Script.java

package org.molgenis.compute.pipelinemodel;

import java.io.*;
import java.util.Timer;
import java.util.TimerTask;
import java.util.Vector;

//now script has
//local name
//remote name

//remote directory

//data - the listing of the script
public abstract class Script implements Serializable
{
	private String ID = null;

	private String localname = null;
	private String remotename = null;

	private byte[] scriptData = null;

	private String remoteDir = null;

	private boolean isFinished = false;
	private boolean isStarted = false;

	private Timer countdown = new Timer();

	private int maxRunTime = 180; // 3 minutes for testing hello world

	public boolean isExpired()
	{
		return expired;
	}

	private boolean expired = false;

	public void setExpired(boolean b)
	{
		System.out.println("... execution time is expired");
		this.expired = b;
	}

	public enum Status
	{
		IDLE
		{
			public String toString()
			{
				return "waiting";
			}
		},

		WAITING
		{
			public String toString()
			{
				return "waiting";
			}
		},

		SCHEDULED
		{
			public String toString()
			{
				return "scheduled";
			}
		},
		RUNNING
		{
			public String toString()
			{
				return "running";
			}
		},
		DONE_SUCCESS
		{
			public String toString()
			{
				return "done success";
			}
		},
		DONE_FAILED
		{
			public String toString()
			{
				return "failed";
			}
		}

	}

	private Status status = Status.IDLE;

	private boolean hasAdditionalFiles = false;
	private Vector<FileToSaveRemotely> filesToSaveRemotely = new Vector();

	private boolean isShort = false;

	public Script(String scriptID, String outputRemoteLocation, byte[] bytes)
	{
		this.ID = scriptID;
		this.remotename = ID + ".sh";
		this.remoteDir = outputRemoteLocation;
		this.scriptData = bytes;
	}

	public String getID()
	{
		return ID;
	}

	public void setID(String ID)
	{
		this.ID = ID;
	}

	// todo delete
	public Script(String localname, String remotename)
	{
		this.localname = localname;
		this.remotename = remotename;

		try
		{
			this.scriptData = getFileAsBytes(localname);
		}
		catch (IOException e)
		{
			e.printStackTrace();
		}
	}

	// todo delete
	public Script(String remotename, byte[] scriptListing)
	{
		this.remotename = remotename;
		this.scriptData = scriptListing;
	}

	public String getLocalname()
	{
		return localname;
	}

	public String getRemotename()
	{
		return remotename;
	}

	private final byte[] getFileAsBytes(String filename) throws IOException
	{

		File file = new File(filename);

		final BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file));
		final byte[] bytes = new byte[(int) file.length()];
		bis.read(bytes);
		bis.close();
		return bytes;
	}

	public byte[] getScriptData()
	{
		return scriptData;
	}

	public String getRemoteDir()
	{
		return remoteDir;
	}

	public void setRemoteDir(String remoteDir)
	{
		this.remoteDir = remoteDir;
	}

	public boolean isHasAdditionalFiles()
	{
		return hasAdditionalFiles;
	}

	public void setHasAdditionalFiles(boolean hasAdditionalFiles)
	{
		this.hasAdditionalFiles = hasAdditionalFiles;
	}

	public void addFileToTransfer(FileToSaveRemotely file)
	{
		filesToSaveRemotely.add(file);
	}

	public FileToSaveRemotely getFileToSaveRemotely(int i)
	{
		return filesToSaveRemotely.elementAt(i);
	}

	public boolean isShort()
	{
		return isShort;
	}

	public void setShort(boolean aShort)
	{
		isShort = aShort;
	}

	public int getNumberFileToSaveRemotely()
	{
		return filesToSaveRemotely.size();
	}

	public boolean isFinished()
	{
		return isFinished;
	}

	public void setFinished(boolean finished)
	{
		isFinished = finished;
	}

	public boolean isStarted()
	{
		return isStarted;
	}

	public void setStarted(boolean started)
	{
		isStarted = started;
		start();
	}

	@Override
	public String toString()
	{
		return "Script{" + "ID='" + ID + '\'' + ", localname='" + localname + '\'' + ", remotename='" + remotename
				+ '\'' + ", scriptData=" + new String(scriptData) + ", remoteDir='" + remoteDir + '\''
				+ ", hasAdditionalFiles=" + hasAdditionalFiles + ", filesToSaveRemotely=" + filesToSaveRemotely + '}';
	}

	public abstract String getSubmitCommand();

	public abstract String getMonitoringCommand();

	public Status getStatus()
	{
		return status;
	}

	public void setStatus(Status status)
	{
		this.status = status;
	}

	private void start()
	{

		isStarted = true;
		countdown.schedule(new TimerTask()
		{
			public void run()
			{
				setExpired(true);
			}
		}, maxRunTime * 1000);
	}
}