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From chath...@apache.org
Subject svn commit: r1164715 [1/2] - in /incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya: ./ appwrapper/ component/ component/dynamic/ component/gui/ component/registry/ component/system/ component/ws/ experiment/gui/ file/gu...
Date Fri, 02 Sep 2011 21:26:07 GMT
Author: chathura
Date: Fri Sep  2 21:26:03 2011
New Revision: 1164715

URL: http://svn.apache.org/viewvc?rev=1164715&view=rev
Log:
Code Cleanup:

Removing noops
Removing Sysouts that are not part of tooling
Remove printing exceptions to logging them

Modified:
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/GpelWorkflowClient.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ProxyServiceTester.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/RegisterThroughFileWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/SearchAndEditWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/StreamSourceComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/CepComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/DynamicInvoker.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/GenericSubWorkflowComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentSelector.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentViewer.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/StreamSourceNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/URLRegistryWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/WebResigtoryWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/LocalComponentRegistry.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/SystemComponentRegistry.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/URLComponentRegistry.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndBlockComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndifComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/SystemComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/InteractionComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentFactory.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/ExperimentMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryLoaderWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryWorkflowPublisherWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/file/gui/FileMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/GPELRegistry.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/SubWorkflowUpdater.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/gui/GPELLoadWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/script/WorkflowWSDL.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/DataPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/EPRPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/amazon/InstanceDataPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/BasicTypeMapping.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/DynamicPort.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/impl/PortImpl.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/subworkflow/SubWorkflowNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/BlockNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndBlockNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndForEachNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndifNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ForEachNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/IfNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ParameterNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ReceiveNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/SystemNode.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/BlockNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/ConstantNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/EndBlockNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/EndForEachNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/EndifNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/ForEachNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/IfNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/InputConfigurationDialog.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/InputNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/MemoNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/OutputNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/gui/ReceiveNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/util/GraphUtil.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gridftp/GridFtpClient.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gui/WaitDialog.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gui/XBayaDialog.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/gui/
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/AsynchronousInvoker.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/GFacInvoker.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/jython/runner/JythonClassLoader.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/jython/script/JythonScript.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/lead/LEADWorkflowInvoker.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/monitor/MonitorEvent.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/monitor/gui/MonitorPanel.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/monitor/gui/MonitorWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/myproxy/gui/MyProxyChecker.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/myproxy/gui/MyProxyMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ode/ODEInvokerWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ode/ODEWSDLTransformer.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/pegasus/gui/PegasusInvokerWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/pegasus/gui/PegasusMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/streaming/StreamReceiveNodeGUI.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/streaming/StreamTransformer.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/test/LEADWorkflowInvokerTestCase.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/test/MetadataTestCase.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/test/WebComponentRegistryClientTestCase.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XMLUtil.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/wf/gui/WorkflowMenu.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/workflow/WorkflowEngineManager.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/workflow/proxy/GPELWorkflowClient.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/workflow/proxy/WorkflowProxyClient.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/xregistry/XRegistryLoaderWindow.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/xsd/LeadContextHeaderXSD.java
    incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/xsd/LeadCrosscutXSD.java

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/GpelWorkflowClient.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/GpelWorkflowClient.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/GpelWorkflowClient.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/GpelWorkflowClient.java Fri Sep  2 21:26:03 2011
@@ -65,53 +65,7 @@ import xsul5.wsdl.WsdlDefinitions;
 
 public class GpelWorkflowClient implements Callback {
 
-    public static void main(String[] args) throws Exception {
-
-        // new GPELClient()
-        String userName = "chathura";
-        String password = "changeme";
-        String topic = "chathura_client";
-        String workflowFile = "/nfs/mneme/home/users/cherath/projects/test/extremeWorkspace/xbaya/workflows/Vortex_Chathura_Dbg2.xwf";
-        Workflow workflow = getWorkflow(workflowFile);
-
-        List<WSComponentPort> inputs = workflow.getInputs();
-
-        for (Iterator iterator = inputs.iterator(); iterator.hasNext();) {
-            WSComponentPort componentPort = (WSComponentPort) iterator.next();
-            if ("CrossCuttingConfigurations".equals(componentPort.getName())) {
-                componentPort
-                        .setDefaultValue("<CrossCuttingConfigurations  xmlns:lcp=\"http://lead.extreme.indiana.edu/namespaces/2006/lead-crosscut-parameters/\">"
-                                + "<lcp:nx>803</lcp:nx>"
-                                + "<lcp:ny>803</lcp:ny>"
-                                + "<lcp:dx>1000</lcp:dx>"
-                                + "<lcp:dy>1000</lcp:dy>"
-                                + "<lcp:ctrlat>35.746513</lcp:ctrlat>"
-                                + "<lcp:ctrlon>-89.64844</lcp:ctrlon>"
-                                + "<lcp:fcst_time>18.0</lcp:fcst_time>"
-                                + "<lcp:start_date>2010/04/08</lcp:start_date>"
-                                + "<lcp:start_hour>3</lcp:start_hour>"
-                                + "<lcp:westbc>-93.2417</lcp:westbc>"
-                                + "<lcp:eastbc>-86.055176</lcp:eastbc>"
-                                + "<lcp:northbc>38.620865</lcp:northbc>"
-                                + "<lcp:southbc>32.763515</lcp:southbc>"
-                                + "</CrossCuttingConfigurations>");
-            } else if ("AssimilatedADASData".equals(componentPort.getName())) {
-                componentPort
-                        .setDefaultValue("gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/other/lead/ADAS/10kmnet000000/ad2010040803.net000000 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/other/lead/ADAS/10kmnetgrdbas/ad2010040803.netgrdbas");
-            } else if ("NAMInitialData".equals(componentPort.getName())) {
-                componentPort
-                        .setDefaultValue("gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f06 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f09 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f12 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f15 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f18 gsiftp://gridftp.bigred.iu.teragrid.org:2812//N/dc/projects/lead/ldm/pub/native/grid/NCEP/LEADNAM/2010040800/nam40grb2.2010040800f21");
-            }
-        }
-
-        invoke(userName, password, topic, workflow, inputs);
-
-        LeadNotificationManager.createMessageBoxSubscription("http://127.0.0.1:13333/MsgBox", "127.0.0.1:12346",
-                "topic123", "", new GpelWorkflowClient(), false);
-
-    }
-
-    /**
+   /**
      * 
      * @param workflowFileName
      * @return

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ProxyServiceTester.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ProxyServiceTester.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ProxyServiceTester.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ProxyServiceTester.java Fri Sep  2 21:26:03 2011
@@ -55,8 +55,6 @@ import edu.indiana.extreme.weps.XMLFile;
 
 public class ProxyServiceTester {
 
-    // private final static MLogger logger = MLogger.getLogger();
-    // private String wsdlLocation = "http://bleu.extreme.indiana.edu:54321/axis2/services/WEPSService?wsdl";
     private String wsdlLoc = "http://localhost:8081/axis2/services/WEPSService?wsdl";
 
     private void runClient() {

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java Fri Sep  2 21:26:03 2011
@@ -322,30 +322,6 @@ public class XBayaEngine {
                         XBayaEngine.this.setXRegistryURL(XBayaEngine.this.configuration.getXRegistryURL());
                         ComponentTreeNode componentTree = client.getComponentTree();
                         componentTreeViewer.addComponentTree(componentTree);
-                        // TreeNode[] path = componentTree.getPath();
-                        // JTree swingComponent = componentTreeViewer.getSwingComponent();
-                        // swingComponent.expandPath(
-                        // new TreePath(path));
-                        // for (int i = 0; i < path.length; i++) {
-                        // Enumeration children = path[i].children();
-                        // while (children.hasMoreElements()) {
-                        // Object elemt = children.nextElement();
-                        // if (elemt instanceof ComponentTreeNode) {
-                        // ComponentTreeNode treeNode = (ComponentTreeNode) elemt;
-                        // TreeNode[] newPath = treeNode.getPath();
-                        // swingComponent.expandPath(
-                        // new TreePath(newPath));
-                        // swingComponent.repaint();
-                        //
-                        // }
-                        // }
-                        // }
-                        // gui.getComponentSelector().refresh();
-                        // int count = gui.getComponentSelector().getSwingComponent().getComponentCount();
-                        // for (int i = 0; i < count; i++) {
-                        //
-                        // gui.getComponentSelector().getSwingComponent().getComponent(i).repaint();
-                        // }
 
                     } catch (ComponentRegistryException e) {
                         getErrorWindow().error(ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/RegisterThroughFileWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/RegisterThroughFileWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/RegisterThroughFileWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/RegisterThroughFileWindow.java Fri Sep  2 21:26:03 2011
@@ -65,7 +65,6 @@ public class RegisterThroughFileWindow {
     }
 
     private RegisterThroughFileWindow() {
-        // initGUI();
     }
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/SearchAndEditWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/SearchAndEditWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/SearchAndEditWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/appwrapper/SearchAndEditWindow.java Fri Sep  2 21:26:03 2011
@@ -88,7 +88,6 @@ public class SearchAndEditWindow {
     }
 
     private SearchAndEditWindow() {
-        // initGUI();
     }
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/StreamSourceComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/StreamSourceComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/StreamSourceComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/StreamSourceComponent.java Fri Sep  2 21:26:03 2011
@@ -54,10 +54,6 @@ public class StreamSourceComponent exten
         setName(NAME);
         setDescription(DESCRIPTION);
 
-        // SystemComponentDataPort port = new
-        // SystemComponentDataPort(PORT_NAME);
-        // port.setDescription(PORT_DESCRIPTION);
-        // this.outputs.add(port);
     }
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/CepComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/CepComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/CepComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/CepComponent.java Fri Sep  2 21:26:03 2011
@@ -44,12 +44,6 @@ public class CepComponent extends Compon
      */
     protected List<CepComponentPort> outputs;
 
-    // protected URL implJarLocation;
-
-    // protected String operationName;
-
-    // protected String className;
-
     public CepComponent() {
         super();
         setName(NAME);

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/DynamicInvoker.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/DynamicInvoker.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/DynamicInvoker.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/DynamicInvoker.java Fri Sep  2 21:26:03 2011
@@ -98,7 +98,6 @@ public class DynamicInvoker implements I
      * @see org.apache.airavata.xbaya.invoker.WorkflowInvoker#setInput(java.lang.String, java.lang.Object)
      */
     public void setInput(String name, Object value) throws XBayaException {
-        // TODO Auto-generated method stub
 
     }
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/GenericSubWorkflowComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/GenericSubWorkflowComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/GenericSubWorkflowComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/dynamic/GenericSubWorkflowComponent.java Fri Sep  2 21:26:03 2011
@@ -62,7 +62,6 @@ public class GenericSubWorkflowComponent
      */
     @Override
     public List<CepComponentPort> getInputPorts() {
-        // TODO Auto-generated method stub
         return this.inputs;
     }
 
@@ -71,7 +70,6 @@ public class GenericSubWorkflowComponent
      */
     @Override
     public List<CepComponentPort> getOutputPorts() {
-        // TODO Auto-generated method stub
         return this.outputs;
     }
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentMenu.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentMenu.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentMenu.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentMenu.java Fri Sep  2 21:26:03 2011
@@ -47,285 +47,310 @@ import org.ogce.xregistry.utils.XRegistr
 
 public class ComponentMenu {
 
-    private XBayaEngine engine;
+	private XBayaEngine engine;
 
-    private JMenu componentMenu;
+	private JMenu componentMenu;
 
-    private JMenuItem fileRegistryItem;
+	private JMenuItem fileRegistryItem;
 
-    private JMenuItem webItem;
+	private JMenuItem webItem;
 
-    private JMenuItem urlItem;
-
-    private JMenuItem removeItem;
-
-    private JMenuItem refreshSelectedItem;
-
-    private JMenuItem refreshAllItem;
-
-    private JMenuItem xregistryItem;
-
-    private JMenuItem streamSourceItem;
-
-    private JMenuItem workflowItem;
-    
-    private JMenuItem jcrRegistryItem;
-
-    /**
-     * Constructs a ComponentMenu.
-     * 
-     * @param engine
-     * 
-     */
-    public ComponentMenu(XBayaEngine engine) {
-        this.engine = engine;
-        createComponentMenu();
-    }
-
-    /**
-     * @return The component menu.
-     */
-    public JMenu getMenu() {
-        return this.componentMenu;
-    }
-
-    private void createComponentMenu() {
-        this.fileRegistryItem = createFileRegistryMenuItem();
-        this.jcrRegistryItem = createJCRRegistryItem();
-        this.xregistryItem = createXRegistryItem();
-        this.webItem = createWebRegistryItem();
-        this.urlItem = createURLRegistryItem();
-        this.workflowItem = createWorkflowItem();
-        this.removeItem = createRemoveRegistryItem();
-        this.refreshSelectedItem = createRefreshSelectedRegistryItem();
-        this.refreshAllItem = createRefreshAllRegistriesItem();
-        this.streamSourceItem = createStreamSourceItem();
-
-        this.componentMenu = new JMenu("Component");
-        this.componentMenu.setMnemonic(KeyEvent.VK_C);
-        this.componentMenu.add(this.fileRegistryItem);
-        this.componentMenu.add(this.xregistryItem);
-        this.componentMenu.add(this.jcrRegistryItem);
-        this.componentMenu.add(this.webItem);
-        this.componentMenu.add(this.urlItem);
-        this.componentMenu.add(this.workflowItem);
-        this.componentMenu.addSeparator();
-        this.componentMenu.add(this.removeItem);
-        this.componentMenu.addSeparator();
-        this.componentMenu.add(this.refreshSelectedItem);
-        this.componentMenu.add(this.refreshAllItem);
-        this.componentMenu.addSeparator();
-        this.componentMenu.add(this.streamSourceItem);
-    }
-
-    /**
-     * @return
-     */
-    private JMenuItem createWorkflowItem() {
-        JMenuItem item = new JMenuItem("Load Workflow Component");
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent event) {
-                new Thread() {
-                    @Override
-                    public void run() {
-                        Workflow workflow = new WorkflowFiler(ComponentMenu.this.engine).getWorkflow();
-                        // //to normalize and build the scripts
-                        // new ODEClient().getInputs(workflow);
-                        try {
-                            ComponentMenu.this.engine.addWorkflowComponent(workflow.getName(),
-                                    SubWorkflowComponent.getInstance(workflow));
-
-                        } catch (ComponentException e) {
-                            // TODO Auto-generated catch block
-                            e.printStackTrace();
-                        }
-                    }
-                }.start();
-            }
-        });
-        return item;
-    }
-
-    /**
-     * @return
-     */
-    private JMenuItem createStreamSourceItem() {
-        JMenuItem item = new JMenuItem("Load Stream Sources");
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent event) {
-                new Thread() {
-                    @Override
-                    public void run() {
-                        try {
-                            ComponentMenu.this.engine.getGUI().addStreamSources(
-                                    new StreamTableModel(ComponentMenu.this.engine));
-                            ComponentMenu.this.streamSourceItem.setEnabled(false);
-                        } catch (MalformedURLException e) {
-                            ComponentMenu.this.engine.getErrorWindow().error(e);
-                        } catch (XRegistryClientException e) {
-                            ComponentMenu.this.engine.getErrorWindow().error(e);
-                        }
-                    }
-                }.start();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createRefreshSelectedRegistryItem() {
-        JMenuItem item = new JMenuItem("Refresh Selected Registry");
-        // this.refreshItem.setMnemonic(KeyEvent.VK_R);
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent event) {
-                new Thread() {
-                    @Override
-                    public void run() {
-                        try {
-                            ComponentMenu.this.engine.getGUI().getComponentSelector().updateSelectedRegistry();
-                        } catch (ComponentRegistryException e) {
-                            ComponentMenu.this.engine.getErrorWindow()
-                                    .error(ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
-                        } catch (RuntimeException e) {
-                            ComponentMenu.this.engine.getErrorWindow()
-                                    .error(ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
-                        } catch (Error e) {
-                            ComponentMenu.this.engine.getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
-                        }
-                    }
-                }.start();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createRefreshAllRegistriesItem() {
-        JMenuItem item = new JMenuItem("Refresh All Registries");
-        // this.refreshItem.setMnemonic(KeyEvent.VK_E);
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent event) {
-                new Thread() {
-                    @Override
-                    public void run() {
-                        try {
-                            ComponentMenu.this.engine.getGUI().getComponentSelector().update();
-                        } catch (ComponentRegistryException e) {
-                            ComponentMenu.this.engine.getErrorWindow()
-                                    .error(ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
-                        } catch (RuntimeException e) {
-                            ComponentMenu.this.engine.getErrorWindow()
-                                    .error(ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
-                        } catch (Error e) {
-                            ComponentMenu.this.engine.getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
-                        }
-                    }
-                }.start();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createRemoveRegistryItem() {
-        JMenuItem item = new JMenuItem("Remove Selected Registry");
-        item.setMnemonic(KeyEvent.VK_R);
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent event) {
-                try {
-                    ComponentMenu.this.engine.getGUI().getComponentSelector().removeSelectedRegistry();
-                } catch (RuntimeException e) {
-                    ComponentMenu.this.engine.getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
-                } catch (Error e) {
-                    ComponentMenu.this.engine.getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
-                }
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createWebRegistryItem() {
-        JMenuItem item = new JMenuItem("Add Web Registry");
-        item.setMnemonic(KeyEvent.VK_W);
-        item.addActionListener(new AbstractAction() {
-            private WebResigtoryWindow window;
-
-            public void actionPerformed(ActionEvent e) {
-                if (this.window == null) {
-                    this.window = new WebResigtoryWindow(ComponentMenu.this.engine);
-                }
-                this.window.show();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createURLRegistryItem() {
-        JMenuItem item = new JMenuItem("Add WSDL by URL");
-        item.setMnemonic(KeyEvent.VK_U);
-        item.addActionListener(new AbstractAction() {
-            private URLRegistryWindow window;
-
-            public void actionPerformed(ActionEvent e) {
-                if (this.window == null) {
-                    this.window = new URLRegistryWindow(ComponentMenu.this.engine);
-                }
-                this.window.show();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createXRegistryItem() {
-        JMenuItem item = new JMenuItem("Add XRegistry");
-        item.setMnemonic(KeyEvent.VK_X);
-        item.addActionListener(new AbstractAction() {
-            private XRegistryWindow window;
-
-            public void actionPerformed(ActionEvent e) {
-                if (this.window == null) {
-                    this.window = new XRegistryWindow(ComponentMenu.this.engine);
-                }
-                this.window.show();
-            }
-        });
-        return item;
-    }
-    
-    private JMenuItem createJCRRegistryItem() {
-        JMenuItem item = new JMenuItem("Add JCR Registry");
-        item.setMnemonic(KeyEvent.VK_J);
-        item.addActionListener(new AbstractAction() {
-            private JCRRegistryWindow window;
-
-            public void actionPerformed(ActionEvent e) {
-                if (this.window == null) {
-                    this.window = new JCRRegistryWindow(ComponentMenu.this.engine);
-                }
-                this.window.show();
-            }
-        });
-        return item;
-    }
-
-    private JMenuItem createFileRegistryMenuItem() {
-        JMenuItem item = new JMenuItem("Add Local Directory");
-        item.setMnemonic(KeyEvent.VK_L);
-        item.addActionListener(new AbstractAction() {
-            public void actionPerformed(ActionEvent e) {
-                registerComponentLocalDirectory();
-            }
-        });
-        return item;
-    }
-
-    private void registerComponentLocalDirectory() {
-        JFileChooser fileChooser = new JFileChooser(XBayaPathConstants.WSDL_DIRECTORY);
-        fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
-        int returnVal = fileChooser.showOpenDialog(this.engine.getGUI().getFrame().getContentPane());
-        if (returnVal == JFileChooser.APPROVE_OPTION) {
-            File directory = fileChooser.getSelectedFile();
-            LocalComponentRegistry registry = new LocalComponentRegistry(directory);
-            // move to another thread using loader.
-            ComponentRegistryLoader loader = new ComponentRegistryLoader(this.engine);
-            loader.load(registry);
-        }
-    }
+	private JMenuItem urlItem;
+
+	private JMenuItem removeItem;
+
+	private JMenuItem refreshSelectedItem;
+
+	private JMenuItem refreshAllItem;
+
+	private JMenuItem xregistryItem;
+
+	private JMenuItem streamSourceItem;
+
+	private JMenuItem workflowItem;
+
+	private JMenuItem jcrRegistryItem;
+
+	/**
+	 * Constructs a ComponentMenu.
+	 * 
+	 * @param engine
+	 * 
+	 */
+	public ComponentMenu(XBayaEngine engine) {
+		this.engine = engine;
+		createComponentMenu();
+	}
+
+	/**
+	 * @return The component menu.
+	 */
+	public JMenu getMenu() {
+		return this.componentMenu;
+	}
+
+	private void createComponentMenu() {
+		this.fileRegistryItem = createFileRegistryMenuItem();
+		this.jcrRegistryItem = createJCRRegistryItem();
+		this.xregistryItem = createXRegistryItem();
+		this.webItem = createWebRegistryItem();
+		this.urlItem = createURLRegistryItem();
+		this.workflowItem = createWorkflowItem();
+		this.removeItem = createRemoveRegistryItem();
+		this.refreshSelectedItem = createRefreshSelectedRegistryItem();
+		this.refreshAllItem = createRefreshAllRegistriesItem();
+		this.streamSourceItem = createStreamSourceItem();
+
+		this.componentMenu = new JMenu("Component");
+		this.componentMenu.setMnemonic(KeyEvent.VK_C);
+		this.componentMenu.add(this.fileRegistryItem);
+		this.componentMenu.add(this.xregistryItem);
+		this.componentMenu.add(this.jcrRegistryItem);
+		this.componentMenu.add(this.webItem);
+		this.componentMenu.add(this.urlItem);
+		this.componentMenu.add(this.workflowItem);
+		this.componentMenu.addSeparator();
+		this.componentMenu.add(this.removeItem);
+		this.componentMenu.addSeparator();
+		this.componentMenu.add(this.refreshSelectedItem);
+		this.componentMenu.add(this.refreshAllItem);
+		this.componentMenu.addSeparator();
+		this.componentMenu.add(this.streamSourceItem);
+	}
+
+	/**
+	 * @return
+	 */
+	private JMenuItem createWorkflowItem() {
+		JMenuItem item = new JMenuItem("Load Workflow Component");
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent event) {
+				new Thread() {
+					@Override
+					public void run() {
+						Workflow workflow = new WorkflowFiler(
+								ComponentMenu.this.engine).getWorkflow();
+						// //to normalize and build the scripts
+						try {
+							ComponentMenu.this.engine.addWorkflowComponent(
+									workflow.getName(),
+									SubWorkflowComponent.getInstance(workflow));
+
+						} catch (ComponentException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (RuntimeException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (Error e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.UNEXPECTED_ERROR, e);
+						}
+					}
+				}.start();
+			}
+		});
+		return item;
+	}
+
+	/**
+	 * @return
+	 */
+	private JMenuItem createStreamSourceItem() {
+		JMenuItem item = new JMenuItem("Load Stream Sources");
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent event) {
+				new Thread() {
+					@Override
+					public void run() {
+						try {
+							ComponentMenu.this.engine.getGUI()
+									.addStreamSources(
+											new StreamTableModel(
+													ComponentMenu.this.engine));
+							ComponentMenu.this.streamSourceItem
+									.setEnabled(false);
+						} catch (MalformedURLException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(e);
+						} catch (XRegistryClientException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(e);
+						}
+					}
+				}.start();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createRefreshSelectedRegistryItem() {
+		JMenuItem item = new JMenuItem("Refresh Selected Registry");
+		// this.refreshItem.setMnemonic(KeyEvent.VK_R);
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent event) {
+				new Thread() {
+					@Override
+					public void run() {
+						try {
+							ComponentMenu.this.engine.getGUI()
+									.getComponentSelector()
+									.updateSelectedRegistry();
+						} catch (ComponentRegistryException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (RuntimeException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (Error e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.UNEXPECTED_ERROR, e);
+						}
+					}
+				}.start();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createRefreshAllRegistriesItem() {
+		JMenuItem item = new JMenuItem("Refresh All Registries");
+		// this.refreshItem.setMnemonic(KeyEvent.VK_E);
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent event) {
+				new Thread() {
+					@Override
+					public void run() {
+						try {
+							ComponentMenu.this.engine.getGUI()
+									.getComponentSelector().update();
+						} catch (ComponentRegistryException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (RuntimeException e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.COMPONENT_LIST_LOAD_ERROR, e);
+						} catch (Error e) {
+							ComponentMenu.this.engine.getErrorWindow().error(
+									ErrorMessages.UNEXPECTED_ERROR, e);
+						}
+					}
+				}.start();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createRemoveRegistryItem() {
+		JMenuItem item = new JMenuItem("Remove Selected Registry");
+		item.setMnemonic(KeyEvent.VK_R);
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent event) {
+				try {
+					ComponentMenu.this.engine.getGUI().getComponentSelector()
+							.removeSelectedRegistry();
+				} catch (RuntimeException e) {
+					ComponentMenu.this.engine.getErrorWindow().error(
+							ErrorMessages.UNEXPECTED_ERROR, e);
+				} catch (Error e) {
+					ComponentMenu.this.engine.getErrorWindow().error(
+							ErrorMessages.UNEXPECTED_ERROR, e);
+				}
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createWebRegistryItem() {
+		JMenuItem item = new JMenuItem("Add Web Registry");
+		item.setMnemonic(KeyEvent.VK_W);
+		item.addActionListener(new AbstractAction() {
+			private WebResigtoryWindow window;
+
+			public void actionPerformed(ActionEvent e) {
+				if (this.window == null) {
+					this.window = new WebResigtoryWindow(
+							ComponentMenu.this.engine);
+				}
+				this.window.show();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createURLRegistryItem() {
+		JMenuItem item = new JMenuItem("Add WSDL by URL");
+		item.setMnemonic(KeyEvent.VK_U);
+		item.addActionListener(new AbstractAction() {
+			private URLRegistryWindow window;
+
+			public void actionPerformed(ActionEvent e) {
+				if (this.window == null) {
+					this.window = new URLRegistryWindow(
+							ComponentMenu.this.engine);
+				}
+				this.window.show();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createXRegistryItem() {
+		JMenuItem item = new JMenuItem("Add XRegistry");
+		item.setMnemonic(KeyEvent.VK_X);
+		item.addActionListener(new AbstractAction() {
+			private XRegistryWindow window;
+
+			public void actionPerformed(ActionEvent e) {
+				if (this.window == null) {
+					this.window = new XRegistryWindow(ComponentMenu.this.engine);
+				}
+				this.window.show();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createJCRRegistryItem() {
+		JMenuItem item = new JMenuItem("Add JCR Registry");
+		item.setMnemonic(KeyEvent.VK_J);
+		item.addActionListener(new AbstractAction() {
+			private JCRRegistryWindow window;
+
+			public void actionPerformed(ActionEvent e) {
+				if (this.window == null) {
+					this.window = new JCRRegistryWindow(
+							ComponentMenu.this.engine);
+				}
+				this.window.show();
+			}
+		});
+		return item;
+	}
+
+	private JMenuItem createFileRegistryMenuItem() {
+		JMenuItem item = new JMenuItem("Add Local Directory");
+		item.setMnemonic(KeyEvent.VK_L);
+		item.addActionListener(new AbstractAction() {
+			public void actionPerformed(ActionEvent e) {
+				registerComponentLocalDirectory();
+			}
+		});
+		return item;
+	}
+
+	private void registerComponentLocalDirectory() {
+		JFileChooser fileChooser = new JFileChooser(
+				XBayaPathConstants.WSDL_DIRECTORY);
+		fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+		int returnVal = fileChooser.showOpenDialog(this.engine.getGUI()
+				.getFrame().getContentPane());
+		if (returnVal == JFileChooser.APPROVE_OPTION) {
+			File directory = fileChooser.getSelectedFile();
+			LocalComponentRegistry registry = new LocalComponentRegistry(
+					directory);
+			// move to another thread using loader.
+			ComponentRegistryLoader loader = new ComponentRegistryLoader(
+					this.engine);
+			loader.load(registry);
+		}
+	}
 }
\ No newline at end of file

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentSelector.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentSelector.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentSelector.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentSelector.java Fri Sep  2 21:26:03 2011
@@ -83,8 +83,6 @@ public class ComponentSelector implement
 
     private JTree tree;
 
-    // private ComponentTreeNode rootNode;
-
     private ComponentTreeModel treeModel;
 
     private ComponentReference selectedComponentReference;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentViewer.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentViewer.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentViewer.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/ComponentViewer.java Fri Sep  2 21:26:03 2011
@@ -47,8 +47,6 @@ public class ComponentViewer implements 
     private static final String DEFAULT_HTML_MESSAGE = "<html> Select a component from the " + ComponentSelector.TITLE
             + ".</html>";
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private Component currentComponent;
 
     private JEditorPane editorPane;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/StreamSourceNodeGUI.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/StreamSourceNodeGUI.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/StreamSourceNodeGUI.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/StreamSourceNodeGUI.java Fri Sep  2 21:26:03 2011
@@ -62,59 +62,6 @@ public class StreamSourceNodeGUI extends
         this.configurationWindow.show();
     }
 
-    // protected void paint(Graphics2D g) {
-    //
-    // Point position = this.node.getPosition();
-    //
-    // // Draws the body.
-    // if (this.dragged) {
-    // g.setColor(DRAGGED_BODY_COLOR);
-    // } else {
-    // g.setColor(this.bodyColor);
-    // }
-    // g.fillRect(position.x, position.y, this.dimension.width,
-    // this.dimension.height);
-    //
-    // // Draws the head.
-    // g.setColor(this.headColor);
-    // g.fillRect(position.x, position.y, this.dimension.width,
-    // this.headHeight);
-    // //Draw a small circle to indicate the break
-    // if(node.isBreak() ){
-    // g.setColor(BREAK_POINT_COLOR);
-    // int r = this.headHeight/4;
-    // g.fillOval( position.x+this.dimension.width - 3*r, position.y +r, 2*r, 2*r);
-    // g.setColor(BREAK_POINT_BORDER_COLOR);
-    // g.drawOval( position.x+this.dimension.width - 3*r, position.y +r, 2*r, 2*r);
-    // }
-    //
-    // // Text
-    // g.setColor(TEXT_COLOR);
-    //
-    // // XXX it's debatable if we should show the ID or the name.
-    // // String name = this.node.getName();
-    // String name = this.node.getID();
-    // g.drawString(name, position.x + TEXT_GAP_X, position.y
-    // + this.headHeight - TEXT_GAP_Y);
-    //
-    // // Edge
-    // g.setColor(EDGE_COLOR);
-    // g.drawRect(position.x, position.y, this.dimension.width,
-    // this.dimension.height);
-    //
-    // // Paint all ports
-    // for (Port port : this.node.getAllPorts()) {
-    // port.getGUI().paint(g);
-    // }
-    //
-    // // Paint extras
-    // for (Paintable paintable : this.paintables) {
-    // paintable.paint(g, this.node.getPosition());
-    // }
-    //
-    //
-    //
-    // }
 
     protected void setSelectedFlag(boolean flag) {
         this.selected = flag;
@@ -125,13 +72,5 @@ public class StreamSourceNodeGUI extends
         }
     }
 
-    // protected void calculatePositions(Graphics g) {
-    // FontMetrics fm = g.getFontMetrics();
-    // this.headHeight = fm.getHeight() + TEXT_GAP_Y * 2;
-    //
-    // this.dimension.height = MINIMUM_HEIGHT*3;
-    // this.dimension.width = MINIMUM_WIDTH*2;
-    //
-    // }
 
 }
\ No newline at end of file

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/URLRegistryWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/URLRegistryWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/URLRegistryWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/URLRegistryWindow.java Fri Sep  2 21:26:03 2011
@@ -40,8 +40,6 @@ import org.apache.airavata.xbaya.gui.XBa
 
 public class URLRegistryWindow {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private XBayaEngine engine;
 
     private ComponentRegistryLoader loader;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/WebResigtoryWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/WebResigtoryWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/WebResigtoryWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/gui/WebResigtoryWindow.java Fri Sep  2 21:26:03 2011
@@ -41,8 +41,6 @@ import org.apache.airavata.xbaya.gui.XBa
 
 public class WebResigtoryWindow {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private XBayaEngine engine;
 
     private ComponentRegistryLoader loader;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/LocalComponentRegistry.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/LocalComponentRegistry.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/LocalComponentRegistry.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/LocalComponentRegistry.java Fri Sep  2 21:26:03 2011
@@ -35,8 +35,6 @@ import org.apache.airavata.xbaya.util.IO
 
 public class LocalComponentRegistry extends ComponentRegistry {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private File directory;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/SystemComponentRegistry.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/SystemComponentRegistry.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/SystemComponentRegistry.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/SystemComponentRegistry.java Fri Sep  2 21:26:03 2011
@@ -46,8 +46,6 @@ import org.apache.airavata.xbaya.compone
 
 public class SystemComponentRegistry extends ComponentRegistry {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private static final String NAME = "System Components";
 
     private Map<String, Component> componentMap;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/URLComponentRegistry.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/URLComponentRegistry.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/URLComponentRegistry.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/registry/URLComponentRegistry.java Fri Sep  2 21:26:03 2011
@@ -35,8 +35,6 @@ import xsul.wsdl.WsdlResolver;
 
 public class URLComponentRegistry extends ComponentRegistry {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private ComponentTreeNode tree;
 
     private URI url;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndBlockComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndBlockComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndBlockComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndBlockComponent.java Fri Sep  2 21:26:03 2011
@@ -34,7 +34,6 @@ public class EndBlockComponent extends S
      */
     public static final String NAME = "EndBlock";
 
-    // TODO
     private static final String DESCRIPTION = "TODO";
 
     private static final String INPUT_PORT_NAME = "Input";
@@ -43,7 +42,6 @@ public class EndBlockComponent extends S
 
     private static final String OUTPUT_PORT_NAME = "Output";
 
-    // TODO
     private static final String OUTPUT_PORT_DESCRIPTION = "";
 
     private SystemComponentDataPort inputPort;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndifComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndifComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndifComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/EndifComponent.java Fri Sep  2 21:26:03 2011
@@ -42,7 +42,6 @@ public class EndifComponent extends Syst
 
     private static final String OUTPUT_PORT_NAME = "Output";
 
-    // TODO
     private static final String OUTPUT_PORT_DESCRIPTION = "";
 
     private SystemComponentDataPort inputPort;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/SystemComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/SystemComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/SystemComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/system/SystemComponent.java Fri Sep  2 21:26:03 2011
@@ -77,8 +77,6 @@ public abstract class SystemComponent ex
             buf.append("<h3>Input" + (i + 1) + "</h3>");
             buf.append("<strong>Name: </strong>");
             buf.append("" + port.getName() + "<br>");
-            // buf.append("<strong>Type: </strong>");
-            // buf.append("" + port.getType().getLocalPart() + "<br>");
             buf.append("<strong>Description: </strong>");
             buf.append("" + port.getDescription());
         }

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponent.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponent.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponent.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponent.java Fri Sep  2 21:26:03 2011
@@ -88,10 +88,6 @@ public class WSComponent extends Compone
 
     }
 
-    // TODO not used now, but parse them from WSDL
-    // private XmlElement inputAppinfo;
-
-    // private XmlElement outputAppinfo;
 
     /**
      * Constructs a WSComponent.

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentFactory.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentFactory.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentFactory.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentFactory.java Fri Sep  2 21:26:03 2011
@@ -38,8 +38,6 @@ import xsul5.wsdl.WsdlPortTypeOperation;
 
 public class WSComponentFactory {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     /**
      * @param wsdlString
      * @return The list of components in the specified WSDL.

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/component/ws/WSComponentPort.java Fri Sep  2 21:26:03 2011
@@ -35,8 +35,6 @@ import xsul5.XmlConstants;
 
 public class WSComponentPort extends ComponentDataPort {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     /**
      * default
      */

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/ExperimentMenu.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/ExperimentMenu.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/ExperimentMenu.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/ExperimentMenu.java Fri Sep  2 21:26:03 2011
@@ -80,8 +80,6 @@ public class ExperimentMenu {
         createLoadWorkflowfromXRegistryItem();
         createSaveWorkflowtoXRegistryItem();
         createDeleteWorkflowtoXRegistryItem();
-        // createDeployWorkflowtoODEItem();
-        // createLaunchODEWorkflowItem();
         createLaunchXBayaInterpreterItem();
         createLaunchGridChemWorkflowItem();
 
@@ -97,10 +95,6 @@ public class ExperimentMenu {
         this.experimentMenu.add(this.launchXBayaInterpreterItem);
         this.experimentMenu.addSeparator();
         this.experimentMenu.add(this.launchGridChemWorkflowItem);
-        // TODO: ODE build has to be improved before it is supported by default.
-        // this.experimentMenu.addSeparator();
-        // this.experimentMenu.add(this.deployWorkflowtoODEItem);
-        // this.experimentMenu.add(this.launchODEWorkflowItem);
     }
 
     /**
@@ -159,47 +153,6 @@ public class ExperimentMenu {
         });
     }
 
-    // private void createDeployWorkflowtoODEItem() {
-    // this.deployWorkflowtoODEItem = new JMenuItem("Deploy Workflow to ODE Engine");
-    // deployWorkflowtoODEItem.addActionListener(new AbstractAction() {
-    // private OGCEODEDeploymentWindow window;
-    //
-    // public void actionPerformed(ActionEvent e) {
-    //
-    // if (this.window == null) {
-    // this.window = new OGCEODEDeploymentWindow(
-    // ExperimentMenu.this.engine);
-    // }
-    // try {
-    // this.window.show();
-    // } catch (Exception e1) {
-    // ExperimentMenu.this.engine.getErrorWindow().error(e1);
-    // }
-    //
-    // }
-    // });
-    // }
-    //
-    // private void createLaunchODEWorkflowItem() {
-    // this.launchODEWorkflowItem = new JMenuItem("Launch Workflow to ODE Engine");
-    // launchODEWorkflowItem.addActionListener(new AbstractAction() {
-    // private ODEInvokerWindow window;
-    //
-    // public void actionPerformed(ActionEvent e) {
-    // if (this.window == null) {
-    // this.window = new ODEInvokerWindow(
-    // ExperimentMenu.this.engine);
-    // }
-    // try {
-    // this.window.show();
-    // } catch (Exception e1) {
-    // ExperimentMenu.this.engine.getErrorWindow().error(e1);
-    // }
-    //
-    // }
-    // });
-    //
-    // }
 
     private void createLaunchXBayaInterpreterItem() {
         this.launchXBayaInterpreterItem = new JMenuItem("Launch Workflow to XBaya Interpreter Server");

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryLoaderWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryLoaderWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryLoaderWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryLoaderWindow.java Fri Sep  2 21:26:03 2011
@@ -49,8 +49,6 @@ import xregistry.generated.OGCEResourceD
 
 public class OGCEXRegistryLoaderWindow {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private XBayaEngine engine;
 
     private XBayaDialog dialog;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryWorkflowPublisherWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryWorkflowPublisherWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryWorkflowPublisherWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/experiment/gui/OGCEXRegistryWorkflowPublisherWindow.java Fri Sep  2 21:26:03 2011
@@ -68,24 +68,12 @@ public class OGCEXRegistryWorkflowPublis
     }
 
     private void ok() {
-        // if(Pattern.matches("[\\s | \\w]+", this.messageField.getText())){
-        // this.okButton.setEnabled(false);
-        // this.hide();
-        // }else{
-        // this.engine.getErrorWindow().warning("Invalid name");
-        // }
         String name = this.nameTextField.getText();
-        // if (name != null && name.equals(StringUtil.convertToJavaIdentifier(name))) {
         String description = this.descriptionTextArea.getText();
 
         GraphCanvas graphCanvas = this.engine.getGUI().getGraphCanvas();
         graphCanvas.setNameAndDescription(name, description);
         hide();
-        // }else{
-        // this.nameTextField.setText(StringUtil.convertToJavaIdentifier(name));
-        // JOptionPane.showMessageDialog(this.engine.getGUI().getFrame(),
-        // "Invalid Name. Please consider the Name suggsted", "Invalid Name", JOptionPane.OK_OPTION);
-        // }
     }
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/file/gui/FileMenu.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/file/gui/FileMenu.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/file/gui/FileMenu.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/file/gui/FileMenu.java Fri Sep  2 21:26:03 2011
@@ -62,8 +62,6 @@ public class FileMenu {
 
     private JMenuItem importWorkflowItem;
 
-    // private JMenuItem exportScuflItem;
-
     private JMenuItem exportODEScriptsItem;
 
     private XBayaEngine engine;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/GPELRegistry.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/GPELRegistry.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/GPELRegistry.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/GPELRegistry.java Fri Sep  2 21:26:03 2011
@@ -45,8 +45,6 @@ import org.ietf.jgss.GSSCredential;
 
 public class GPELRegistry extends ComponentRegistry {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private WorkflowClient workflowClient;
 
     private WorkflowType type;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/SubWorkflowUpdater.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/SubWorkflowUpdater.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/SubWorkflowUpdater.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/component/SubWorkflowUpdater.java Fri Sep  2 21:26:03 2011
@@ -75,7 +75,6 @@ public class SubWorkflowUpdater {
             }
             for (WorkflowNode node : updatingNodes) {
                 Point position = node.getPosition();
-                // TODO remember connections too
                 graph.removeNode(node);
 
                 WorkflowNode newNode = newComponent.createNode(graph);

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/gui/GPELLoadWindow.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/gui/GPELLoadWindow.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/gui/GPELLoadWindow.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/gui/GPELLoadWindow.java Fri Sep  2 21:26:03 2011
@@ -51,8 +51,6 @@ import org.gpel.client.GcSearchResult;
 
 public class GPELLoadWindow {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private XBayaEngine engine;
 
     private GPELLoader loader;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/script/WorkflowWSDL.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/script/WorkflowWSDL.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/script/WorkflowWSDL.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/gpel/script/WorkflowWSDL.java Fri Sep  2 21:26:03 2011
@@ -107,8 +107,6 @@ public class WorkflowWSDL {
 
     private static final String TYPE_SUFFIX = "Type";
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private Workflow workflow;
 
     private WSGraph graph;

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/DataPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/DataPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/DataPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/DataPort.java Fri Sep  2 21:26:03 2011
@@ -53,7 +53,6 @@ public abstract class DataPort extends P
     @SuppressWarnings("unchecked")
     @Override
     public List<DataEdge> getEdges() {
-        // TODO Auto-generated method stub
         return (List<DataEdge>) super.getEdges();
     }
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/EPRPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/EPRPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/EPRPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/EPRPort.java Fri Sep  2 21:26:03 2011
@@ -60,7 +60,6 @@ public class EPRPort extends DataPort {
      */
     @Override
     public QName getType() {
-        // TODO Auto-generated method stub
         return WSConstants.XSD_ANY_TYPE;
     }
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/amazon/InstanceDataPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/amazon/InstanceDataPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/amazon/InstanceDataPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/amazon/InstanceDataPort.java Fri Sep  2 21:26:03 2011
@@ -79,7 +79,7 @@ public class InstanceDataPort extends Da
      */
     @Override
     public void copyType(DataPort port) throws GraphException {
-        // TODO Auto-generated method stub
+        // left blank
 
     }
 }
\ No newline at end of file

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/BasicTypeMapping.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/BasicTypeMapping.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/BasicTypeMapping.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/BasicTypeMapping.java Fri Sep  2 21:26:03 2011
@@ -55,8 +55,6 @@ public class BasicTypeMapping {
      */
     private static final int NUM = 2;
 
-    // public static Map<QName, String> TYPE_MAPPER = new HashMap<QName, String>();
-
     private static QName[] TYPES = new QName[NUM];
 
     private static String[] NAMES = new String[NUM * 2];

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepNode.java Fri Sep  2 21:26:03 2011
@@ -95,15 +95,8 @@ public class CepNode extends NodeImpl im
     @Override
     protected void edgeWasAdded(Edge edge) throws GraphException {
         GraphUtil.validateConnection(edge);
-        // Node node = edge.getFromPort().getNode();
-        // if (node instanceof StreamSourceNode){
-        // ((StreamSourceNode)node).getSample
-        // }
     }
 
-    // protected void edgeWasRemoved(Edge edge){
-    // super.edgeWasRemoved(edge);
-    // }
 
     public void setName(String name) {
         super.setName(name);

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/CepPort.java Fri Sep  2 21:26:03 2011
@@ -39,7 +39,6 @@ public class CepPort extends DataPort {
 
     private CepComponentPort componentPort;
 
-    // private String uuid;
 
     public CepPort(XmlElement portElement) {
         super(portElement);
@@ -52,7 +51,6 @@ public class CepPort extends DataPort {
     public CepPort() {
         super();
         this.id = UUID.randomUUID().toString();
-        // TODO Auto-generated constructor stub
     }
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/DynamicPort.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/DynamicPort.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/DynamicPort.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/dynamic/DynamicPort.java Fri Sep  2 21:26:03 2011
@@ -40,7 +40,6 @@ public class DynamicPort extends DataPor
      */
     public DynamicPort() {
         super();
-        // TODO Auto-generated constructor stub
     }
 
     /**
@@ -48,7 +47,6 @@ public class DynamicPort extends DataPor
      */
     @Override
     public void copyType(DataPort port) throws GraphException {
-        // TODO Auto-generated method stub
 
     }
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/impl/PortImpl.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/impl/PortImpl.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/impl/PortImpl.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/impl/PortImpl.java Fri Sep  2 21:26:03 2011
@@ -42,7 +42,6 @@ import org.xmlpull.infoset.XmlElement;
  */
 public abstract class PortImpl implements Port {
 
-    // private static final MLogger logger = MLogger.getLogger();
 
     /**
      * The graph this edge belogs to

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/subworkflow/SubWorkflowNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/subworkflow/SubWorkflowNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/subworkflow/SubWorkflowNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/subworkflow/SubWorkflowNode.java Fri Sep  2 21:26:03 2011
@@ -73,26 +73,6 @@ public class SubWorkflowNode extends Nod
         GraphUtil.validateConnection(edge);
     }
 
-    // /**
-    // * @return the node xml
-    // */
-    // @Override
-    // protected XmlElement toXML() {
-    // return null;
-    // }
-    //
-    // /**
-    // * @see org.apache.airavata.xbaya.graph.impl.NodeImpl#parse(org.xmlpull.infoset.XmlElement)
-    // */
-    // @Override
-    // protected void parse(XmlElement nodeElement) throws GraphException {
-    //
-    // }
-    //
-    // @Deprecated
-    // protected void parseComponent(XmlElement componentElement){
-    //
-    // }
 
     /**
      * @param workflow

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/BlockNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/BlockNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/BlockNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/BlockNode.java Fri Sep  2 21:26:03 2011
@@ -31,8 +31,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class BlockNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private BlockNodeGUI gui;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndBlockNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndBlockNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndBlockNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndBlockNode.java Fri Sep  2 21:26:03 2011
@@ -40,7 +40,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class EndBlockNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
 
     private EndBlockNodeGUI gui;
 

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndForEachNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndForEachNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndForEachNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndForEachNode.java Fri Sep  2 21:26:03 2011
@@ -44,8 +44,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class EndForEachNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private EndForEachNodeGUI gui;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndifNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndifNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndifNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/EndifNode.java Fri Sep  2 21:26:03 2011
@@ -40,8 +40,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class EndifNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private EndifNodeGUI gui;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ForEachNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ForEachNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ForEachNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ForEachNode.java Fri Sep  2 21:26:03 2011
@@ -44,8 +44,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class ForEachNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private ForEachNodeGUI gui;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/IfNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/IfNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/IfNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/IfNode.java Fri Sep  2 21:26:03 2011
@@ -37,8 +37,6 @@ public class IfNode extends SystemNode {
 
     private static final String XPATH_TAG_NAME = "xpath";
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private IfNodeGUI gui;
 
     private String xpath;
@@ -134,7 +132,6 @@ public class IfNode extends SystemNode {
         super.parseConfiguration(configElement);
         XmlElement element = configElement.element(null, XPATH_TAG_NAME);
         if (element != null) {
-            // TODO
             this.xpath = element.requiredText();
         }
     }

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ParameterNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ParameterNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ParameterNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ParameterNode.java Fri Sep  2 21:26:03 2011
@@ -46,8 +46,6 @@ abstract public class ParameterNode exte
 
     private static final String METADATA_TAG = "metadata";
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private boolean configured;
 
     /**

Modified: incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ReceiveNode.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ReceiveNode.java?rev=1164715&r1=1164714&r2=1164715&view=diff
==============================================================================
--- incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ReceiveNode.java (original)
+++ incubator/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/graph/system/ReceiveNode.java Fri Sep  2 21:26:03 2011
@@ -36,8 +36,6 @@ import org.xmlpull.infoset.XmlElement;
 
 public class ReceiveNode extends SystemNode {
 
-    // private static final MLogger logger = MLogger.getLogger();
-
     private ReceiveNodeGUI gui;
 
     /**



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