetchFile, Bag bag) throws IOException{
+  public Bag readFetch(Path fetchFile, Bag bag) throws IOException{
     logger.info("Attempting to read [{}]", fetchFile);
     Bag newBag = new Bag(bag);
-    BufferedReader br = Files.newBufferedReader(Paths.get(fetchFile.toURI()));
+    BufferedReader br = Files.newBufferedReader(fetchFile);
 
     String line = br.readLine();
     while(line != null){
@@ -247,9 +245,9 @@ public Bag readFetch(File fetchFile, Bag bag) throws IOException{
     return newBag;
   }
 
-  protected static List<Pair<String, String>> readKeyValuesFromFile(File file, String splitRegex) throws IOException{
+  protected static List<Pair<String, String>> readKeyValuesFromFile(Path file, String splitRegex) throws IOException{
     List<Pair<String, String>> keyValues = new ArrayList<>();
-    BufferedReader br = Files.newBufferedReader(Paths.get(file.toURI()));
+    BufferedReader br = Files.newBufferedReader(file);
 
     String line = br.readLine();
     while(line != null){

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

@@ -1,25 +1,26 @@
 package gov.loc.repository.bagit.tasks;
 
-import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
 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.
  */
 public class CheckIfFileExistsTask implements Runnable {
-  private final File file;
+  private final Path file;
   private final StringBuilder messageBuilder;
   private final CountDownLatch latch;
 
-  public CheckIfFileExistsTask(File file, StringBuilder messageBuilder, CountDownLatch latch) {
+  public CheckIfFileExistsTask(Path file, StringBuilder messageBuilder, CountDownLatch latch) {
     this.file = file;
     this.messageBuilder = messageBuilder;
     this.latch = latch;
   }
 
   @Override
   public void run() {
-    if(!file.exists()){
+    if(!Files.exists(file)){
       messageBuilder.append("Manifest lists file [").append(file).append("] but it does not exist").append(System.lineSeparator());
     }
     latch.countDown();