refactor to remove payload oxum fields from Bag domain object

Author: johnscancella

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

@@ -64,7 +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)");
@@ -105,7 +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

@@ -35,10 +35,6 @@ public final class Bag {
   //the current location of the bag on the filesystem
   private Path rootDir;
 
-  private Long payloadFileCount;
-  
-  private Long payloadByteCount;
-  
   /**
    * empty bag with an invalid version
    */
@@ -172,19 +168,4 @@ 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/reader/BagReader.java

@@ -1,10 +1,13 @@
 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;
@@ -50,7 +53,10 @@ public Bag read(final Path rootDir) throws IOException, UnparsableVersionExcepti
     }
     bag.setRootDir(rootDir);
 
-    BagitTextFileReader.readBagitTextFile(bag);
+    final Path bagitFile = bagitDir.resolve("bagit.txt");
+    final SimpleImmutableEntry<Version, Charset> bagitInfo = BagitTextFileReader.readBagitTextFile(bagitFile);
+    bag.setVersion(bagitInfo.getKey());
+    bag.setFileEncoding(bagitInfo.getValue());
 
     ManifestReader.readAllManifests(nameMapping, bagitDir, bag);
 

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

@@ -3,15 +3,13 @@
 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.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;
@@ -36,58 +34,65 @@ private BagitTextFileReader(){
   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);
+    return new SimpleImmutableEntry<Version, Charset>(values.getVersion(), values.getEncoding());
   }
 
   /**
-   * 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
+   * Read the Payload-Byte-Count and Payload-File-Count from the bagit.txt file
+   * @since bagic specification 1.0
    * 
-   * @param bag the to read that contains the bagit.txt file and set the values in the bag
+   * @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 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"));
+  public static SimpleImmutableEntry<Long, Long> readPayloadByteAndFileCount(final Path bagitFile) throws UnparsableVersionException, IOException, InvalidBagMetadataException{
+    final BagitFileValues values = parseValues(bagitFile);
 
-    bag.setVersion(values.version);
-    bag.setFileEncoding(values.encoding);
-    bag.setPayloadByteCount(values.payloadByteCount);
-    bag.setPayloadFileCount(values.payloadFileCount);
+    return new SimpleImmutableEntry<Long, Long>(values.getPayloadByteCount(), values.getPayloadFileCount());
   }
 
-  private static BagitFileValues parseValues(final Path bagitFile) throws UnparsableVersionException, IOException, InvalidBagMetadataException{
+  /**
+   * 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);
-    final BagitFileValues values = new BagitFileValues();
 
-    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();
-        values.version = parseVersion(version);
+        version = parseVersion(pair.getValue());
       }
       if("Tag-File-Character-Encoding".equals(pair.getKey())){
         encoding = Charset.forName(pair.getValue());
-        values.encoding = encoding;
       }
       if("Payload-Byte-Count".equals(pair.getKey())){ //assume version is 1.0+
-        values.payloadByteCount = Long.valueOf(pair.getValue());
+        payloadByteCount = Long.valueOf(pair.getValue());
       }
       if("Payload-File-Count".equals(pair.getKey())){ //assume version is 1.0+
-        values.payloadFileCount = Long.valueOf(pair.getValue());
+        payloadFileCount = Long.valueOf(pair.getValue());
       }
       logger.debug("[{}] is [{}]", pair.getKey(), pair.getValue());
     }
 
-    return values;
+    return new BagitFileValues(version, encoding, payloadByteCount, payloadFileCount);
   }
 
   /*
@@ -104,12 +109,4 @@ 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/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);
   }
 

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

@@ -9,8 +9,12 @@
 import org.slf4j.LoggerFactory;
 
 import gov.loc.repository.bagit.domain.Bag;
+import gov.loc.repository.bagit.exceptions.InvalidBagMetadataException;
 import gov.loc.repository.bagit.exceptions.InvalidPayloadOxumException;
 import gov.loc.repository.bagit.exceptions.PayloadOxumDoesNotExistException;
+import gov.loc.repository.bagit.exceptions.UnparsableVersionException;
+import gov.loc.repository.bagit.reader.BagitFileValues;
+import gov.loc.repository.bagit.reader.BagitTextFileReader;
 import gov.loc.repository.bagit.util.PathUtils;
 
 /**
@@ -32,16 +36,22 @@ private QuickVerifier() {
    * 
    * @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 static boolean canQuickVerify(final Bag bag) {
+  public static boolean canQuickVerify(final Bag bag) throws UnparsableVersionException, IOException, InvalidBagMetadataException {
     boolean payloadInfoExists = false;
     final String payloadOxum = getPayloadOxum(bag);
+    final BagitFileValues bagitValues = BagitTextFileReader.parseValues(bag.getRootDir().resolve("bagit.txt"));
 
-    if (bag.getPayloadByteCount() != null && bag.getPayloadFileCount() != null) {
+    if (bagitValues.getPayloadByteCount() != null && bagitValues.getPayloadFileCount() != null) {
       logger.debug("Found payload byte and file count, using that instead of payload-oxum");
       if(payloadOxum != null){
-        comparePayloadOxumWithByteAndFileCount(payloadOxum, bag.getPayloadByteCount(), bag.getPayloadFileCount());
+        comparePayloadOxumWithByteAndFileCount(payloadOxum, bagitValues.getPayloadByteCount(), bagitValues.getPayloadFileCount());
       }
       payloadInfoExists = true;
     }
@@ -83,23 +93,22 @@ private static void comparePayloadOxumWithByteAndFileCount(final String payloadO
    * Quickly verify by comparing the number of files and the total number of
    * bytes expected
    * 
-   * @param bag
-   *          the bag to quickly verify
-   * @param ignoreHiddenFiles
-   *          ignore hidden files found in payload directory
+   * @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
+   * @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 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 static void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles)
-      throws IOException, InvalidPayloadOxumException {
+      throws IOException, InvalidPayloadOxumException, UnparsableVersionException, InvalidBagMetadataException {
     final SimpleImmutableEntry<Long, Long> byteAndFileCount = getByteAndFileCount(bag);
 
     final Path payloadDir = PathUtils.getDataDir(bag);
@@ -124,11 +133,18 @@ public static void quicklyVerify(final Bag bag, final boolean ignoreHiddenFiles)
    * 
    * @param bag
    *          the bag to get the payload info from
+   *          
    * @return the byte count, the file count
+   * 
+   * @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
    */
-  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());
+  private static SimpleImmutableEntry<Long, Long> getByteAndFileCount(final Bag bag) throws UnparsableVersionException, IOException, InvalidBagMetadataException {
+    final BagitFileValues bagitValues = BagitTextFileReader.parseValues(bag.getRootDir().resolve("bagit.txt"));
+    
+    if (bagitValues.getPayloadByteCount() != null && bagitValues.getPayloadFileCount() != null) {
+      return new SimpleImmutableEntry<Long, Long>(bagitValues.getPayloadByteCount(), bagitValues.getPayloadFileCount());
     }
 
     final String payloadOxum = getPayloadOxum(bag);