Merge pull request #410 from osbornjd/jay/MarkIII

FileHandler Changed to Using Accessors
Signed-off-by: Jay Jay Billings <billingsjj@ornl.gov>

org.eclipse.ice.commands/src/main/java/org/eclipse/ice/commands/Command.java

@@ -168,8 +168,7 @@ protected CommandStatus setConfiguration() {
 		// Check the info and return failure if something was not set
 		if (commandConfig.getExecutable() == null || commandConfig.getInputFile() == null
 				|| commandConfig.getOutFileName() == null || commandConfig.getErrFileName() == null
-				|| commandConfig.getNumProcs() == null || commandConfig.getOS() == null
-				|| commandConfig.getWorkingDirectory() == null)
+				|| commandConfig.getNumProcs() == null || commandConfig.getWorkingDirectory() == null)
 			return CommandStatus.INFOERROR;
 
 		// Set the command to actually run and execute
@@ -435,6 +434,8 @@ protected boolean logOutput(final InputStream output, final InputStream errors)
 			// Write to the stdOut file
 			while ((nextLine = stdOutReader.readLine()) != null) {
 				commandConfig.getStdOut().write(nextLine);
+
+				commandConfig.addToStdOutputString(nextLine);
 				// MUST put a new line for this type of writer. "\r\n" works on
 				// Windows and Unix-based systems.
 				commandConfig.getStdOut().write("\r\n");

org.eclipse.ice.commands/src/main/java/org/eclipse/ice/commands/CommandConfiguration.java

@@ -81,17 +81,16 @@ public class CommandConfiguration {
 	 */
 	private String installDirectory;
 
-	/**
-	 * The operating system on which the job will run
-	 */
-	private String os;
-
 	/**
 	 * The working directory for the job to be executed in, and thus where e.g. the
 	 * output files will be located
 	 */
 	private String workingDirectory;
 
+	/**
+	 * The operating system that the command will be run on. Set as a default to the local OS
+	 */
+	private String os;
 	/**
 	 * The hostname that the command will be executed on. This is the same as the
 	 * hostname in {@link org.eclipse.ice.commands.Connection} and is just used for
@@ -104,6 +103,13 @@ public class CommandConfiguration {
 	 */
 	private BufferedWriter stdOut = null, stdErr = null;
 
+	/**
+	 * This is a string that contains all of the output of the job. This is the same
+	 * text that gets written out to
+	 * {@link org.eclipse.ice.commands.CommandConfiguration#stdOut}
+	 */
+	String stdOutput = "";
+
 	/**
 	 * A flag to mark whether or not the input file name should be appended to the
 	 * executable command. Marked as true by default so that the user (by default)
@@ -129,6 +135,7 @@ public class CommandConfiguration {
 	public CommandConfiguration() {
 		// Assume some default variables
 		commandId = -999;
+		os = System.getProperty("os.name");
 	}
 
 	/**
@@ -210,7 +217,7 @@ public String createOutputHeader(String logName) {
 		header += new SimpleDateFormat("yyyyMMdd_HHmmss").format(Calendar.getInstance().getTime()) + "\n";
 
 		// Add the point of origin
-		header += "# Launch host: " + localHostname + "\n";
+		header += "# Launch host: " + hostname + "\n";
 
 		// Add the target machine
 		header += "# Target host: " + hostname + "\n";
@@ -446,24 +453,24 @@ public String getInstallDirectory() {
 	}
 
 	/**
-	 * Setter for operating system, see
+	 * Getter for os, see
 	 * {@link org.eclipse.ice.commands.CommandConfiguration#os}
+	 * Note that this is set to the default of the local OS
 	 * 
-	 * @param operatingSys
+	 * @return os
 	 */
-	public void setOS(String operatingSys) {
-		os = operatingSys;
-		return;
+	public String getOS() {
+		return os;
 	}
 
 	/**
-	 * Getter for operating system, see
+	 * Setter for operating system, see
 	 * {@link org.eclipse.ice.commands.CommandConfiguration#os}
 	 * 
-	 * @return os
+	 * @param OS
 	 */
-	public String getOS() {
-		return os;
+	public void setOS(String OS) {
+		os = OS;
 	}
 
 	/**
@@ -573,6 +580,36 @@ public BufferedWriter getStdOut() {
 		return stdOut;
 	}
 
+	/**
+	 * Setter for stdOutput, see
+	 * {@link org.eclipse.ice.commands.CommandConfiguration#stdOutput}
+	 * 
+	 * @return stdOutput
+	 */
+	public void setStdOutputString(String out) {
+		stdOutput = out;
+	}
+
+	/**
+	 * This function adds the String string to the String
+	 * {@link org.eclipse.ice.commands.CommandConfiguration#stdOutput}
+	 * 
+	 * @param string
+	 */
+	public void addToStdOutputString(String string) {
+		stdOutput += " " + string;
+	}
+
+	/**
+	 * Getter for stdOutput, see
+	 * {@link org.eclipse.ice.commands.CommandConfiguration#stdOutput}
+	 * 
+	 * @return stdOutput
+	 */
+	public String getStdOutputString() {
+		return stdOutput;
+	}
+
 	/**
 	 * Getter for splitCommand, see
 	 * {@link org.eclipse.ice.commands.CommandConfiguration#splitCommand} No setter

org.eclipse.ice.commands/src/main/java/org/eclipse/ice/commands/FileHandler.java

@@ -37,21 +37,11 @@ public abstract class FileHandler implements IFileHandler {
 	protected static final Logger logger = LoggerFactory.getLogger(FileHandler.class);
 
 	/**
-	 * The command member variable that will actually execute the move or copy that
-	 * was requested by the user
+	 * The command member variable that will actually execute the transfer that was
+	 * requested by the user
 	 */
 	Command command;
 
-	/**
-	 * The ConnectionConfiguration associated with the source file
-	 */
-	ConnectionConfiguration sourceConfiguration;
-
-	/**
-	 * The ConnectionConfiguration associated with the destination file
-	 */
-	ConnectionConfiguration destinationConfiguration;
-
 	/**
 	 * A status member variable that indicates the status of the file transfer. See
 	 * also {@link org.eclipse.ice.commands.CommandStatus}
@@ -72,7 +62,20 @@ public FileHandler() {
 	 *         was successful
 	 * @throws IOException
 	 */
-	public abstract CommandStatus move(final String source, final String destination) throws IOException;
+	public CommandStatus move(final String source, final String destination) throws IOException {
+
+		// Check the file existence. If they don't exist, an exception is thrown
+		checkExistence(source, destination);
+
+		// Set the commands to have the appropriate properties
+		configureMoveCommand(source, destination);
+
+		// Execute and process the file transfer
+		transferStatus = executeTransfer(destination);
+
+		// Return whether or not it succeeded
+		return transferStatus;
+	}
 
 	/**
 	 * This method is responsible for copying a file from a source to a destination
@@ -82,8 +85,41 @@ public FileHandler() {
 	 *         was successful
 	 * @throws IOException
 	 */
-	public abstract CommandStatus copy(final String source, final String destination) throws IOException;
+	public CommandStatus copy(final String source, final String destination) throws IOException {
+		// Check the file existence. If one or both don't exist, an exception is thrown
+		checkExistence(source, destination);
+
+		// Set the commands to have the appropriate properties
+		configureCopyCommand(source, destination);
+
+		// Execute and process the file transfer
+		transferStatus = executeTransfer(destination);
+
+		// Return whether or not it succeeded
+		return transferStatus;
+	}
+
+	/**
+	 * This function sets the command member variables to have the source and
+	 * destination strings. It is delegated to the subclasses so that the commands
+	 * can be cast appropriately
+	 * 
+	 * @param source
+	 * @param destination
+	 */
+	protected abstract void configureMoveCommand(final String source, final String destination);
+
+	/**
+	 * This function sets the command member variables to have the source and
+	 * destination strings. It is delegated to the subclasses so that the commands
+	 * can be cast appropriately
+	 * 
+	 * @param source
+	 * @param destination
+	 */
+	protected abstract void configureCopyCommand(final String source, final String destination);
 
+
 	/**
 	 * This method is responsible for determining whether or not a file or directory
 	 * already exists for a given path.
@@ -109,15 +145,16 @@ public FileHandler() {
 	public abstract void checkExistence(final String source, final String destination) throws IOException;
 
 	/**
-	 * This function gets and returns the private member variable command of type
-	 * Command
+	 * This function gets and returns the private member variable command of
+	 * type Command
 	 * 
 	 * @return Command - the command associated with this FileHandler
 	 */
 	public Command getCommand() {
 		return command;
 	}
 
+
 	/**
 	 * This operation creates all the directories that are parents of the
 	 * destination.
@@ -144,6 +181,14 @@ protected boolean createDirectories(String dest) throws IOException {
 		return exists;
 	}
 
+	/**
+	 * This function actually executes the file transfer and then checks that it was
+	 * completed correctly
+	 * 
+	 * @param destination - destination for the file to go to
+	 * @return - CommandStatus indicating whether or not the transfer completed
+	 *         successfully
+	 */
 	protected CommandStatus executeTransfer(final String destination) {
 		// Execute the file transfer
 		transferStatus = command.execute();
@@ -163,13 +208,14 @@ protected CommandStatus executeTransfer(final String destination) {
 	}
 
 	/**
-	 * This function returns the current status of the copy or move, as it is given
-	 * by the member variable {@link org.eclipse.ice.commands.FileHandler#command}
+	 * This function returns the current status of the transfer, as it is given by the
+	 * member variable {@link org.eclipse.ice.commands.FileHandler#copyCommand}
 	 * 
 	 * @return - CommandStatus indicating the status of the file transfer
 	 */
 	public CommandStatus getStatus() {
 		return command.getStatus();
 	}
 
+
 }

org.eclipse.ice.commands/src/main/java/org/eclipse/ice/commands/LocalCopyFileCommand.java

@@ -44,19 +44,6 @@ public class LocalCopyFileCommand extends LocalCommand {
 	public LocalCopyFileCommand() {
 	}
 
-	/**
-	 * Constructor which sets the two paths, source and destination, to those given
-	 * by the arguments of the constructor. See
-	 * {@link org.eclipse.ice.tests.commands.CopyFileCommand} for member variable
-	 * descriptions.
-	 * 
-	 * @param src
-	 * @param dest
-	 */
-	public LocalCopyFileCommand(final String src, final String dest) {
-		source = Paths.get(src);
-		destination = Paths.get(dest);
-	}
 
 	/**
 	 * This function actually executes the copy file command. It checks that the
@@ -103,6 +90,18 @@ public CommandStatus cancel() {
 		return CommandStatus.CANCELED;
 	}
 
+
+	/**
+	 * This function sets the Paths for source and destination to the given strings
+	 * @param src - string corresponding to the source file
+	 * @param dest - string corresponding to the destination file
+	 */
+	public void setConfiguration(String src, String dest) {
+		source = Paths.get(src);
+		destination = Paths.get(dest);
+		return;
+	}
+
 	/**
 	 * A function that returns the source path in string form
 	 * 
@@ -111,7 +110,8 @@ public CommandStatus cancel() {
 	public String getSource() {
 		return source.toString();
 	}
-
+
+
 	/**
 	 * A function that returns the destination path in string form
 	 * 
@@ -120,4 +120,5 @@ public String getSource() {
 	public String getDestination() {
 		return destination.toString();
 	}
+
 }

org.eclipse.ice.commands/src/main/java/org/eclipse/ice/commands/LocalFileHandler.java

@@ -29,47 +29,30 @@ public class LocalFileHandler extends FileHandler {
 	 * Default constructor
 	 */
 	public LocalFileHandler() {
-
 	}
 
 	/**
-	 * See {@link org.eclipse.ice.commands.FileHandler#move()}
+	 * See {@link org.eclipse.ice.commands.FileHandler#setConfiguration(String, String)}
 	 */
 	@Override
-	public CommandStatus move(final String source, final String destination) throws IOException {
-
-		// Check the file existence. If they don't exist, an exception is thrown
-		checkExistence(source, destination);
-
-		// Make the command
-		command = new LocalMoveFileCommand(source, destination);
-
-		// Execute and process the file transfer
-		transferStatus = executeTransfer(destination);
-
-		// Return whether or not it succeeded
-		return transferStatus;
+	protected void configureMoveCommand(final String source, final String destination) {
+		command = new LocalMoveFileCommand();
+		// Cast the Command as a LocalMoveFileCommand to set the source and destination paths
+		((LocalMoveFileCommand) command).setConfiguration(source, destination);
 	}
 
 	/**
-	 * See {@link org.eclipse.ice.commands.FileHandler#copy()}
+	 * See {@link org.eclipse.ice.commands.FileHandler#setConfiguration(String, String)}
 	 */
 	@Override
-	public CommandStatus copy(final String source, final String destination) throws IOException {
-		// Check the file existence. If one or both don't exist, an exception is thrown
-		checkExistence(source, destination);
-
-		// Make the command
-		command = new LocalCopyFileCommand(source, destination);
-
-		// Execute and process the file transfer
-		transferStatus = executeTransfer(destination);
-
-		// Return whether or not it succeeded
-		return transferStatus;
+	protected void configureCopyCommand(final String source, final String destination) {
+		command = new LocalCopyFileCommand();
+		// Cast the Command as a LocalCopyFileCommand to set the source and destination paths
+		((LocalCopyFileCommand) command).setConfiguration(source, destination);
 
 	}
 
+
 	/**
 	 * See {@link org.eclipse.ice.commands.FileHandler#exists(String)}
 	 */