Emergency PR: remove Hex reference to pass build

components/blitz/src/ome/services/blitz/impl/ScriptI.java

@@ -38,6 +38,7 @@
 import ome.tools.hibernate.QueryBuilder;
 import ome.util.Utils;
 import ome.util.checksum.ChecksumProviderFactory;
+import ome.util.checksum.ChecksumType;
 
 import omero.ApiUsageException;
 import omero.RInt;
@@ -586,8 +587,8 @@ private OriginalFile makeFile(final String path, final String script,
         file.setPath(FilenameUtils.getFullPath(path));
         file.setMimetype(ParamsHelper.PYTHONSCRIPT);
         file.setSize((long) script.getBytes().length);
-        file.setSha1(Utils.bytesToHex(
-                cpf.getProvider().getChecksum(script.getBytes())));
+        file.setSha1(cpf.getProvider(ChecksumType.SHA1)
+                .putBytes(script.getBytes()).checksumAsString());
         return updateFile(file, current);
     }
 

components/blitz/src/ome/services/scripts/ScriptFinder.java

@@ -20,6 +20,7 @@
 import ome.util.Utils;
 import ome.util.checksum.ChecksumProviderFactory;
 import ome.util.checksum.ChecksumProviderFactoryImpl;
+import ome.util.checksum.ChecksumType;
 import omero.model.OriginalFileI;
 import omero.model.ScriptJob;
 import omero.model.ScriptJobI;
@@ -86,7 +87,8 @@ public OriginalFileI getFile(ServiceFactory sf) {
         ChecksumProviderFactory cpf = new ChecksumProviderFactoryImpl();
         try {
             final byte[] buf = FileUtils.readFileToByteArray(source);
-            final String sha1 = Utils.bytesToHex(cpf.getProvider().getChecksum(buf));
+            final String sha1 = cpf.getProvider(ChecksumType.SHA1)
+                    .putBytes(buf).checksumAsString();
             log.debug("Loading script: " + sha1);
 
             Parameters p = new Parameters();

components/blitz/src/omero/client.java

@@ -29,6 +29,7 @@
 import ome.util.Utils;
 import ome.util.checksum.ChecksumProviderFactory;
 import ome.util.checksum.ChecksumProviderFactoryImpl;
+import ome.util.checksum.ChecksumType;
 import omero.api.ClientCallback;
 import omero.api.ClientCallbackPrxHelper;
 import omero.api.IAdminPrx;
@@ -928,9 +929,8 @@ public int killSession() {
      */
     public String sha1(File file) {
         ChecksumProviderFactory cpf = new ChecksumProviderFactoryImpl();
-        return Utils.bytesToHex(
-                cpf.getProvider().getChecksum(
-                        file.getAbsolutePath()));
+        return cpf.getProvider(ChecksumType.SHA1).putBytes(
+                        file.getAbsolutePath()).checksumAsString();
     }
 
     public OriginalFile upload(File file) throws ServerError, IOException {

components/common/src/ome/util/checksum/AbstractChecksumProvider.java

@@ -0,0 +1,134 @@
+/*
+ * Copyright (C) 2013 University of Dundee & Open Microscopy Environment.
+ * All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package ome.util.checksum;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.MappedByteBuffer;
+import java.nio.channels.FileChannel;
+
+import ome.util.Utils;
+
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hasher;
+
+/**
+ * Abstract skeleton class implementing {@link ChecksumProvider} and providing
+ * implementations of the interface methods using a universal checksum class
+ * object. Classes extending this class shall pass in a concrete checksum
+ * algorithm implementation (a {@link HashFunction} instance) as the constructor
+ * parameter.
+ *
+ * @author Blazej Pindelski, bpindelski at dundee.ac.uk
+ * @since 4.4.7
+ */
+public class AbstractChecksumProvider implements ChecksumProvider {
+
+    private final HashFunction hashFunction;
+
+    private Hasher hasher;
+
+    // Array size for buffered file reads
+    private static final int BYTEARRAYSIZE = 8192;
+
+    /**
+     * Protected ctor. There should not be an instance of this class.
+     * @param hashFunction
+     */
+    protected AbstractChecksumProvider(HashFunction hashFunction) {
+        this.hashFunction = hashFunction;
+        this.hasher = this.hashFunction.newHasher();
+    }
+
+    /**
+     * @see ChecksumProvider#putBytes(byte[])
+     */
+    public ChecksumProvider putBytes(byte[] byteArray) {
+        this.hasher.putBytes(byteArray);
+        return this;
+    }
+
+    /**
+     * @see ChecksumProvider#putBytes(ByteBuffer)
+     */
+    public ChecksumProvider putBytes(ByteBuffer byteBuffer) {
+        if (byteBuffer.hasArray()) {
+            this.hasher.putBytes(byteBuffer.array());
+            return this;
+        } else {
+            throw new IllegalArgumentException("Supplied ByteBuffer has " +
+                    "inaccessible array.");
+        }
+    }
+
+    /**
+     * @see ChecksumProvider#putBytes(String)
+     */
+    public ChecksumProvider putBytes(String filePath) {
+        FileInputStream fis = null;
+        FileChannel fch = null;
+        try {
+            fis = new FileInputStream(filePath);
+            fch = fis.getChannel();
+            MappedByteBuffer mbb = fch.map(FileChannel.MapMode.READ_ONLY, 0L,
+                    fch.size());
+            byte[] byteArray = new byte[BYTEARRAYSIZE];
+            int byteCount;
+            while (mbb.hasRemaining()) {
+                byteCount = Math.min(mbb.remaining(), BYTEARRAYSIZE);
+                mbb.get(byteArray, 0, byteCount);
+                this.hasher.putBytes(byteArray, 0, byteCount);
+            }
+            return this;
+        } catch (IOException io) {
+            throw new RuntimeException(io);
+        } finally {
+            Utils.closeQuietly(fis);
+            Utils.closeQuietly(fch);
+        }
+    }
+
+    public ChecksumProvider reset() {
+        this.hasher = this.hashFunction.newHasher();
+        return this;
+    }
+
+    /**
+     * @see ChecksumProvider#checksumAsBytes()
+     */
+    public byte[] checksumAsBytes() {
+        byte[] result = this.hasher.hash().asBytes();
+        this.reset();
+        return result;
+    }
+
+    /**
+     * @see ChecksumProvider#checksumAsString()
+     */
+    public String checksumAsString() {
+        try {
+            return this.hasher.hash().toString();
+        } finally {
+            this.reset();
+        }
+    }
+
+}

components/common/src/ome/util/checksum/ChecksumProvider.java

@@ -22,45 +22,74 @@
 import java.nio.ByteBuffer;
 
 /**
- * A provider producing checksum or message digests (depending on the
- * implementing class) of a given type of input. Inside the
- * <code>ome.util.checksum</code> package, the term <i>checksum</i>
+ * A provider producing checksums or message digests (depending on the
+ * implementing class) of a given type of input. The object's internal state
+ * represents the current checksum value and each call to <code>putBytes()</code>
+ * updates this object's internal state. This is a fluent interface allowing
+ * for method chaining.
+ * <br/>
+ * Inside the <code>ome.util.checksum</code> package, the term <i>checksum</i>
  * is understood as an "umbrella" term covering checksums, message digests and
- * hashes. An UnsupportedOperationException is thrown for methods which were
- * not present in the Utils class, which this interface supersedes.
+ * hashes.
  *
  * @author Blazej Pindelski, bpindelski at dundee.ac.uk
  * @since 4.4.7
  */
 public interface ChecksumProvider {
 
     /**
-     * Returns a checksum of a byte array. If the array is null, throws NPE.
-     * Note that, although checksum results are consistent for any given hash
-     * function and byte array, different hash functions may calculate different
-     * checksums for an empty array despite its lack of content.
+     * Updates the internal checksum value with data from a byte array.
+     * If the array is null, throws NPE. Note that, although checksum results
+     * are consistent for any given hash function and byte array, different hash
+     * functions may calculate different checksums for an empty array despite
+     * its lack of content.
      *
-     * @param buffer The input byte array.
-     * @return Checksum bytes inside an array.
+     * @param byteArray The input byte array.
+     * @return ChecksumProvider
      */
-    byte[] getChecksum(byte[] buffer);
+    ChecksumProvider putBytes(byte[] byteArray);
 
     /**
-     * Returns a checksum of a file identified by a path. Throws a
-     * RuntimeException in a case of an IO error.
+     * Updates the internal checksum value with data from a byte buffer.
+     * If the array underlying the byte buffer is not accessible, throws an
+     * IllegalArgumentException.
      *
-     * @param fileName <code>String</code> representing the absolute file path.
-     * @return Checksum bytes inside an array.
+     * @param byteBuffer The input byte buffer.
+     * @return ChecksumProvider
      */
-    byte[] getChecksum(String fileName);
+    ChecksumProvider putBytes(ByteBuffer byteBuffer);
 
     /**
-     * Returns a checksum of a byte buffer. If the array underlying the byte
-     * buffer is not accessible, throws an IllegalArgumentException.
+     * Updates the internal checksum value with data from a file identified by a
+     * path. Throws a RuntimeException in a case of an IO error.
      *
-     * @param buffer The input byte buffer.
-     * @return Checksum bytes inside an array.
+     * @param filePath <code>String</code> representing the absolute file path.
+     * @return ChecksumProvider
      */
-    byte[] getChecksum(ByteBuffer buffer);
+    ChecksumProvider putBytes(String filePath);
 
+    /**
+     * Resets the internal state of the object by clearing the checksum value.
+     *
+     * @return ChecksumProvider
+     */
+    ChecksumProvider reset();
+
+    /**
+     * Returns a byte array representation of the calculated checksum.
+     * Internally this method calls {@link ChecksumProvider#reset()}.
+     * Subsequent calls to this method will yield unspecified results.
+     *
+     * @return <code>byte[]</code> The checksum in a byte array.
+     */
+    byte[] checksumAsBytes();
+
+    /**
+     * Returns a <code>String</code> representing the checksum in hex form.
+     * Internally this method calls {@link ChecksumProvider#reset()}.
+     * Subsequent calls to this method will yield unspecified results.
+     *
+     * @return <code>String</code> The hexadecimal value of the checksum.
+     */
+    String checksumAsString();
 }

components/common/src/ome/util/checksum/ChecksumProviderFactory.java

@@ -21,20 +21,12 @@
 
 /**
  * A factory producing throw-away objects of the {@link ChecksumProvider} type.
- * If no {@link ChecksumType} given, defaults to SHA1.
  *
  * @author Blazej Pindelski, bpindelski at dundee.ac.uk
  * @since 4.4.7
  */
 public interface ChecksumProviderFactory {
 
-    /**
-     * Returns the default SHA1 {@link ChecksumProvider}.
-     *
-     * @return A SHA1 {@link ChecksumProvider}.
-     */
-    ChecksumProvider getProvider();
-
     /**
      * Returns an implementation of {@link ChecksumProvider} depending on the
      * specified {@link ChecksumType}.

components/common/src/ome/util/checksum/ChecksumProviderFactoryImpl.java

@@ -27,13 +27,6 @@
  */
 public class ChecksumProviderFactoryImpl implements ChecksumProviderFactory {
 
-    /**
-     * @see ChecksumProviderFactory#getProvider()
-     */
-    public ChecksumProvider getProvider() {
-        return this.getProvider(ChecksumType.SHA1);
-    }
-
     /**
      * @see ChecksumProviderFactory#getProvider(ChecksumType)
      */

components/common/src/ome/util/checksum/MD5ChecksumProviderImpl.java

@@ -19,47 +19,19 @@
 
 package ome.util.checksum;
 
-import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
 
-import java.nio.ByteBuffer;
-
 /**
  * An implementation of the {@link ChecksumProvider} interface using MD5
  * as the message digest algorithm.
  *
  * @author Blazej Pindelski, bpindelski at dundee.ac.uk
  * @since 4.4.7
  */
-public class MD5ChecksumProviderImpl implements ChecksumProvider {
-
-    private final HashFunction md5 = Hashing.md5();
-
-    /**
-     * @see ChecksumProvider#getChecksum(byte[])
-     */
-    public byte[] getChecksum(byte[] rawData) {
-        return this.md5.newHasher().putBytes(rawData).hash().asBytes();
-    }
-
-    /**
-     * @see ChecksumProvider#getChecksum(ByteBuffer)
-     */
-    public byte[] getChecksum(ByteBuffer byteBuffer) {
-        if (byteBuffer.hasArray()) {
-            return this.md5.newHasher().putBytes(byteBuffer.array()).hash().asBytes();
-        } else {
-            throw new IllegalArgumentException("Supplied ByteBuffer has " +
-                    "inaccessible array.");
-        }
-    }
+public final class MD5ChecksumProviderImpl extends AbstractChecksumProvider {
 
-    /**
-     * @see ChecksumProvider#getChecksum(String)
-     */
-    public byte[] getChecksum(String filePath) {
-        throw new UnsupportedOperationException("Method not "
-                + "implemented for file path String.");
+    public MD5ChecksumProviderImpl() {
+        super(Hashing.md5());
     }
 
 }