Merge pull request #128 from DICE-UNC/issue87

Issue87

jargon-core/src/main/java/org/irods/jargon/core/checksum/AbstractChecksumComputeStrategy.java

@@ -24,7 +24,7 @@ public abstract class AbstractChecksumComputeStrategy {
 	 * @throws FileNotFoundException
 	 * @throws JargonException
 	 */
-	public abstract ChecksumValue instanceChecksumForPackingInstruction(
+	public abstract ChecksumValue computeChecksumValueForLocalFile(
 			final String localFileAbsolutePath) throws FileNotFoundException,
 			JargonException;
 

jargon-core/src/main/java/org/irods/jargon/core/checksum/LocalChecksumComputerFactory.java

@@ -1,10 +1,13 @@
 package org.irods.jargon.core.checksum;
 
+import org.irods.jargon.core.connection.IRODSSession;
 import org.irods.jargon.core.protovalues.ChecksumEncodingEnum;
 
 /**
  * Factory interface to create methods to compute local checksums based on a
  * type that can be derived from the {@link ChecksumManager}.
+ * <p/>
+ * This factory is available from the {@link IRODSSession}
  * 
  * @author Mike Conway - DICE
  */

jargon-core/src/main/java/org/irods/jargon/core/checksum/LocalChecksumComputerFactoryImpl.java

@@ -3,11 +3,14 @@
  */
 package org.irods.jargon.core.checksum;
 
+import org.irods.jargon.core.connection.IRODSSession;
 import org.irods.jargon.core.protovalues.ChecksumEncodingEnum;
 
 /**
  * Factory to create methods to compute local checksums based on a type that can
- * be derived from the {@link ChecksumManager}.
+ * be derived from the {@link ChecksumManager}. *
+ * <p/>
+ * This factory is available from the {@link IRODSSession}
  * 
  * @author Mike Conway - DICE
  * 

jargon-core/src/main/java/org/irods/jargon/core/checksum/MD5LocalChecksumComputerStrategy.java

@@ -29,7 +29,7 @@ public class MD5LocalChecksumComputerStrategy extends
 	 * instanceChecksumForPackingInstruction(java.lang.String)
 	 */
 	@Override
-	public ChecksumValue instanceChecksumForPackingInstruction(
+	public ChecksumValue computeChecksumValueForLocalFile(
 			final String localFileAbsolutePath) throws FileNotFoundException,
 			JargonException {
 

jargon-core/src/main/java/org/irods/jargon/core/checksum/SHA256LocalChecksumComputerStrategy.java

@@ -30,7 +30,7 @@ public class SHA256LocalChecksumComputerStrategy extends
 	 * instanceChecksumForPackingInstruction(java.lang.String)
 	 */
 	@Override
-	public ChecksumValue instanceChecksumForPackingInstruction(
+	public ChecksumValue computeChecksumValueForLocalFile(
 			final String localFileAbsolutePath) throws FileNotFoundException,
 			JargonException {
 

jargon-core/src/main/java/org/irods/jargon/core/exception/ChecksumInvalidException.java

@@ -0,0 +1,65 @@
+/**
+ * 
+ */
+package org.irods.jargon.core.exception;
+
+/**
+ * @author Mike Conway - DICE General exception for checksum mismatches
+ *
+ */
+public class ChecksumInvalidException extends JargonException {
+
+	private static final long serialVersionUID = 6069493884085439471L;
+
+	/**
+	 * @param message
+	 */
+	public ChecksumInvalidException(String message) {
+		super(message);
+	}
+
+	/**
+	 * @param message
+	 * @param cause
+	 */
+	public ChecksumInvalidException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
+	/**
+	 * @param cause
+	 */
+	public ChecksumInvalidException(Throwable cause) {
+		super(cause);
+	}
+
+	/**
+	 * @param message
+	 * @param cause
+	 * @param underlyingIRODSExceptionCode
+	 */
+	public ChecksumInvalidException(String message, Throwable cause,
+			int underlyingIRODSExceptionCode) {
+		super(message, cause, underlyingIRODSExceptionCode);
+		// TODO Auto-generated constructor stub
+	}
+
+	/**
+	 * @param cause
+	 * @param underlyingIRODSExceptionCode
+	 */
+	public ChecksumInvalidException(Throwable cause,
+			int underlyingIRODSExceptionCode) {
+		super(cause, underlyingIRODSExceptionCode);
+	}
+
+	/**
+	 * @param message
+	 * @param underlyingIRODSExceptionCode
+	 */
+	public ChecksumInvalidException(String message,
+			int underlyingIRODSExceptionCode) {
+		super(message, underlyingIRODSExceptionCode);
+	}
+
+}

jargon-core/src/main/java/org/irods/jargon/core/pub/DataAOHelper.java

@@ -523,7 +523,7 @@ ChecksumValue computeLocalFileChecksum(final File localFile,
 				.getIrodsSession().getLocalChecksumComputerFactory()
 				.instance(checksumEncoding);
 		try {
-			return strategy.instanceChecksumForPackingInstruction(localFile
+			return strategy.computeChecksumValueForLocalFile(localFile
 					.getAbsolutePath());
 		} catch (FileNotFoundException e) {
 			log.error("cannot find file for computing local checksum", e);

jargon-core/src/main/java/org/irods/jargon/core/pub/DataObjectAOImpl.java

@@ -3096,7 +3096,7 @@ public boolean verifyChecksumBetweenLocalAndIrods(
 			ChecksumValue localChecksum = getIRODSSession()
 					.getLocalChecksumComputerFactory()
 					.instance(irodsChecksum.getChecksumEncoding())
-					.instanceChecksumForPackingInstruction(
+					.computeChecksumValueForLocalFile(
 							localFile.getAbsolutePath());
 			log.info("localChecksum:{}", localChecksum);
 			return irodsChecksum.getChecksumStringValue().equals(

jargon-core/src/main/java/org/irods/jargon/core/pub/DataObjectChecksumUtilitiesAO.java

@@ -1,6 +1,7 @@
 package org.irods.jargon.core.pub;
 
 import org.irods.jargon.core.checksum.ChecksumValue;
+import org.irods.jargon.core.exception.ChecksumInvalidException;
 import org.irods.jargon.core.exception.FileNotFoundException;
 import org.irods.jargon.core.exception.JargonException;
 import org.irods.jargon.core.pub.domain.ObjStat;
@@ -48,4 +49,25 @@ ChecksumValue computeChecksumValueFromIrodsData(String irodsValue)
 	ChecksumValue computeChecksumOnDataObject(IRODSFile irodsFile)
 			throws JargonException;
 
+	/**
+	 * Compare a local file against iRODS using the configured checksum algo on
+	 * the iRODS side. Return the checksum information, or throw an exception if
+	 * the checksums do not match
+	 * 
+	 * @param localAbsolutePath
+	 *            <code>String</code> with the local file absolute path
+	 * @param irodsAbsolutePath
+	 *            <code>String</code> with the irods file absolute path
+	 * @return {@link ChecksumValue} for a validated checksum
+	 * @throws FileNotFoundException
+	 *             if either file is missing
+	 * @throws ChecksumInvalidException
+	 *             if the checksums do not match
+	 * @throws JargonException
+	 */
+	ChecksumValue verifyLocalFileAgainstIrodsFileChecksum(
+			final String localAbsolutePath, final String irodsAbsolutePath)
+			throws FileNotFoundException, ChecksumInvalidException,
+			JargonException;
+
 }

jargon-core/src/main/java/org/irods/jargon/core/pub/DataObjectChecksumUtilitiesAOImpl.java

@@ -3,11 +3,15 @@
  */
 package org.irods.jargon.core.pub;
 
+import java.io.File;
+
+import org.irods.jargon.core.checksum.AbstractChecksumComputeStrategy;
 import org.irods.jargon.core.checksum.ChecksumManager;
 import org.irods.jargon.core.checksum.ChecksumManagerImpl;
 import org.irods.jargon.core.checksum.ChecksumValue;
 import org.irods.jargon.core.connection.IRODSAccount;
 import org.irods.jargon.core.connection.IRODSSession;
+import org.irods.jargon.core.exception.ChecksumInvalidException;
 import org.irods.jargon.core.exception.FileNotFoundException;
 import org.irods.jargon.core.exception.JargonException;
 import org.irods.jargon.core.packinstr.DataObjInp;
@@ -124,4 +128,81 @@ public ChecksumValue computeChecksumValueFromIrodsData(
 				.determineChecksumEncodingFromIrodsData(irodsValue.trim());
 	}
 
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.irods.jargon.core.pub.DataObjectChecksumUtilitiesAO#
+	 * verifyLocalFileAgainstIrodsFileChecksum(java.lang.String,
+	 * java.lang.String)
+	 */
+	@Override
+	public ChecksumValue verifyLocalFileAgainstIrodsFileChecksum(
+			final String localAbsolutePath, final String irodsAbsolutePath)
+			throws FileNotFoundException, ChecksumInvalidException,
+			JargonException {
+		log.info("verifyLocalFileAgainstIrodsFileChecksum()");
+		if (localAbsolutePath == null || localAbsolutePath.isEmpty()) {
+			throw new IllegalArgumentException(
+					"null or empty localAbsolutePath");
+		}
+
+		if (irodsAbsolutePath == null || irodsAbsolutePath.isEmpty()) {
+			throw new IllegalArgumentException(
+					"null or empty irodsAbsolutePath");
+		}
+
+		log.info("localAbsolutePath:{}", localAbsolutePath);
+		log.info("irodsAbsolutePath:{}", irodsAbsolutePath);
+
+		File localFile = new File(localAbsolutePath);
+
+		if (!localFile.exists()) {
+			throw new FileNotFoundException("local file does not exist");
+		}
+
+		if (!localFile.isFile()) {
+			throw new JargonException(
+					"local file is not a file, it is a collection");
+		}
+
+		IRODSFile irodsFile = this.getIRODSFileFactory().instanceIRODSFile(
+				irodsAbsolutePath);
+
+		if (!irodsFile.exists()) {
+			throw new FileNotFoundException("irods file does not exist");
+		}
+
+		if (!irodsFile.isFile()) {
+			throw new JargonException(
+					"irods file is not a file, it is a collection");
+		}
+
+		ChecksumValue checksumValue = this
+				.computeChecksumOnDataObject(irodsFile);
+
+		AbstractChecksumComputeStrategy checksumComputeStrategy = this
+				.getIRODSSession().getLocalChecksumComputerFactory()
+				.instance(checksumValue.getChecksumEncoding());
+		ChecksumValue localValue;
+		try {
+			localValue = checksumComputeStrategy
+					.computeChecksumValueForLocalFile(localAbsolutePath);
+		} catch (java.io.FileNotFoundException e) {
+			// Jargon has it's own file not found exception, dumb or not
+			throw new FileNotFoundException(
+					"local file not found during checksum");
+		}
+
+		if (!localValue.equals(checksumValue)) {
+			log.error("checksum mismatch");
+			log.error("local checksum:{}", localValue);
+			log.error("irods checksum:{}", checksumValue);
+			throw new ChecksumInvalidException(
+					"checksum mismatch between local and iRODS");
+		}
+
+		return checksumValue;
+
+	}
+
 }

jargon-core/src/main/java/org/irods/jargon/core/pub/io/IRODSFileInputStream.java

@@ -197,7 +197,6 @@ private int openIRODSFile() throws JargonException {
 	@Override
 	public int read() throws IOException {
 		try {
-			// openFile();
 			byte buffer[] = new byte[1];
 
 			int temp = fileIOOperations.fileRead(fd, buffer, 0, 1);
@@ -296,7 +295,6 @@ public int read(final byte b[], final int off, final int len)
 
 		int temp;
 		try {
-			// openFile();
 			temp = fileIOOperations.fileRead(fd, b, off, len);
 		} catch (JargonException e) {
 			log.error(
@@ -360,7 +358,6 @@ public int read(final byte b[], final int off, final int len)
 	 */
 	@Override
 	public int read(final byte b[]) throws IOException {
-		// openFile();
 		return read(b, 0, b.length);
 	}