Add public API method 'getHexDigest()' plus new junit tests and clean…

… up code

src/main/java/org/dataone/hashstore/HashAddress.java

@@ -11,11 +11,11 @@
  * know the underlying file system details.
  */
 public class HashAddress {
-    private String id;
-    private String relPath;
-    private Path absPath;
-    private boolean isDuplicate;
-    private Map<String, String> hexDigests;
+    private final String id;
+    private final String relPath;
+    private final Path absPath;
+    private final boolean isDuplicate;
+    private final Map<String, String> hexDigests;
 
     /**
      * Creates a new instance of HashAddress with the given properties.

src/main/java/org/dataone/hashstore/HashStore.java

@@ -105,7 +105,7 @@ String storeMetadata(InputStream metadata, String pid, String formatId)
          * @throws FileNotFoundException    When requested pid has no associated object
          * @throws IOException              I/O error when creating InputStream to
          *                                  object
-         * @throws NoSuchAlgorithmException When algorithm used to calcualte object
+         * @throws NoSuchAlgorithmException When algorithm used to calculate object
          *                                  address is not supported
          */
         InputStream retrieveObject(String pid)
@@ -123,21 +123,21 @@ InputStream retrieveObject(String pid)
          *                                  associated object
          * @throws IOException              I/O error when creating InputStream to
          *                                  metadata
-         * @throws NoSuchAlgorithmException When algorithm used to calcualte metadata
+         * @throws NoSuchAlgorithmException When algorithm used to calculate metadata
          *                                  address is not supported
          */
         InputStream retrieveMetadata(String pid, String formatId) throws Exception;
 
         /**
          * The 'deleteObject' method deletes an object permanently from disk using a
-         * given persistent identifier and any empty subdirecetories.
+         * given persistent identifier and any empty subdirectories.
          * 
          * @param pid Authority-based identifier
-         * @return
+         * @return True if successful
          * @throws IllegalArgumentException When pid is null or empty
          * @throws FileNotFoundException    When requested pid has no associated object
          * @throws IOException              I/O error when deleting empty directories
-         * @throws NoSuchAlgorithmException When algorithm used to calcualte object
+         * @throws NoSuchAlgorithmException When algorithm used to calculate object
          *                                  address is not supported
          */
         boolean deleteObject(String pid) throws Exception;
@@ -149,11 +149,11 @@ InputStream retrieveObject(String pid)
          * 
          * @param pid      Authority-based identifier
          * @param formatId Metadata namespace/format
-         * @return
+         * @return True if successfulÏ
          * @throws IllegalArgumentException When pid or formatId is null or empty
          * @throws FileNotFoundException    When requested pid has no metadata
          * @throws IOException              I/O error when deleting empty directories
-         * @throws NoSuchAlgorithmException When algorithm used to calcualte object
+         * @throws NoSuchAlgorithmException When algorithm used to calculate object
          *                                  address is not supported
          */
         boolean deleteMetadata(String pid, String formatId) throws Exception;
@@ -164,8 +164,12 @@ InputStream retrieveObject(String pid)
          * 
          * @param pid       Authority-based identifier
          * @param algorithm Algorithm of desired hex digest
-         * @return
-         * @throws Exception TODO: Add specific exceptions
+         * @return String hex digest of requested pid
+         * @throws IllegalArgumentException When pid or formatId is null or empty
+         * @throws FileNotFoundException    When requested pid object does not exist
+         * @throws IOException              I/O error when calculating hex digests
+         * @throws NoSuchAlgorithmException When algorithm used to calculate object
+         *                                  address is not supported
          */
         String getHexDigest(String pid, String algorithm) throws Exception;
 }

src/main/java/org/dataone/hashstore/HashStoreFactory.java

@@ -26,8 +26,8 @@ public class HashStoreFactory {
      *                        (int)
      *                        storeAlgorithm
      * 
-     * @return
-     * @throws HashStoreFactoryException When HashStore fails to initialize due to
+     * @return HashStore instance ready to store objects and metadata
+     * @throws HashStoreFactoryException When HashStore failÏs to initialize due to
      *                                   permissions or class-related issues
      * @throws IOException               When there is an issue with properties
      */

src/main/java/org/dataone/hashstore/filehashstore/FileHashStore.java

@@ -302,7 +302,7 @@ protected void checkConfigurationEquality(String propertyName, Object suppliedVa
      * @param storeWidth             Width of store
      * @param storeAlgorithm         Algorithm to use to calculate the hex digest
      *                               for the
-     *                               permanent address of a data sobject
+     *                               permanent address of a data object
      * @param storeMetadataNamespace default formatId of hashstore metadata
      * @return String that representing the contents of 'hashstore.yaml'
      */
@@ -533,7 +533,7 @@ public InputStream retrieveObject(String pid)
         }
 
         // Get permanent address of the pid by calculating its sha-256 hex digest
-        String objectCid = this.getPidHexDigest(pid, OBJECT_STORE_ALGORITHM);
+        String objectCid = this.getPidHexDigest(pid, this.OBJECT_STORE_ALGORITHM);
         String objShardString = this.getHierarchicalPathString(this.DIRECTORY_DEPTH, this.DIRECTORY_WIDTH,
                 objectCid);
         Path objHashAddressPath = this.OBJECT_STORE_DIRECTORY.resolve(objShardString);
@@ -579,7 +579,7 @@ public InputStream retrieveMetadata(String pid, String formatId) throws Exceptio
         }
 
         // Get permanent address of the pid by calculating its sha-256 hex digest
-        String metadataCid = this.getPidHexDigest(pid + formatId, OBJECT_STORE_ALGORITHM);
+        String metadataCid = this.getPidHexDigest(pid + formatId, this.OBJECT_STORE_ALGORITHM);
         String metadataShardString = this.getHierarchicalPathString(this.DIRECTORY_DEPTH, this.DIRECTORY_WIDTH,
                 metadataCid);
         Path metadataHashAddressPath = this.METADATA_STORE_DIRECTORY.resolve(metadataShardString);
@@ -620,7 +620,7 @@ public boolean deleteObject(String pid)
         }
 
         // Get permanent address of the pid by calculating its sha-256 hex digest
-        String objectCid = this.getPidHexDigest(pid, OBJECT_STORE_ALGORITHM);
+        String objectCid = this.getPidHexDigest(pid, this.OBJECT_STORE_ALGORITHM);
         String objShardString = this.getHierarchicalPathString(this.DIRECTORY_DEPTH, this.DIRECTORY_WIDTH,
                 objectCid);
         Path objHashAddressPath = this.OBJECT_STORE_DIRECTORY.resolve(objShardString);
@@ -673,7 +673,7 @@ public boolean deleteMetadata(String pid, String formatId)
         }
 
         // Get permanent address of the pid by calculating its sha-256 hex digest
-        String metadataCid = this.getPidHexDigest(pid + formatId, OBJECT_STORE_ALGORITHM);
+        String metadataCid = this.getPidHexDigest(pid + formatId, this.OBJECT_STORE_ALGORITHM);
         String metadataCidShardString = this.getHierarchicalPathString(this.DIRECTORY_DEPTH, this.DIRECTORY_WIDTH,
                 metadataCid);
         Path metadataCidPath = this.METADATA_STORE_DIRECTORY.resolve(metadataCidShardString);
@@ -710,9 +710,57 @@ public boolean deleteMetadata(String pid, String formatId)
     }
 
     @Override
-    public String getHexDigest(String pid, String algorithm) throws Exception {
-        // TODO: Implement method
-        return null;
+    public String getHexDigest(String pid, String algorithm)
+            throws NoSuchAlgorithmException, FileNotFoundException, IOException {
+        logFileHashStore.debug("FileHashStore.getHexDigest - Called to calculate hex digest for pid: " + pid);
+
+        if (pid == null || pid.trim().isEmpty()) {
+            String errMsg = "FileHashStore.getHexDigest - pid cannot be null or empty, pid: " + pid;
+            logFileHashStore.error(errMsg);
+            throw new IllegalArgumentException(errMsg);
+        }
+        this.validateAlgorithm(algorithm);
+
+        // Get permanent address of the pid by calculating its sha-256 hex digest
+        String objectCid = this.getPidHexDigest(pid, this.OBJECT_STORE_ALGORITHM);
+        String objShardString = this.getHierarchicalPathString(this.DIRECTORY_DEPTH, this.DIRECTORY_WIDTH,
+                objectCid);
+        Path objHashAddressPath = this.OBJECT_STORE_DIRECTORY.resolve(objShardString);
+
+        // Check to see if object exists
+        if (!Files.exists(objHashAddressPath)) {
+            String errMsg = "FileHashStore.getHexDigest - File does not exist for pid: " + pid
+                    + " with object address: " + objHashAddressPath;
+            logFileHashStore.warn(errMsg);
+            throw new FileNotFoundException(errMsg);
+        }
+
+        // If so, calculate hex digest/checksum
+        MessageDigest mdObject = MessageDigest.getInstance(algorithm);
+        try {
+            InputStream dataStream = Files.newInputStream(objHashAddressPath);
+            byte[] buffer = new byte[8192];
+            int bytesRead;
+            while ((bytesRead = dataStream.read(buffer)) != -1) {
+                mdObject.update(buffer, 0, bytesRead);
+
+            }
+            // Close datastream
+            dataStream.close();
+
+        } catch (IOException ioe) {
+            String errMsg = "FileHashStore.getHexDigest - Unexpected IOException encountered: "
+                    + ioe.getMessage();
+            logFileHashStore.error(errMsg);
+            throw ioe;
+
+        }
+
+        String mdObjectHexDigest = DatatypeConverter.printHexBinary(mdObject.digest()).toLowerCase();
+        logFileHashStore
+                .info("FileHashStore.getHexDigest - Hex digest calculated for pid: " + pid + ", with hex digest value: "
+                        + mdObjectHexDigest);
+        return mdObjectHexDigest;
     }
 
     /**