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

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

@@ -35,6 +35,13 @@ public final class Bag {
   //the current location of the bag on the filesystem
   private Path rootDir;
 
+  private Long payloadFileCount;
+
+  private Long payloadByteCount;
+
+  //TODO
+//  add payload file and byte count here and to reader. Use in verifier and writer
+
   /**
    * empty bag with an invalid version
    */
@@ -167,4 +174,20 @@ public void setRootDir(final Path rootDir) {
   public void setVersion(final Version version) {
     this.version = version;
   }
+
+  public Long getPayloadFileCount() {
+    return payloadFileCount;
+  }
+
+  public void setPayloadFileCount(final Long payloadFileCount) {
+    this.payloadFileCount = payloadFileCount;
+  }
+
+  public Long getPayloadByteCount() {
+    return payloadByteCount;
+  }
+
+  public void setPayloadByteCount(final Long payloadByteCount) {
+    this.payloadByteCount = payloadByteCount;
+  }
 }

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/BagReader.java

@@ -1,13 +1,10 @@
 package gov.loc.repository.bagit.reader;
 
 import java.io.IOException;
-import java.nio.charset.Charset;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.AbstractMap.SimpleImmutableEntry;
 
 import gov.loc.repository.bagit.domain.Bag;
-import gov.loc.repository.bagit.domain.Version;
 import gov.loc.repository.bagit.exceptions.InvalidBagMetadataException;
 import gov.loc.repository.bagit.exceptions.InvalidBagitFileFormatException;
 import gov.loc.repository.bagit.exceptions.MaliciousPathException;
@@ -53,10 +50,7 @@ public Bag read(final Path rootDir) throws IOException, UnparsableVersionExcepti
     }
     bag.setRootDir(rootDir);
 
-    final Path bagitFile = bagitDir.resolve("bagit.txt");
-    final SimpleImmutableEntry<Version, Charset> bagitInfo = BagitTextFileReader.readBagitTextFile(bagitFile);
-    bag.setVersion(bagitInfo.getKey());
-    bag.setFileEncoding(bagitInfo.getValue());
+    BagitTextFileReader.readBagitTextFile(bag);
 
     ManifestReader.readAllManifests(nameMapping, bagitDir, bag);
 

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

@@ -3,13 +3,15 @@
 import java.io.IOException;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 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;
 
+import gov.loc.repository.bagit.domain.Bag;
 import gov.loc.repository.bagit.domain.Version;
 import gov.loc.repository.bagit.exceptions.InvalidBagMetadataException;
 import gov.loc.repository.bagit.exceptions.UnparsableVersionException;
@@ -32,23 +34,63 @@ 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.version, values.encoding);
+  }
+
+  /**
+   * Read the bagit.txt file and get the version and encoding. In version 1.0+ also check for
+   * payload-byte-count and payload-file-count
+   * 
+   * @param bag the to read that contains the bagit.txt file and set the values in the bag
+   * 
+   * @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 void readBagitTextFile(final Bag bag) throws IOException, UnparsableVersionException, InvalidBagMetadataException{
+    Path bagitDir = bag.getRootDir().resolve(".bagit");
+    if(!Files.exists(bagitDir)){
+      bagitDir = bag.getRootDir();
+    }
+    final BagitFileValues values = parseValues(bagitDir.resolve("bagit.txt"));
+
+    bag.setVersion(values.version);
+    bag.setFileEncoding(values.encoding);
+    bag.setPayloadByteCount(values.payloadByteCount);
+    bag.setPayloadFileCount(values.payloadFileCount);
+  }
+
+  private 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);
+    final BagitFileValues values = new BagitFileValues();
 
     String version = "";
     Charset encoding = StandardCharsets.UTF_8;
     for(final SimpleImmutableEntry<String, String> pair : pairs){
       if("BagIt-Version".equals(pair.getKey())){
         version = pair.getValue();
         logger.debug("BagIt-Version is [{}]", version);
+        values.version = parseVersion(version);
       }
       if("Tag-File-Character-Encoding".equals(pair.getKey())){
         encoding = Charset.forName(pair.getValue());
         logger.debug("Tag-File-Character-Encoding is [{}]", encoding);
+        values.encoding = encoding;
+      }
+      if("Payload-Byte-Count".equals(pair.getKey())){ //assume version is 1.0+
+        logger.debug("Payload-Byte-Count is [{}]", pair.getKey());
+        values.payloadByteCount = Long.valueOf(pair.getValue());
+      }
+      if("Payload-File-Count".equals(pair.getKey())){ //assume version is 1.0+
+        logger.debug("Payload-File-Count is [{}]", pair.getKey());
+        values.payloadFileCount = Long.valueOf(pair.getValue());
       }
     }
 
-    return new SimpleImmutableEntry<Version, Charset>(parseVersion(version), encoding);
+    return values;
   }
 
   /*
@@ -65,4 +107,12 @@ static Version parseVersion(final String version) throws UnparsableVersionExcept
 
     return new Version(major, minor);
   }
+
+  @SuppressWarnings({"PMD.BeanMembersShouldSerialize"})
+  private static class BagitFileValues{
+    public Version version;
+    public Charset encoding;
+    public Long payloadByteCount;
+    public Long payloadFileCount;
+  }
 }

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

@@ -33,9 +33,21 @@ private QuickVerifier(){
    * @return true if the bag can be quickly verified
    */
   public static boolean canQuickVerify(final Bag bag){
+    boolean payloadInfoExists = false;
+
+    if(bag.getPayloadByteCount() != null && bag.getPayloadFileCount() != null){
+      logger.debug("Found payload byte and file count, using that instead of payload-oxum");
+      //TODO check if it matches payload-oxum, and if not issue warning?
+      payloadInfoExists = true;
+    }
+
     final String payloadOxum = getPayloadOxum(bag);
-    logger.debug("Found payload-oxum [{}] for bag [{}]", payloadOxum, bag.getRootDir());
-    return payloadOxum != null && payloadOxum.matches(PAYLOAD_OXUM_REGEX) && bag.getItemsToFetch().size() == 0;
+    if(payloadOxum != null && payloadOxum.matches(PAYLOAD_OXUM_REGEX)){
+      logger.debug("Found payload-oxum [{}] for bag [{}]", payloadOxum, bag.getRootDir());
+      payloadInfoExists = true;
+    }
+
+    return payloadInfoExists && bag.getItemsToFetch().size() == 0;
   }
 
   /*
@@ -53,7 +65,7 @@ private static String getPayloadOxum(final Bag bag){
   /**
    * Quickly verify by comparing the number of files and the total number of bytes expected
    * 
-   * @param bag the bag to verify by payload-oxum
+   * @param bag the bag to quickly verify
    * @param ignoreHiddenFiles ignore hidden files found in payload directory
    * 
    * @throws IOException if there is an error reading a file
@@ -63,9 +75,36 @@ private static String getPayloadOxum(final Bag bag){
    * To check, run {@link BagVerifier#canQuickVerify}
    */
   public static void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles) throws IOException, InvalidPayloadOxumException{
+    final SimpleImmutableEntry<Long, Long> byteAndFileCount = getByteAndFileCount(bag);
+
+    final Path payloadDir = PathUtils.getDataDir(bag);
+    final FileCountAndTotalSizeVistor vistor = new FileCountAndTotalSizeVistor(ignoreHiddenFiles);
+    Files.walkFileTree(payloadDir, vistor);
+    logger.info("supplied payload-oxum: [{}.{}], Calculated payload-oxum: [{}.{}], for payload directory [{}]", 
+        byteAndFileCount.getKey(), byteAndFileCount.getValue(), vistor.getTotalSize(), vistor.getCount(), payloadDir);
+
+    if(byteAndFileCount.getKey() != vistor.getTotalSize()){
+      throw new InvalidPayloadOxumException("Invalid total size. Expected " + byteAndFileCount.getKey() + " but calculated " + vistor.getTotalSize());
+    }
+    if(byteAndFileCount.getValue() != vistor.getCount()){
+      throw new InvalidPayloadOxumException("Invalid file count. Expected " + byteAndFileCount.getValue() + " but found " + vistor.getCount() + " files");
+    }
+  }
+
+  /**
+   * get either the payload-oxum values or the payload-byte-count and payload-file-count
+   * 
+   * @param bag the bag to get the payload info from
+   * @return the byte count, the file count
+   */
+  private static SimpleImmutableEntry<Long, Long> getByteAndFileCount(final Bag bag){
+    if(bag.getPayloadByteCount() != null && bag.getPayloadFileCount() != null){
+      return new SimpleImmutableEntry<Long, Long>(bag.getPayloadByteCount(), bag.getPayloadFileCount());
+    }
+
     final String payloadOxum = getPayloadOxum(bag);
     if(payloadOxum == null || !payloadOxum.matches(PAYLOAD_OXUM_REGEX)){
-      throw new PayloadOxumDoesNotExistException("Payload-Oxum does not exist in bag.");
+      throw new PayloadOxumDoesNotExistException("Payload-Oxum or payload-byte-count and payload-file-count does not exist in bag.");
     }
 
     final String[] parts = payloadOxum.split("\\.");
@@ -74,16 +113,6 @@ public static void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles)
     logger.debug("Parsing [{}] for the number of files to find in the payload directory", parts[1]);
     final long numberOfFiles = Long.parseLong(parts[1]);
 
-    final Path payloadDir = PathUtils.getDataDir(bag);
-    final FileCountAndTotalSizeVistor vistor = new FileCountAndTotalSizeVistor(ignoreHiddenFiles);
-    Files.walkFileTree(payloadDir, vistor);
-    logger.info("supplied payload-oxum: [{}], Calculated payload-oxum: [{}.{}], for payload directory [{}]", payloadOxum, vistor.getTotalSize(), vistor.getCount(), payloadDir);
-
-    if(totalSize != vistor.getTotalSize()){
-      throw new InvalidPayloadOxumException("Invalid total size. Expected " + totalSize + "but calculated " + vistor.getTotalSize());
-    }
-    if(numberOfFiles != vistor.getCount()){
-      throw new InvalidPayloadOxumException("Invalid file count. Expected " + numberOfFiles + "but found " + vistor.getCount() + " files");
-    }
+    return new SimpleImmutableEntry<>(totalSize, numberOfFiles);
   }
 }

src/main/java/gov/loc/repository/bagit/writer/BagWriter.java

@@ -43,7 +43,7 @@ public static void write(final Bag bag, final Path outputDir) throws IOException
     final Path bagitDir = PayloadWriter.writeVersionDependentPayloadFiles(bag, outputDir);
 
     logger.debug("writing the bagit.txt file");
-    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), bagitDir);
+    BagitFileWriter.writeBagitFile(bag.getVersion(), bag.getFileEncoding(), bag.getPayloadByteCount(), bag.getPayloadFileCount(), bagitDir);
 
     logger.debug("writing the payload manifest(s)");
     ManifestWriter.writePayloadManifests(bag.getPayLoadManifests(), bagitDir, bag.getRootDir(), bag.getFileEncoding());

src/main/java/gov/loc/repository/bagit/writer/BagitFileWriter.java

@@ -15,6 +15,8 @@
 public final class BagitFileWriter {
   private static final Logger logger = LoggerFactory.getLogger(BagitFileWriter.class);
 
+  private static final Version ONE_DOT_ZERO = new Version(1, 0);
+
   private BagitFileWriter(){
     //intentionally left empty
   }
@@ -29,6 +31,27 @@ private BagitFileWriter(){
    * @throws IOException if there was a problem writing the file
    */
   public static void writeBagitFile(final Version version, final Charset encoding, final Path outputDir) throws IOException{
+    writeBagitFileInternal(version, encoding, null, null, outputDir);
+  }
+
+  /**
+   * Write the bagit.txt file in required UTF-8 encoding for versions 1.0+
+   * 
+   * @param version the version of the bag to write out
+   * @param encoding the encoding of the tag files
+   * @param payloadByteCount the total number of bytes for all files in the payload directory
+   * @param payloadFileCount the total number of files in the payload directory
+   * @param outputDir the root of the bag
+   * 
+   * @throws IOException if there was a problem writing the file
+   */
+  public static void writeBagitFile(final Version version, final Charset encoding, final Long payloadByteCount, 
+      final Long payloadFileCount, final Path outputDir) throws IOException{
+    writeBagitFileInternal(version, encoding, payloadByteCount, payloadFileCount, outputDir);
+  }
+
+  private static void writeBagitFileInternal(final Version version, final Charset encoding, final Long payloadByteCount, 
+      final Long payloadFileCount, final Path outputDir) throws IOException{
     final Path bagitPath = outputDir.resolve("bagit.txt");
     logger.debug("Writing bagit.txt file to [{}]", outputDir);
 
@@ -41,5 +64,13 @@ public static void writeBagitFile(final Version version, final Charset encoding,
     final String secondLine = "Tag-File-Character-Encoding : " + encoding + System.lineSeparator();
     logger.debug("Writing line [{}] to [{}]", secondLine, bagitPath);
     Files.write(bagitPath, secondLine.getBytes(StandardCharsets.UTF_8), StandardOpenOption.WRITE, StandardOpenOption.APPEND);
+
+    if(version.compareTo(ONE_DOT_ZERO) >= 0 && payloadByteCount != null && payloadFileCount != null){ //if it is 1.0 or greater
+      final String thirdLine = "Payload-Byte-Count : " + payloadByteCount + System.lineSeparator();
+      Files.write(bagitPath, thirdLine.getBytes(StandardCharsets.UTF_8), StandardOpenOption.WRITE, StandardOpenOption.APPEND);
+
+      final String fourthLine = "Payload-File-Count : " + payloadFileCount + System.lineSeparator();
+      Files.write(bagitPath, fourthLine.getBytes(StandardCharsets.UTF_8), StandardOpenOption.WRITE, StandardOpenOption.APPEND);
+    }
   }
 }

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

@@ -1,5 +1,6 @@
 package gov.loc.repository.bagit.reader;
 
+import java.io.File;
 import java.lang.reflect.InvocationTargetException;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
@@ -10,6 +11,7 @@
 import org.junit.Test;
 
 import gov.loc.repository.bagit.PrivateConstructorTest;
+import gov.loc.repository.bagit.domain.Bag;
 import gov.loc.repository.bagit.domain.Version;
 import gov.loc.repository.bagit.exceptions.UnparsableVersionException;
 
@@ -32,4 +34,17 @@ public void testReadBagitFile()throws Exception{
     assertEquals(new Version(0, 97), actualBagitInfo.getKey());
     assertEquals(StandardCharsets.UTF_8, actualBagitInfo.getValue());
   }
+
+  @Test
+  public void testReadingPayloadByteAndFileCount() throws Exception{
+    Path passingRootDir = Paths.get(new File("src/test/resources/bags/v1_0/bag").toURI());
+    BagReader reader = new BagReader();
+    Bag bag = reader.read(passingRootDir);
+
+    BagitTextFileReader.readBagitTextFile(bag);
+    assertNotNull(bag.getVersion());
+    assertNotNull(bag.getFileEncoding());
+    assertNotNull(bag.getPayloadByteCount());
+    assertNotNull(bag.getPayloadFileCount());
+  }
 }

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

@@ -36,13 +36,21 @@ public void testCanQuickVerify() throws Exception{
   }
 
   @Test 
-  public void testQuickVerify() throws Exception{
+  public void testQuickVerifyUsingPayloadOxum() throws Exception{
     Path passingRootDir = Paths.get(new File("src/test/resources/bags/v0_94/bag").toURI());
     Bag bag = reader.read(passingRootDir);
 
     QuickVerifier.quicklyVerify(bag, true);
   }
 
+  @Test 
+  public void testQuickVerifyUsingPayloadByteAndFileCount() throws Exception{
+    Path passingRootDir = Paths.get(new File("src/test/resources/bags/v1_0/bag").toURI());
+    Bag bag = reader.read(passingRootDir);
+
+    QuickVerifier.quicklyVerify(bag, true);
+  }
+
   @Test(expected=PayloadOxumDoesNotExistException.class)
   public void testExceptionIsThrownWhenPayloadOxumDoesntExist() throws Exception{
     Bag bag = reader.read(rootDir);

src/test/java/gov/loc/repository/bagit/writer/BagitFileWriterTest.java

@@ -43,4 +43,29 @@ public void testWriteBagitFile() throws Exception{
         Files.getLastModifiedTime(bagit).toMillis() >= originalModified);
     assertEquals(size, Files.size(bagit));
   }
+
+  @Test
+  public void testBagitFileWritesOptionalLines() throws Exception{
+    File rootDir = folder.newFolder();
+    Path rootDirPath = Paths.get(rootDir.toURI());
+    Path bagit = rootDirPath.resolve("bagit.txt");
+
+    assertFalse(Files.exists(bagit));
+    BagitFileWriter.writeBagitFile(new Version(1, 0), StandardCharsets.UTF_8, 5l, 5l, rootDirPath);
+    assertTrue(Files.exists(bagit));
+    assertEquals(4, Files.readAllLines(bagit).size());
+  }
+
+  @Test //should not write payload byte and file count lines for version older than 1.0
+  public void testBagitFileDoesntWritesOptionalLines() throws Exception{
+    File rootDir = folder.newFolder();
+    Path rootDirPath = Paths.get(rootDir.toURI());
+    Path bagit = rootDirPath.resolve("bagit.txt");
+
+    assertFalse(Files.exists(bagit));
+    BagitFileWriter.writeBagitFile(new Version(0, 97), StandardCharsets.UTF_8, 5l, 5l, rootDirPath);
+    assertTrue(Files.exists(bagit));
+    assertEquals(2, Files.readAllLines(bagit).size());
+  }
+
 }