* create thumbnails in a temporary directory, not next to the dataset.

* disable ManagerHandler by default, enable by "-m" command line option.
* do not use StatisticsHandler if ManagerHandler is off.
* clean up ManagerHandler, fix deploy and undeploy dataset context paths.
* ManagerHandler obtains manager.ts template from resource (should work from inside jar).
* only deploy new dataset if context does not exist yet.

src/main/java/bdv/server/BigDataServer.java

@@ -6,11 +6,11 @@ import org.apache.commons.cli.*;
 import org.apache.commons.lang.StringUtils;
 import org.eclipse.jetty.server.Connector;
 import org.eclipse.jetty.server.ConnectorStatistics;
+import org.eclipse.jetty.server.Handler;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.server.ServerConnector;
 import org.eclipse.jetty.server.handler.ContextHandlerCollection;
 import org.eclipse.jetty.server.handler.HandlerCollection;
-import org.eclipse.jetty.server.handler.RequestLogHandler;
 import org.eclipse.jetty.server.handler.StatisticsHandler;
 import org.eclipse.jetty.util.log.Log;
 import org.eclipse.jetty.util.thread.QueuedThreadPool;
@@ -61,7 +61,8 @@ public class BigDataServer
 		{
 			hostname = "localhost";
 		}
-		return new Parameters( port, hostname, new HashMap< String, String >() );
+		final boolean enableManagerContext = false;
+		return new Parameters( port, hostname, new HashMap< String, String >(), enableManagerContext );
 	}
 
 	public static void main( final String[] args ) throws Exception
@@ -72,6 +73,8 @@ public class BigDataServer
 		if ( params == null )
 			return;
 
+		final String thumbnailsDirectoryName = getThumbnailDirectoryPath( params );
+
 		// Threadpool for multiple connections
 		final Server server = new Server( new QueuedThreadPool( 1000, 10 ) );
 
@@ -81,29 +84,32 @@ public class BigDataServer
 		connector.setPort( params.getPort() );
 		LOG.info( "Set connectors: " + connector );
 		server.setConnectors( new Connector[] { connector } );
-
-		// Add Statistics bean to the connector
-		final ConnectorStatistics connectorStats = new ConnectorStatistics();
-		connector.addBean( connectorStats );
-
 		final String baseURL = "http://" + server.getURI().getHost() + ":" + params.getPort();
-		LOG.info( "Server Base URL: " + baseURL );
 
 		// Handler initialization
-		final StatisticsHandler statHandler = new StatisticsHandler();
-
 		final HandlerCollection handlers = new HandlerCollection();
 
-		final ContextHandlerCollection datasetHandlers = createHandlers( baseURL, params.getDatasets() );
+		final ContextHandlerCollection datasetHandlers = createHandlers( baseURL, params.getDatasets(), thumbnailsDirectoryName );
 		handlers.addHandler( datasetHandlers );
-		handlers.addHandler( new ManagerHandler( baseURL, server, connectorStats, statHandler, datasetHandlers ) );
-		handlers.addHandler( new RequestLogHandler() );
 		handlers.addHandler( new JsonDatasetListHandler( server, datasetHandlers ) );
 
-		statHandler.setHandler( handlers );
+		Handler handler = handlers;
+		if ( params.enableManagerContext() )
+		{
+			// Add Statistics bean to the connector
+			final ConnectorStatistics connectorStats = new ConnectorStatistics();
+			connector.addBean( connectorStats );
+
+			// create StatisticsHandler wrapper and ManagerHandler
+			final StatisticsHandler statHandler = new StatisticsHandler();
+			handlers.addHandler( new ManagerHandler( baseURL, server, connectorStats, statHandler, datasetHandlers, thumbnailsDirectoryName ) );
+			statHandler.setHandler( handlers );
+			handler = statHandler;
+		}
 
-		LOG.info( "Set handler: " + statHandler );
-		server.setHandler( statHandler );
+		LOG.info( "Set handler: " + handler );
+		server.setHandler( handler );
+		LOG.info( "Server Base URL: " + baseURL );
 		LOG.info( "BigDataServer starting" );
 		server.start();
 		server.join();
@@ -123,11 +129,14 @@ public class BigDataServer
 		 */
 		private final Map< String, String > datasetNameToXml;
 
-		Parameters( final int port, final String hostname, final Map< String, String > datasetNameToXml )
+		private final boolean enableManagerContext;
+
+		Parameters( final int port, final String hostname, final Map< String, String > datasetNameToXml, final boolean enableManagerContext )
 		{
 			this.port = port;
 			this.hostname = hostname;
 			this.datasetNameToXml = datasetNameToXml;
+			this.enableManagerContext = enableManagerContext;
 		}
 
 		public int getPort()
@@ -140,6 +149,11 @@ public class BigDataServer
 			return hostname;
 		}
 
+		public String getThumbnailDirectory()
+		{
+			return null;
+		}
+
 		/**
 		 * Get datasets.
 		 *
@@ -149,6 +163,11 @@ public class BigDataServer
 		{
 			return datasetNameToXml;
 		}
+
+		public boolean enableManagerContext()
+		{
+			return enableManagerContext;
+		}
 	}
 
 	@SuppressWarnings( "static-access" )
@@ -182,6 +201,10 @@ public class BigDataServer
 				.withArgName( "FILE" )
 				.create( "d" ) );
 
+		options.addOption( OptionBuilder
+				.withDescription( "enable statistics and manager context. EXPERIMENTAL!" )
+				.create( "m" ) );
+
 		try
 		{
 			final CommandLineParser parser = new BasicParser();
@@ -197,6 +220,10 @@ public class BigDataServer
 
 			final HashMap< String, String > datasets = new HashMap< String, String >( defaultParameters.getDatasets() );
 
+			boolean enableManagerContext = false;
+			if ( cmd.hasOption( "m" ) )
+				enableManagerContext = true;
+
 			if ( cmd.hasOption( "d" ) )
 			{
 				// process the file given with "-d"
@@ -243,7 +270,7 @@ public class BigDataServer
 			if ( datasets.isEmpty() )
 				throw new IllegalArgumentException( "Dataset list is empty." );
 
-			return new Parameters( port, serverName, datasets );
+			return new Parameters( port, serverName, datasets, enableManagerContext );
 		}
 		catch ( final ParseException | IllegalArgumentException e )
 		{
@@ -267,7 +294,39 @@ public class BigDataServer
 		LOG.info( "Dataset added: {" + name + ", " + xmlpath + "}" );
 	}
 
-	private static ContextHandlerCollection createHandlers( final String baseURL, final Map< String, String > dataSet ) throws SpimDataException, IOException
+	private static String getThumbnailDirectoryPath( final Parameters params ) throws IOException
+	{
+		final String thumbnailDirectoryName = params.getThumbnailDirectory();
+		if ( thumbnailDirectoryName != null )
+		{
+			Path thumbnails = Paths.get( thumbnailDirectoryName );
+			if ( ! Files.exists( thumbnails ) )
+			{
+				try
+				{
+					thumbnails = Files.createDirectories( thumbnails );
+					return thumbnails.toFile().getAbsolutePath();
+				}
+				catch ( final IOException e )
+				{
+					LOG.warn( e.getMessage() );
+					LOG.warn( "Could not create thumbnails directory \"" + thumbnailDirectoryName + "\".\n Trying to create temporary directory." );
+				}
+			}
+			else
+			{
+				if ( ! Files.isDirectory( thumbnails ) )
+					LOG.warn( "Thumbnails directory \"" + thumbnailDirectoryName + "\" is not a directory.\n Trying to create temporary directory." );
+				else
+					return thumbnails.toFile().getAbsolutePath();
+			}
+		}
+		final Path thumbnails = Files.createTempDirectory( "thumbnails" );
+		thumbnails.toFile().deleteOnExit();
+		return thumbnails.toFile().getAbsolutePath();
+	}
+
+	private static ContextHandlerCollection createHandlers( final String baseURL, final Map< String, String > dataSet, final String thumbnailsDirectoryName ) throws SpimDataException, IOException
 	{
 		final ContextHandlerCollection handlers = new ContextHandlerCollection();
 
@@ -276,7 +335,7 @@ public class BigDataServer
 			final String name = entry.getKey();
 			final String xmlpath = entry.getValue();
 			final String context = "/" + name;
-			final CellHandler ctx = new CellHandler( baseURL + context + "/", xmlpath );
+			final CellHandler ctx = new CellHandler( baseURL + context + "/", xmlpath, name, thumbnailsDirectoryName );
 			ctx.setContextPath( context );
 			handlers.addHandler( ctx );
 		}

src/main/java/bdv/server/CellHandler.java

@@ -78,7 +78,12 @@ public class CellHandler extends ContextHandler
 	 */
 	private final String settingsXmlString;
 
-	public CellHandler( final String baseUrl, final String xmlFilename ) throws SpimDataException, IOException
+	/**
+	 * Full path to thumbnail png.
+	 */
+	private final String thumbnailFilename;
+
+	public CellHandler( final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory ) throws SpimDataException, IOException
 	{
 		final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
 		final SpimDataMinimal spimData = io.load( xmlFilename );
@@ -97,7 +102,7 @@ public class CellHandler extends ContextHandler
 		datasetXmlString = buildRemoteDatasetXML( io, spimData, baseUrl );
 		metadataJson = buildMetadataJsonString( imgLoader, seq );
 		settingsXmlString = buildSettingsXML( baseFilename );
-		createThumbnail( spimData, baseFilename );
+		thumbnailFilename = createThumbnail( spimData, baseFilename, datasetName, thumbnailsDirectory );
 	}
 
 	@Override
@@ -170,9 +175,7 @@ public class CellHandler extends ContextHandler
 
 	private void provideThumbnail( final Request baseRequest, final HttpServletResponse response ) throws IOException
 	{
-		// Just check it once
-		final Path path = Paths.get( baseFilename + ".png" );
-
+		final Path path = Paths.get( thumbnailFilename );
 		if ( Files.exists( path ) )
 		{
 			final byte[] imageData = Files.readAllBytes(path);
@@ -270,19 +273,25 @@ public class CellHandler extends ContextHandler
 	/**
 	 * Create PNG thumbnail file named "{@code <baseFilename>.png}".
 	 */
-	private static void createThumbnail( final SpimDataMinimal spimData, final String baseFilename )
+	private static String createThumbnail( final SpimDataMinimal spimData, final String baseFilename, final String datasetName, final String thumbnailsDirectory )
 	{
-		final File thumbnailFile = new File( baseFilename + ".png" );
-		final BufferedImage bi = ThumbnailGenerator.makeThumbnail( spimData, baseFilename, Constants.THUMBNAIL_WIDTH, Constants.THUMBNAIL_HEIGHT );
-		try
-		{
-			ImageIO.write( bi, "png", thumbnailFile );
-		}
-		catch ( final IOException e )
+		final String thumbnailFileName = thumbnailsDirectory + "/" + datasetName + ".png";
+		final File thumbnailFile = new File( thumbnailFileName );
+		if ( !thumbnailFile.isFile() ) // do not recreate thumbnail if it
+										// already exists
 		{
-			LOG.warn( "Could not create thumbnail png for dataset \"" + baseFilename + "\"" );
-			LOG.warn( e.getMessage() );
+			final BufferedImage bi = ThumbnailGenerator.makeThumbnail( spimData, baseFilename, Constants.THUMBNAIL_WIDTH, Constants.THUMBNAIL_HEIGHT );
+			try
+			{
+				ImageIO.write( bi, "png", thumbnailFile );
+			}
+			catch ( final IOException e )
+			{
+				LOG.warn( "Could not create thumbnail png for dataset \"" + baseFilename + "\"" );
+				LOG.warn( e.getMessage() );
+			}
 		}
+		return thumbnailFileName;
 	}
 
 	/**

src/main/java/bdv/server/ManagerHandler.java

@@ -23,6 +23,10 @@ import java.io.PrintWriter;
 import java.net.URISyntaxException;
 import java.text.DecimalFormat;
 
+/**
+ * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ */
 public class ManagerHandler extends ContextHandler
 {
 	private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( ManagerHandler.class );
@@ -43,13 +47,23 @@ public class ManagerHandler extends ContextHandler
 
 	private long sizeDataSets = 0;
 
-	public ManagerHandler( final String baseURL, final Server server, final ConnectorStatistics connectorStats, final StatisticsHandler statHandler, final ContextHandlerCollection handlers ) throws IOException, URISyntaxException
+	private final String thumbnailsDirectoryName;
+
+	public ManagerHandler(
+			final String baseURL,
+			final Server server,
+			final ConnectorStatistics connectorStats,
+			final StatisticsHandler statHandler,
+			final ContextHandlerCollection handlers,
+			final String thumbnailsDirectoryName )
+					throws IOException, URISyntaxException
 	{
 		this.baseURL = baseURL;
 		this.server = server;
 		this.handlers = handlers;
 		this.statHandler = statHandler;
 		this.connectorStats = connectorStats;
+		this.thumbnailsDirectoryName = thumbnailsDirectoryName;
 		setContextPath( "/" + Constants.MANAGER_CONTEXT_NAME );
 	}
 
@@ -77,7 +91,6 @@ public class ManagerHandler extends ContextHandler
 		{
 			return;
 		}
-
 	}
 
 	public String getByteSizeString( final long size )
@@ -103,11 +116,8 @@ public class ManagerHandler extends ContextHandler
 
 	private String getHtml()
 	{
-		// manager.st should be under {WorkingFolder}/templates/
-		final StringTemplateGroup templates =
-				new StringTemplateGroup( "manager", "templates" );
-
-		final StringTemplate t = templates.getInstanceOf( "manager" );
+		final StringTemplateGroup templates = new StringTemplateGroup( "manager" );
+		final StringTemplate t = templates.getInstanceOf( "templates/manager" );
 
 		t.setAttribute( "bytesSent", getByteSizeString( statHandler.getResponsesBytesTotal() ) );
 		t.setAttribute( "msgPerSec", connectorStats.getMessagesOutPerSecond() );
@@ -136,16 +146,12 @@ public class ManagerHandler extends ContextHandler
 			final StringBuilder sb = new StringBuilder();
 			for ( final Handler handler : server.getChildHandlersByClass( CellHandler.class ) )
 			{
-				CellHandler contextHandler = null;
-				if ( handler instanceof CellHandler )
-				{
-					sb.append( "<tr>\n<th>" );
-					contextHandler = ( CellHandler ) handler;
-					sb.append( contextHandler.getContextPath() + "</th>\n<td>" );
-					sb.append( contextHandler.getXmlFile() + "</td>\n</tr>\n" );
-					noDataSets++;
-					sizeDataSets += new File( contextHandler.getXmlFile().replace( ".xml", ".h5" ) ).length();
-				}
+				sb.append( "<tr>\n<th>" );
+				final CellHandler contextHandler = ( CellHandler ) handler;
+				sb.append( contextHandler.getContextPath() + "</th>\n<td>" );
+				sb.append( contextHandler.getXmlFile() + "</td>\n</tr>\n" );
+				noDataSets++;
+				sizeDataSets += new File( contextHandler.getXmlFile().replace( ".xml", ".h5" ) ).length();
 			}
 			contexts = sb.toString();
 		}
@@ -154,25 +160,45 @@ public class ManagerHandler extends ContextHandler
 	private void deploy( final String datasetName, final String fileLocation, final Request baseRequest, final HttpServletResponse response ) throws IOException
 	{
 		LOG.info( "Add new context: " + datasetName );
-		CellHandler ctx = null;
-		try
+		final String context = "/" + datasetName;
+
+		boolean alreadyExists = false;
+		for ( final Handler handler : server.getChildHandlersByClass( CellHandler.class ) )
 		{
-			ctx = new CellHandler( baseURL + datasetName + "/", fileLocation );
+			final CellHandler contextHandler = ( CellHandler ) handler;
+			if ( context.equals( contextHandler.getContextPath() ) )
+			{
+				LOG.info( "Context " + datasetName + " already exists.");
+				alreadyExists = true;
+				break;
+			}
 		}
-		catch ( final SpimDataException e )
+
+		if ( ! alreadyExists )
 		{
-			LOG.warn( "Failed to create a CellHandler", e );
-			e.printStackTrace();
+			CellHandler ctx = null;
+			try
+			{
+				ctx = new CellHandler( baseURL + context + "/", fileLocation, datasetName, thumbnailsDirectoryName );
+			}
+			catch ( final SpimDataException e )
+			{
+				LOG.warn( "Failed to create a CellHandler", e );
+				e.printStackTrace();
+			}
+			ctx.setContextPath( context );
+			handlers.addHandler( ctx );
 		}
-		ctx.setContextPath( "/" + datasetName );
-		handlers.addHandler( ctx );
 
 		response.setContentType( "text/html" );
 		response.setStatus( HttpServletResponse.SC_OK );
 		baseRequest.setHandled( true );
 
 		final PrintWriter ow = response.getWriter();
-		ow.write( datasetName + " registered." );
+		if ( alreadyExists )
+			ow.write( datasetName + " already exists. Not registered." );
+		else
+			ow.write( datasetName + " registered." );
 		ow.close();
 	}
 
@@ -181,27 +207,24 @@ public class ManagerHandler extends ContextHandler
 		LOG.info( "Remove the context: " + datasetName );
 		boolean ret = false;
 
+		final String context = "/" + datasetName;
 		for ( final Handler handler : server.getChildHandlersByClass( CellHandler.class ) )
 		{
-			CellHandler contextHandler = null;
-			if ( handler instanceof CellHandler )
+			final CellHandler contextHandler = ( CellHandler ) handler;
+			if ( context.equals( contextHandler.getContextPath() ) )
 			{
-				contextHandler = ( CellHandler ) handler;
-				if ( datasetName.equals( contextHandler.getContextPath() ) )
+				try
+				{
+					contextHandler.stop();
+				}
+				catch ( final Exception e )
 				{
-					try
-					{
-						contextHandler.stop();
-					}
-					catch ( final Exception e )
-					{
-						e.printStackTrace();
-					}
-					contextHandler.destroy();
-					handlers.removeHandler( contextHandler );
-					ret = true;
-					break;
+					e.printStackTrace();
 				}
+				contextHandler.destroy();
+				handlers.removeHandler( contextHandler );
+				ret = true;
+				break;
 			}
 		}