DatabaseUpdaterCluster.java

package org.molgenis.compute.monitor;

import org.molgenis.compute.ComputeJob;
import org.molgenis.compute.scriptserver.MCF;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;

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

/**
 * Created by IntelliJ IDEA. User: georgebyelas Date: 21/06/2011 Time: 13:10 To
 * change this template use File | Settings | File Templates.
 */

public abstract class DatabaseUpdaterCluster implements DatabaseUpdater
{
	protected int delay = -1;
	protected int period = -1; // repeat every sec.

	protected Timer timer = new Timer();

	protected Vector<ComputeAppPaths> activeComputeApps = new Vector<ComputeAppPaths>();
	protected Database db = null;

	protected boolean isStarted = false;
	protected MCF mcf = null;

	public void start()
	{

		isStarted = true;
		timer.scheduleAtFixedRate(new TimerTask()
		{
			public void run()
			{
				// System.out.println(">>> updater report");

				// first "cache" all log files of active pipelines
				// this is more efficient than read it every log file to find
				// application status later
				Vector<String> allLogs = readAllLogs();

				// System.out.println("size of active compute apps" +
				// activeComputeApps.size());

				Vector<ComputeAppPaths> appToRemove = new Vector<ComputeAppPaths>();
				for (int i = 0; i < activeComputeApps.size(); i++)
				{
					ComputeAppPaths appPaths = activeComputeApps.elementAt(i);
					ComputeJob application = appPaths.getApplication();

					String name = application.getName();

					// to avoid transaction if the status is not changed
					ComputeAppPaths.AppStatus prevStatus = appPaths.getPrevStatus();
					ComputeAppPaths.AppStatus status = findStatus(name, allLogs);

					if (prevStatus.equals(status)) continue;

					appPaths.setPrevStatus(status);

					if (status.equals(ComputeAppPaths.AppStatus.started))
					{
						application.setStatusCode("started");
						try
						{
							db.beginTx();
							db.update(application);
							db.commitTx();
						}
						catch (DatabaseException e)
						{
							e.printStackTrace();
						}
					}
					else if (status.equals(ComputeAppPaths.AppStatus.finished))
					{
						application.setStatusCode("finished");

						String error = readRemoteFile(appPaths.getErrpath());
						// application.setErrorFile(error);
						String extralog = readRemoteFile(appPaths.getExtralog());
						String output = readRemoteFile(appPaths.getOutpath());
						application.setOutputFile(error);

						if (appPaths.getLogpathSize() > 0)
						{
							for (int iii = 0; iii < appPaths.getLogpathSize(); iii++)
							{
								String log = readRemoteFile(appPaths.getLogpath(iii));
								// application.setLogFile(log);
								extralog += "\n-------------------------------------\n";
								extralog += log;
							}

						}

						application.setLogFile(extralog);

						try
						{
							db.beginTx();
							db.update(application);
							db.commitTx();
						}
						catch (DatabaseException e)
						{
							e.printStackTrace();
						}
						appToRemove.addElement(appPaths);
					}
				}

				activeComputeApps.removeAll(appToRemove);
				mcf.removeFinishedPipelines();
				if (activeComputeApps.size() == 0) cancel();

			}
		}, delay * 1000, period * 1000);
	}

	protected ComputeAppPaths.AppStatus findStatus(String name, Vector<String> allLogs)
	{

		for (int i = 0; i < allLogs.size(); i++)
		{
			String logfile = allLogs.elementAt(i);
			if (!logfile.equalsIgnoreCase(RemoteFileToStringReader.FILE_IS_NOT_EXISTS))
			{
				int index_started = logfile.indexOf(name + ClusterLoggingReaderGridGain._STARTED);
				int index_finished = logfile.indexOf(name + ClusterLoggingReaderGridGain._FINISHED);

				if (index_finished > -1) return ComputeAppPaths.AppStatus.finished;
				else if (index_started > -1) return ComputeAppPaths.AppStatus.started;
			}

		}
		return ComputeAppPaths.AppStatus.idle;
	}

	protected Vector<String> readAllLogs()
	{
		Vector<String> allLogs = new Vector<String>();

		for (int i = 0; i < mcf.getNumberActivePipelines(); i++)
		{
			String path = mcf.getActivePipeline(i).getPipelinelogpath();
			String logfile = readRemoteFile(path);
			allLogs.addElement(logfile);
		}

		return allLogs;
	}

	abstract String readRemoteFile(String path);

	public void stop()
	{
		timer.cancel();
		isStarted = false;
	}

	// set settings in seconds
	public void setSettings(int delay, int period)
	{
		this.delay = delay;
		this.period = period;
	}

	public void addComputeAppPath(ComputeAppPaths computeAppPath)
	{
		activeComputeApps.addElement(computeAppPath);
	}

	public boolean isStarted()
	{
		return isStarted;
	}

	public void setDatabase(Database db)
	{
		this.db = db;
	}

}