as per the proposed spec, allow for payload-oxum to be in bagit.txt

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

@@ -18,6 +18,7 @@
 import gov.loc.repository.bagit.domain.Version;
 import gov.loc.repository.bagit.hash.Hasher;
 import gov.loc.repository.bagit.hash.SupportedAlgorithm;
+import gov.loc.repository.bagit.util.PathUtils;
 import gov.loc.repository.bagit.writer.BagitFileWriter;
 import gov.loc.repository.bagit.writer.ManifestWriter;
 
@@ -26,6 +27,8 @@
  */
 public final class BagCreator {
   private static final Logger logger = LoggerFactory.getLogger(BagCreator.class);
+  private static final int LATEST_MAJOR_VERSION = 0;
+  private static final int LATEST_MINOR_VERSION = 97;
 
   private BagCreator(){}
 
@@ -42,11 +45,11 @@ private BagCreator(){}
    * @return a {@link Bag} object representing the newly created bagit bag
    */
   public static Bag bagInPlace(final Path root, final Collection<SupportedAlgorithm> algorithms, final boolean includeHidden) throws NoSuchAlgorithmException, IOException{
-    final Bag bag = new Bag(new Version(0, 97));
+    final Bag bag = new Bag(new Version(LATEST_MAJOR_VERSION, LATEST_MINOR_VERSION));
     bag.setRootDir(root);
     logger.info("Creating a bag with version: [{}] in directory: [{}]", bag.getVersion(), root);
 
-    final Path dataDir = root.resolve("data");
+    final Path dataDir = PathUtils.getDataDir(bag);
     Files.createDirectory(dataDir);
     final DirectoryStream<Path> directoryStream = Files.newDirectoryStream(root);
     for(final Path path : directoryStream){
@@ -61,7 +64,7 @@ public static Bag bagInPlace(final Path root, final Collection<SupportedAlgorith
     Files.walkFileTree(dataDir, payloadVisitor);
 
     bag.getPayLoadManifests().addAll(payloadFilesMap.keySet());
-    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), root);
+    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), null, null, root);
     ManifestWriter.writePayloadManifests(bag.getPayLoadManifests(), root, root, bag.getFileEncoding());
 
     logger.info("Creating tag manifest(s)");
@@ -102,7 +105,7 @@ public static Bag createDotBagit(final Path root, final Collection<SupportedAlgo
     Files.walkFileTree(root, visitor);
 
     bag.getPayLoadManifests().addAll(map.keySet());
-    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), dotbagitDir);
+    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), null, null, dotbagitDir);
     ManifestWriter.writePayloadManifests(bag.getPayLoadManifests(), dotbagitDir, root, bag.getFileEncoding());
 
     logger.info("Creating tag manifest(s)");

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

@@ -66,50 +66,6 @@ public Bag(final Bag bag){
     this.rootDir = bag.getRootDir();
   }
 
-  public Version getVersion(){
-    return version;
-  }
-
-  public Set<Manifest> getPayLoadManifests() {
-    return payLoadManifests;
-  }
-
-  public void setPayLoadManifests(final Set<Manifest> payLoadManifests) {
-    this.payLoadManifests = payLoadManifests;
-  }
-
-  public Set<Manifest> getTagManifests() {
-    return tagManifests;
-  }
-
-  public void setTagManifests(final Set<Manifest> tagManifests) {
-    this.tagManifests = tagManifests;
-  }
-
-  public List<FetchItem> getItemsToFetch() {
-    return itemsToFetch;
-  }
-
-  public void setItemsToFetch(final List<FetchItem> itemsToFetch) {
-    this.itemsToFetch = itemsToFetch;
-  }
-
-  public List<SimpleImmutableEntry<String, String>> getMetadata() {
-    return metadata;
-  }
-
-  public void setMetadata(final List<SimpleImmutableEntry<String, String>> metadata) {
-    this.metadata = metadata;
-  }
-
-  public Charset getFileEncoding() {
-    return fileEncoding;
-  }
-
-  public void setFileEncoding(final Charset fileEncoding) {
-    this.fileEncoding = fileEncoding;
-  }
-
   @Override
   public String toString() {
     final StringBuilder sb = new StringBuilder(95);
@@ -155,6 +111,50 @@ public boolean equals(final Object obj) {
         Objects.equals(this.itemsToFetch, other.getItemsToFetch()) &&
         Objects.equals(this.metadata, other.getMetadata());
   }
+
+  public Version getVersion(){
+    return version;
+  }
+
+  public Set<Manifest> getPayLoadManifests() {
+    return payLoadManifests;
+  }
+
+  public void setPayLoadManifests(final Set<Manifest> payLoadManifests) {
+    this.payLoadManifests = payLoadManifests;
+  }
+
+  public Set<Manifest> getTagManifests() {
+    return tagManifests;
+  }
+
+  public void setTagManifests(final Set<Manifest> tagManifests) {
+    this.tagManifests = tagManifests;
+  }
+
+  public List<FetchItem> getItemsToFetch() {
+    return itemsToFetch;
+  }
+
+  public void setItemsToFetch(final List<FetchItem> itemsToFetch) {
+    this.itemsToFetch = itemsToFetch;
+  }
+
+  public List<SimpleImmutableEntry<String, String>> getMetadata() {
+    return metadata;
+  }
+
+  public void setMetadata(final List<SimpleImmutableEntry<String, String>> metadata) {
+    this.metadata = metadata;
+  }
+
+  public Charset getFileEncoding() {
+    return fileEncoding;
+  }
+
+  public void setFileEncoding(final Charset fileEncoding) {
+    this.fileEncoding = fileEncoding;
+  }
 
   public Path getRootDir() {
     return rootDir;
@@ -167,4 +167,5 @@ public void setRootDir(final Path rootDir) {
   public void setVersion(final Version version) {
     this.version = version;
   }
+
 }

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

@@ -5,6 +5,7 @@
 /**
  * The {@link Bag} object should contain the Payload-Oxum metatdata key value pair, 
  * this class represents the error when trying to calculate the payload-oxum and it doesn't exist on the bag object.
+ * Or if the payload-byte-count and payload-file-count don't exist for versions 1.0+
  */
 public class PayloadOxumDoesNotExistException extends RuntimeException {
   private static final long serialVersionUID = 1L;

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

@@ -0,0 +1,35 @@
+package gov.loc.repository.bagit.reader;
+
+import java.nio.charset.Charset;
+
+import gov.loc.repository.bagit.domain.Version;
+
+/**
+ * A simple data object for passing around all the bagit.txt file values
+ */
+public class BagitFileValues {
+  private final Version version;
+  private final Charset encoding;
+  private final Long payloadByteCount;
+  private final Long payloadFileCount;
+
+  public BagitFileValues(final Version version, final Charset encoding, final Long payloadByteCount, final Long payloadFileCount){
+    this.version = version;
+    this.encoding = encoding;
+    this.payloadByteCount = payloadByteCount;
+    this.payloadFileCount = payloadFileCount;
+  }
+
+  public Version getVersion() {
+    return version;
+  }
+  public Charset getEncoding() {
+    return encoding;
+  }
+  public Long getPayloadByteCount() {
+    return payloadByteCount;
+  }
+  public Long getPayloadFileCount() {
+    return payloadFileCount;
+  }
+}

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

@@ -4,8 +4,8 @@
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
-import java.util.List;
 import java.util.AbstractMap.SimpleImmutableEntry;
+import java.util.List;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -32,23 +32,67 @@ private BagitTextFileReader(){
    * @throws InvalidBagMetadataException if the bagit.txt file does not conform to the bagit spec
    */
   public static SimpleImmutableEntry<Version, Charset> readBagitTextFile(final Path bagitFile) throws IOException, UnparsableVersionException, InvalidBagMetadataException{
+    final BagitFileValues values = parseValues(bagitFile);
+
+    return new SimpleImmutableEntry<Version, Charset>(values.getVersion(), values.getEncoding());
+  }
+
+  /**
+   * Read the Payload-Byte-Count and Payload-File-Count from the bagit.txt file
+   * @since bagic specification 1.0
+   * 
+   * @param bagitFile the bagit.txt file to read
+   * 
+   * @return the payload byte count, payload file count (in that order)
+   * 
+   * @throws IOException if there is a problem reading a file
+   * @throws UnparsableVersionException if there is a problem parsing the bagit version number
+   * @throws InvalidBagMetadataException if the bagit.txt file does not conform to the bagit spec
+   */
+  public static SimpleImmutableEntry<Long, Long> readPayloadByteAndFileCount(final Path bagitFile) throws UnparsableVersionException, IOException, InvalidBagMetadataException{
+    final BagitFileValues values = parseValues(bagitFile);
+
+    return new SimpleImmutableEntry<Long, Long>(values.getPayloadByteCount(), values.getPayloadFileCount());
+  }
+
+  /**
+   * Read version, file encoding, and (possibly) payload byte and file count
+   * 
+   * @param bagitFile the bagit.txt file to read
+   * 
+   * @return all the possible bagit.txt file field values
+   * 
+   * @throws IOException if there is a problem reading a file
+   * @throws UnparsableVersionException if there is a problem parsing the bagit version number
+   * @throws InvalidBagMetadataException if the bagit.txt file does not conform to the bagit spec
+   */
+  public static BagitFileValues parseValues(final Path bagitFile) throws UnparsableVersionException, IOException, InvalidBagMetadataException{
     logger.debug("Reading [{}] file", bagitFile);
     final List<SimpleImmutableEntry<String, String>> pairs = KeyValueReader.readKeyValuesFromFile(bagitFile, ":", StandardCharsets.UTF_8);
 
-    String version = "";
+
+    Version version = null;
     Charset encoding = StandardCharsets.UTF_8;
+    Long payloadByteCount = null;
+    Long payloadFileCount = null;
+
     for(final SimpleImmutableEntry<String, String> pair : pairs){
       if("BagIt-Version".equals(pair.getKey())){
-        version = pair.getValue();
-        logger.debug("BagIt-Version is [{}]", version);
+        version = parseVersion(pair.getValue());
       }
       if("Tag-File-Character-Encoding".equals(pair.getKey())){
         encoding = Charset.forName(pair.getValue());
-        logger.debug("Tag-File-Character-Encoding is [{}]", encoding);
       }
+      if("Payload-Byte-Count".equals(pair.getKey())){ //assume version is 1.0+
+        payloadByteCount = Long.valueOf(pair.getValue());
+      }
+      if("Payload-File-Count".equals(pair.getKey())){ //assume version is 1.0+
+        payloadFileCount = Long.valueOf(pair.getValue());
+      }
+      logger.debug("[{}] is [{}]", pair.getKey(), pair.getValue());
     }
 
-    return new SimpleImmutableEntry<Version, Charset>(parseVersion(version), encoding);
+    return new BagitFileValues(version, encoding, payloadByteCount, payloadFileCount);
   }
 
   /*

src/main/java/gov/loc/repository/bagit/util/PathUtils.java

@@ -67,9 +67,6 @@ public static boolean isHidden(final Path path) throws IOException{
     return Files.isHidden(path);
   }
 
-  /*
-   * Get the directory that contains the payload files.
-   */
   /**
    * With bagit version 2.0 (.bagit)
    * payload files are no longer in the "data" directory. This method accounts for this

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

@@ -18,13 +18,15 @@
 import gov.loc.repository.bagit.domain.Manifest;
 import gov.loc.repository.bagit.exceptions.CorruptChecksumException;
 import gov.loc.repository.bagit.exceptions.FileNotInPayloadDirectoryException;
+import gov.loc.repository.bagit.exceptions.InvalidBagMetadataException;
 import gov.loc.repository.bagit.exceptions.InvalidBagitFileFormatException;
 import gov.loc.repository.bagit.exceptions.InvalidPayloadOxumException;
 import gov.loc.repository.bagit.exceptions.MaliciousPathException;
 import gov.loc.repository.bagit.exceptions.MissingBagitFileException;
 import gov.loc.repository.bagit.exceptions.MissingPayloadDirectoryException;
 import gov.loc.repository.bagit.exceptions.MissingPayloadManifestException;
 import gov.loc.repository.bagit.exceptions.PayloadOxumDoesNotExistException;
+import gov.loc.repository.bagit.exceptions.UnparsableVersionException;
 import gov.loc.repository.bagit.exceptions.UnsupportedAlgorithmException;
 import gov.loc.repository.bagit.exceptions.VerificationException;
 import gov.loc.repository.bagit.hash.BagitAlgorithmNameToSupportedAlgorithmMapping;
@@ -61,8 +63,12 @@ public BagVerifier(final ExecutorService executor, final BagitAlgorithmNameToSup
    * 
    * @param bag the {@link Bag} object you wish to check
    * @return true if the bag can be quickly verified
+   * 
+   * @throws IOException if there is a problem reading a file
+   * @throws UnparsableVersionException if there is a problem parsing the bagit version number
+   * @throws InvalidBagMetadataException if the bagit.txt file does not conform to the bagit spec
    */
-  public boolean canQuickVerify(final Bag bag){
+  public boolean canQuickVerify(final Bag bag) throws UnparsableVersionException, IOException, InvalidBagMetadataException{
     return QuickVerifier.canQuickVerify(bag);
   }
 
@@ -72,13 +78,15 @@ public boolean canQuickVerify(final Bag bag){
    * @param bag the bag to verify by payload-oxum
    * @param ignoreHiddenFiles ignore hidden files found in payload directory
    * 
-   * @throws IOException if there is an error reading a file
    * @throws InvalidPayloadOxumException if either the total bytes or the number of files 
    * calculated for the payload directory of the bag is different than the supplied values
+   * @throws IOException if there is a problem reading a file
+   * @throws UnparsableVersionException if there is a problem parsing the bagit version number
+   * @throws InvalidBagMetadataException if the bagit.txt file does not conform to the bagit spec
    * @throws PayloadOxumDoesNotExistException if the bag does not contain a payload-oxum.
    * To check, run {@link BagVerifier#canQuickVerify}
    */
-  public void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles) throws IOException, InvalidPayloadOxumException{
+  public void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles) throws IOException, InvalidPayloadOxumException, UnparsableVersionException, InvalidBagMetadataException{
     QuickVerifier.quicklyVerify(bag, ignoreHiddenFiles);
   }
 
@@ -150,7 +158,7 @@ void checkHashes(final Manifest manifest) throws CorruptChecksumException, Inter
    * <li>every element is present
    * <li>every file in the payload manifest(s) are present
    * <li>every file in the tag manifest(s) are present. Tag files not listed in a tag manifest may be present.
-   * <li>every file in the data directory must be listed in at least one payload manifest
+   * <li>every file in the payload directory must be listed in at least one payload manifest
    * <li>each element must comply with the bagit spec
    * </ul>
    * 

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

@@ -33,7 +33,7 @@ private MandatoryVerifier(){
   }
 
   /**
-   * make sure all the fetch items exist in the data directory
+   * make sure all the fetch items exist in the payload directory
    * 
    * @param items the items that needed to be fetched for the bag to be complete
    * @param bagDir the root directory of the bag
@@ -76,8 +76,8 @@ public static void checkBagitFileExists(final Path rootDir, final Version versio
    * @throws MissingPayloadDirectoryException if the bag does not contain the payload directory
    */
   public static void checkPayloadDirectoryExists(final Bag bag) throws MissingPayloadDirectoryException{
-    logger.info("Checking if special payload directory exists (only for version 0.97 and earlier)");
     final Path dataDir = PathUtils.getDataDir(bag);
+    logger.info("Checking if payload directory [{}] exists", dataDir);
 
     if(!Files.exists(dataDir)){
       throw new MissingPayloadDirectoryException("File [" + dataDir + "] should exist but it doesn't");