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From samin...@apache.org
Subject svn commit: r1430653 - in /airavata/trunk/modules: airavata-client/src/main/java/org/apache/airavata/client/ airavata-client/src/main/java/org/apache/airavata/client/api/ commons/utils/src/main/java/org/apache/airavata/common/utils/ integration-tests/s...
Date Wed, 09 Jan 2013 01:52:14 GMT
Author: samindaw
Date: Wed Jan  9 01:52:13 2013
New Revision: 1430653

URL: http://svn.apache.org/viewvc?rev=1430653&view=rev
Log:
adding security settings - however not supported for 0.6 release

Added:
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java   (with props)
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java   (with props)
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java   (with props)
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java   (with props)
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java   (with props)
Modified:
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
    airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/ExperimentAdvanceOptions.java
    airavata/trunk/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/XMLUtil.java
    airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java
    airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/TestMonitorListener.java
    airavata/trunk/modules/integration-tests/src/test/resources/registry.properties
    airavata/trunk/modules/registry/registry-api/src/main/java/org/apache/airavata/registry/api/util/RegistrySettings.java
    airavata/trunk/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/wf/Workflow.java

Modified: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java (original)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java Wed Jan  9 01:52:13 2013
@@ -78,12 +78,10 @@ public class AiravataClient extends Obse
 	public static final String WORKFLOWSERVICEURL = "xbaya.service.url";
 	public static final String TRUSTED_CERT_LOCATION = "trusted.cert.location";
 	private AiravataClientConfiguration clientConfiguration;
-	private MonitorConfiguration monitorConfiguration;
-	private static String workflow = "";
 	private static WorkflowContextHeaderBuilder builder;
 	private String currentUser;
-    private URI regitryURI;
-    private PasswordCallback callBack;
+	private URI regitryURI;
+	private PasswordCallback callBack;
 
 	private AiravataRegistry2 registry;
 
@@ -95,92 +93,24 @@ public class AiravataClient extends Obse
 	private UserManagerImpl userManagerImpl;
 	private ExecutionManagerImpl executionManagerImpl;
 	private String gateway;
-	private boolean configCreated=false;
-
-	// private NameValue[] configurations = new NameValue[7];
+	private boolean configCreated = false;
 
 	private static final Version API_VERSION = new Version("Airavata", 0, 6,
 			null, null, null);
-//
-//	@Deprecated
-//	protected AiravataClient(Map<String, String> configuration)
-//			throws MalformedURLException {
-//		this.configuration = configuration;
-//		try {
-//			initialize();
-//		} catch (AiravataConfigurationException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (RepositoryException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (RegistryException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		}
-//	}
 
 	// FIXME: Need a constructor to set registry URL
 	protected AiravataClient() {
 	}
 
-//	@Deprecated
-//	protected AiravataClient(String fileName) throws RegistryException,
-//			MalformedURLException, IOException {
-//		URL url = this.getClass().getClassLoader().getResource(fileName);
-//		if (url == null) {
-//			url = (new File(fileName)).toURL();
-//		}
-//		Properties properties = new Properties();
-//		properties.load(url.openStream());
-//		configuration.put(GFAC,
-//				validateAxisService(properties.getProperty(DEFAULT_GFAC_URL)));
-//		configuration.put(MSGBOX, validateAxisService(properties
-//				.getProperty(DEFAULT_MESSAGE_BOX_URL)));
-//		configuration
-//				.put(BROKER, validateAxisService(properties
-//						.getProperty(DEFAULT_BROKER_URL)));
-//		configuration
-//				.put(WORKFLOWSERVICEURL, validateAxisService(properties
-//						.getProperty(WORKFLOWSERVICEURL)));
-//		configuration.put(WITHLISTENER, properties.getProperty(WITHLISTENER));
-//
-//		try {
-//			initialize();
-//		} catch (AiravataConfigurationException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (RepositoryException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		}
-//	}
-//
-//	protected AiravataClient(URI registryUrl, String username, String password)
-//			throws MalformedURLException, RepositoryException,
-//			RegistryException, AiravataConfigurationException {
-//		Map<String, String> configuration=createConfig(registryUrl, username, password);
-//		this.configuration = configuration;
-//		try {
-//			initialize();
-//		} catch (AiravataConfigurationException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (RepositoryException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		} catch (RegistryException e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		}
-//	}
-//	
-	 private static HashMap<String, String> createConfig(URI registryUrl,String username, String password) throws RepositoryException,	 RegistryException, AiravataConfigurationException {
+	private static HashMap<String, String> createConfig(URI registryUrl,
+			String username, String password) throws RepositoryException,
+			RegistryException, AiravataConfigurationException {
 		HashMap<String, String> config = new HashMap<String, String>();
-		if (registryUrl!=null) {
+		if (registryUrl != null) {
 			config.put(AiravataClient.REGISTRY, registryUrl.toString());
 		}
-		AiravataRegistry2 registryObject = getRegistry(registryUrl, "default", username, new PasswordCallBackImpl(username, password));
+		AiravataRegistry2 registryObject = getRegistry(registryUrl, "default",
+				username, new PasswordCallBackImpl(username, password));
 		if (registryObject != null) {
 			URI uri = registryObject.getEventingServiceURI();
 			config.put(
@@ -205,30 +135,33 @@ public class AiravataClient extends Obse
 			config.put(AiravataClient.WITHLISTENER, "true");
 		}
 		return config;
-	 }
-	 
-	 @Override
+	}
+
+	@Override
 	public void initialize() throws AiravataAPIInvocationException {
 		try {
-			if (!configCreated){
-				configuration=createConfig(getRegitryURI(), getCurrentUser(), getPassword());
-				configCreated=true;
+			if (!configCreated) {
+				configuration = createConfig(getRegitryURI(), getCurrentUser(),
+						getPassword());
+				configCreated = true;
 			}
 			updateClientConfiguration(configuration);
 
 			// At this point we do not know the workflowExperimentId
 			// FIXME: Registry URL is set null as its not used. Set this when we
 			// have rest services
-			builder = new WorkflowContextHeaderBuilder(configuration.get(BROKER),
-					configuration.get(GFAC), null, null, null,
-					configuration.get(MSGBOX));
+			builder = new WorkflowContextHeaderBuilder(
+					configuration.get(BROKER), configuration.get(GFAC), null,
+					null, null, configuration.get(MSGBOX));
 
-			// TODO: At some point this should contain the current user the airavata
+			// TODO: At some point this should contain the current user the
+			// airavata
 			// client is
 			// logged in to the Airavata system
 			setCurrentUser(getClientConfiguration().getJcrUsername());
 		} catch (Exception e) {
-			throw new AiravataAPIInvocationException("Error while initializing the Airavata API",e);
+			throw new AiravataAPIInvocationException(
+					"Error while initializing the Airavata API", e);
 		}
 	}
 
@@ -246,9 +179,6 @@ public class AiravataClient extends Obse
 			clientConfiguration.setMessagebrokerURL(new URL(configuration
 					.get(BROKER)));
 		}
-//		if (configuration.containsKey(REGISTRY)) {
-//			 clientConfiguration.setRegistryURL(new URL(configuration.get(REGISTRY)));
-//		}
 		if (configuration.get(WORKFLOWSERVICEURL) != null) {
 			clientConfiguration.setXbayaServiceURL(new URL(configuration
 					.get(WORKFLOWSERVICEURL)));
@@ -261,8 +191,8 @@ public class AiravataClient extends Obse
 		if (clientConfiguration.getRegistryURL() != null
 				&& clientConfiguration.getGfacURL() == null) {
 			try {
-				clientConfiguration.setGfacURL(getRegistryClient().getGFacURIs()
-						.get(0).toURL());
+				clientConfiguration.setGfacURL(getRegistryClient()
+						.getGFacURIs().get(0).toURL());
 				configuration.put(GFAC, clientConfiguration.getGfacURL()
 						.toString());
 			} catch (Exception e) {
@@ -271,287 +201,20 @@ public class AiravataClient extends Obse
 		}
 	}
 
-//	public void loadWorkflowFromaFile(String workflowFile)
-//			throws URISyntaxException, IOException {
-//		File workflow = null;
-//		URL url = AiravataClient.class.getClassLoader().getResource(
-//				workflowFile);
-//		if (url == null) {
-//			url = (new File(workflowFile)).toURL();
-//		}
-//		try {
-//			workflow = new File(url.toURI());
-//		} catch (URISyntaxException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		}
-//		FileInputStream stream = new FileInputStream(workflow);
-//		try {
-//			FileChannel fc = stream.getChannel();
-//			MappedByteBuffer bb = fc.map(FileChannel.MapMode.READ_ONLY, 0,
-//					fc.size());
-//			/* Instead of using default, pass in a decoder. */
-//			this.workflow = Charset.defaultCharset().decode(bb).toString();
-//		} finally {
-//			stream.close();
-//		}
-//	}
-//
-//	public void loadWorkflowasaString(String workflowAsaString) {
-//		this.workflow = workflowAsaString;
-//	}
-
-//	public static void updateWorkflowInputValuesFromProperties(
-//			List<WorkflowInput> inputs, String fileName) throws IOException {
-//		URL url = AiravataClient.class.getClassLoader().getResource(fileName);
-//		if (url == null) {
-//			url = (new File(fileName)).toURL();
-//		}
-//		Properties properties = new Properties();
-//		properties.load(url.openStream());
-//		for (WorkflowInput workflowInput : inputs) {
-//			if (properties.containsKey(workflowInput.getName())) {
-//				workflowInput.setValue(properties.get(workflowInput.getName()));
-//			}
-//		}
-//	}
-
-//	public NameValue[] setInputs(String fileName) throws IOException {
-//		URL url = this.getClass().getClassLoader().getResource(fileName);
-//		if (url == null) {
-//			url = (new File(fileName)).toURL();
-//		}
-//		Properties properties = new Properties();
-//		properties.load(url.openStream());
-//		try {
-//			Workflow workflow = new Workflow(this.workflow);
-//			List<NodeImpl> inputs = workflow.getGraph().getNodes();
-//			int inputSize = 0;
-//			for (NodeImpl input : inputs) {
-//				if (input instanceof InputNode) {
-//					inputSize++;
-//				}
-//			}
-//			NameValue[] inputNameVals = new NameValue[inputSize];
-//			int index = 0;
-//			for (NodeImpl input : inputs) {
-//				if (input instanceof InputNode) {
-//					inputNameVals[index] = new NameValue();
-//					String name = input.getName();
-//					inputNameVals[index].setName(name);
-//					inputNameVals[index].setValue(properties.getProperty(name));
-//					((InputNode) input).setDefaultValue(properties
-//							.getProperty(name));
-//					index++;
-//				}
-//			}
-//			// setWorkflow(XMLUtil.xmlElementToString((workflow.toXML()));
-//			return inputNameVals;
-//		} catch (GraphException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		} catch (ComponentException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		}
-//		return null;
-//	}
-//
-//	public void setInputs(Properties inputList) {
-//		try {
-//			Workflow workflow = new Workflow(this.workflow);
-//			List<WSComponentPort> inputs = workflow.getInputs();
-//			for (WSComponentPort input : inputs) {
-//				input.setValue(inputList.getProperty(input.getName()));
-//			}
-//		} catch (GraphException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		} catch (ComponentException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		}
-//	}
-//
-//	public String runWorkflow(String topic) throws AiravataConfigurationException {
-//		return runWorkflow(topic, (String) null);
-//	}
-//
-//	public String runWorkflow(String topic, String user) throws AiravataConfigurationException {
-//		return runWorkflow(topic, user, null, topic);
-//	}
-//
-//	public String runWorkflow(String topic, String user, String metadata,
-//			String workflowInstanceName) throws AiravataConfigurationException {
-//		return runWorkflow(topic, user, metadata, workflowInstanceName, builder);
-//	}
-//
-//	public String runWorkflow(String topic, String user, String metadata,
-//			String workflowInstanceName, WorkflowContextHeaderBuilder builder) throws AiravataConfigurationException {
-//		String worflowoutput = null;
-//		try {
-//            builder.setUserIdentifier(getCurrentUser());
-//			WorkflowInterpretorStub stub = new WorkflowInterpretorStub(
-//					getClientConfiguration().getXbayaServiceURL().toString());
-//			OMElement omElement = AXIOMUtil.stringToOM(XMLUtil
-//					.xmlElementToString(builder.getXml()));
-//			stub._getServiceClient().addHeader(omElement);
-//			worflowoutput = stub.launchWorkflow(workflow, topic, null);
-//			runPreWorkflowExecutionTasks(worflowoutput, user, metadata,
-//					workflowInstanceName);
-//
-//		} catch (AxisFault e) {
-//
-//		} catch (RemoteException e) {
-//			// log.fine(e.getMessage(), e);
-//		} catch (RegistryException e) {
-//			// log.fine(e.getMessage(), e);
-//		} catch (XMLStreamException e) {
-//			e.printStackTrace(); // To change body of catch statement use File |
-//									// Settings | File Templates.
-//		}
-//		// log.info("Workflow output : " + worflowoutput);
-//		return worflowoutput;
-//	}
-//
-//	public Monitor getWorkflowExecutionMonitor(String topic) {
-//		return getWorkflowExecutionMonitor(topic, null);
-//	}
-//
-//	public Monitor getWorkflowExecutionMonitor(String topic,
-//			MonitorEventListener listener) {
-//		final String fTopic = topic;
-//		MonitorConfiguration monitorConfiguration;
-//		try {
-//			monitorConfiguration = new MonitorConfiguration(
-//					getClientConfiguration().getMessagebrokerURL().toURI(), fTopic,
-//					true, getClientConfiguration().getMessageboxURL().toURI());
-//			final Monitor monitor = new Monitor(monitorConfiguration);
-//			monitor.printRawMessage(false);
-//			monitor.getEventDataRepository().registerEventListener(listener);
-//			listener.setExperimentMonitor(monitor);
-//			return monitor;
-//		} catch (URISyntaxException e) {
-//			e.printStackTrace();
-//		}
-//		
-//	}
-//
-//	private void runPreWorkflowExecutionTasks(String topic, String user,
-//			String metadata, String experimentName) throws RegistryException, AiravataConfigurationException {
-//		if (user != null) {
-//			getRegistryClient().updateExperimentExecutionUser(topic, user);
-//		}
-//		if (metadata != null) {
-//            getRegistryClient().updateExperimentMetadata(topic, metadata);
-//		}
-//		if (experimentName == null) {
-//			experimentName = topic;
-//		}
-//        getRegistryClient().updateExperimentName(topic, experimentName);
-//	}
-//
-//	public String runWorkflow(String topic, NameValue[] inputs)
-//			throws Exception {
-//		return runWorkflow(topic, inputs, null);
-//	}
-//
-//	public String runWorkflow(String topic, NameValue[] inputs, String user)
-//			throws Exception {
-//		return runWorkflow(topic, inputs, user, null, topic);
-//	}
-//
-//	public String runWorkflow(final String topic, final NameValue[] inputs,
-//			final String user, final String metadata,
-//			final String experimentName) throws Exception {
-//		return runWorkflow(topic, inputs, user, metadata, experimentName,
-//				builder);
-//	}
-//
-//	public String runWorkflow(final String topic, final NameValue[] inputs,
-//			final String user, final String metadata,
-//			final String experimentName,
-//			final WorkflowContextHeaderBuilder builder) throws AiravataAPIInvocationException, AiravataConfigurationException {
-//		return runWorkflow(topic, inputs, user, metadata, experimentName,
-//				builder, true);
-//	}
-//
-//	private static int TIMEOUT_STEP = 1000;
-//	private static int MAX_TIMEOUT = 60000;
-//
-//	public String runWorkflow(final String topic, final NameValue[] inputs,
-//			final String user, final String metadata,
-//			final String experimentName,
-//			final WorkflowContextHeaderBuilder builder, boolean launchOnThread)
-//			throws AiravataAPIInvocationException, AiravataConfigurationException {
-//
-//        //TODO - fix user passing
-//        builder.setUserIdentifier(getCurrentUser());
-//		try {
-//			runPreWorkflowExecutionTasks(topic, user, metadata, experimentName);
-//		} catch (RegistryException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		}
-//		if (launchOnThread) {
-//			new Thread(new Runnable() {
-//				public void run() {
-//					launchWorkflow(topic, inputs, builder);
-//				}
-//			}).start();
-//			int timeout = 0;
-//			try {
-//				while (!getRegistryClient().isExperimentExists(topic)
-//						&& timeout < MAX_TIMEOUT) {
-//					Thread.sleep(TIMEOUT_STEP);
-//					timeout += MAX_TIMEOUT;
-//				}
-//			} catch (InterruptedException e) {
-//				throw new AiravataAPIInvocationException(e);
-//			} catch (RegistryException e) {
-//                throw new AiravataAPIInvocationException(e);
-//            }
-//        } else {
-//			launchWorkflow(topic, inputs, builder);
-//		}
-//		return topic;
-//	}
-//
-//	public List<ExperimentData> getWorkflowExecutionDataByUser(String user)
-//			throws RegistryException, AiravataConfigurationException {
-//		return getRegistryClient().getExperimentByUser(user);
-//	}
-//
-//	public ExperimentData getWorkflowExecutionData(String topic)
-//			throws RegistryException, AiravataConfigurationException {
-//		return getRegistryClient().getExperiment(topic);
-//	}
-//
-//	public List<ExperimentData> getWorkflowExecutionData(String user,
-//			int pageSize, int PageNo) throws RegistryException {
-//        return null;
-////		return getProvenanceResouceClient().getExperimentByUser(user, pageSize, PageNo);
-//	}
-//
-//	public static String getWorkflow() {
-//		return workflow;
-//	}
-//
-//	public static void setWorkflow(String workflow) {
-//		AiravataClient.workflow = workflow;
-//	}
-
-	public AiravataRegistry2 getRegistryClient() throws AiravataConfigurationException, RegistryException{
-		if (registry==null) {
-			registry = getRegistry(getRegitryURI(),
-					getGateway(),getCurrentUser(), getCallBack());
-		}
-        return registry;
-    }
-	
-    public static AiravataRegistry2 getRegistry(URI registryURI, String gateway, String username, PasswordCallback callback) throws RegistryException, AiravataConfigurationException {
-    	return AiravataRegistryFactory.getRegistry(registryURI,
-				new Gateway(gateway), new AiravataUser(
-						username), callback);
+	public AiravataRegistry2 getRegistryClient()
+			throws AiravataConfigurationException, RegistryException {
+		if (registry == null) {
+			registry = getRegistry(getRegitryURI(), getGateway(),
+					getCurrentUser(), getCallBack());
+		}
+		return registry;
+	}
+
+	public static AiravataRegistry2 getRegistry(URI registryURI,
+			String gateway, String username, PasswordCallback callback)
+			throws RegistryException, AiravataConfigurationException {
+		return AiravataRegistryFactory.getRegistry(registryURI, new Gateway(
+				gateway), new AiravataUser(username), callback);
 	}
 
 	public AiravataClientConfiguration getClientConfiguration() {
@@ -561,382 +224,6 @@ public class AiravataClient extends Obse
 		return clientConfiguration;
 	}
 
-//	private String validateAxisService(String urlString)
-//			throws RegistryException {
-//		String originalURL = urlString;
-//		if (!urlString.endsWith("?wsdl")) {
-//			urlString = urlString + "?wsdl";
-//		}
-//		try {
-//			URL url = new URL(urlString);
-//			URLConnection conn = url.openConnection();
-//			conn.connect();
-//		} catch (MalformedURLException e) {
-//			// the URL is not in a valid form
-//			throw new RegistryException("Given Axis2 Service URL : "
-//					+ urlString + " is Invalid", e);
-//		} catch (IOException e) {
-//			// the connection couldn't be established
-//			throw new RegistryException("Given Axis2 Service URL : "
-//					+ urlString + " is Invalid", e);
-//		}
-//		return originalURL;
-//	}
-//
-//	private String validateURL(String urlString) throws RegistryException {
-//		try {
-//			URL url = new URL(urlString);
-//			URLConnection conn = url.openConnection();
-//			conn.connect();
-//		} catch (MalformedURLException e) {
-//			// the URL is not in a valid form
-//			throw new RegistryException("Given URL: " + urlString
-//					+ " is Invalid", e);
-//		} catch (IOException e) {
-//			// the connection couldn't be established
-//			throw new RegistryException("Given URL: " + urlString
-//					+ " is Invalid", e);
-//		}
-//		return urlString;
-//	}
-//
-//	public List<String> getWorkflowTemplateIds() {
-//		List<String> workflowList = new ArrayList<String>();
-//		Map<String, String> workflows;
-//		try {
-//			workflows = getRegistryClient().getWorkflows();
-//			for (String name : workflows.keySet()) {
-//				workflowList.add(name);
-//			}
-//		} catch (Exception e) {
-//			// TODO Auto-generated catch block
-//			e.printStackTrace();
-//		}
-//		return workflowList;
-//	}
-
-//	public String runWorkflow(String workflowTemplateId,
-//			List<WorkflowInput> inputs) throws Exception {
-//		return runWorkflow(workflowTemplateId, inputs, getRegistryClient().getUser()
-//				.getUserName(), null, workflowTemplateId + "_"
-//				+ Calendar.getInstance().getTime().toString());
-//	}
-//
-//	public String runWorkflow(String workflowTemplateId,
-//			List<WorkflowInput> inputs, String workflowInstanceName)
-//			throws Exception {
-//		return runWorkflow(workflowTemplateId, inputs, getRegistryClient().getUser()
-//				.getUserName(), null, workflowInstanceName);
-//	}
-//
-//	public String runWorkflow(String workflowTemplateId,
-//			List<WorkflowInput> inputs, String user, String metadata,
-//			String workflowInstanceName) throws Exception {
-//		Workflow workflowObj = getWorkflow(workflowTemplateId);
-//		return runWorkflow(workflowObj, inputs, user, metadata,
-//				workflowInstanceName, builder);
-//	}
-
-//	public String runWorkflow(String workflowTemplateId,
-//			List<WorkflowInput> inputs, String user, String metadata,
-//			String workflowInstanceName, WorkflowContextHeaderBuilder builder)
-//			throws Exception {
-//        Workflow workflowObj = getWorkflowManager().getWorkflowFromString(workflowTemplateId);
-////		Workflow workflowObj = extractWorkflow(workflowTemplateId);
-//		return runWorkflow(workflowObj, inputs, user, metadata,
-//				workflowInstanceName, builder);
-//	}
-
-//	public String runWorkflow(Workflow workflow, List<WorkflowInput> inputs,
-//			String workflowInstanceName) throws GraphException,
-//			ComponentException, Exception {
-//		return runWorkflow(workflow, inputs, null, null, workflowInstanceName,
-//				builder);
-//	}
-//
-//	public String runWorkflow(Workflow workflowObj, List<WorkflowInput> inputs,
-//			String user, String metadata, String workflowInstanceName)
-//			throws GraphException, ComponentException, Exception {
-//		return runWorkflow(workflowObj, inputs, user, metadata,
-//				workflowInstanceName, builder);
-//	}
-
-//	public String runWorkflow(Workflow workflowObj, List<WorkflowInput> inputs,
-//			String user, String metadata, String workflowInstanceName,
-//			WorkflowContextHeaderBuilder builder) throws AiravataAPIInvocationException{
-//		try {
-//			String workflowString = XMLUtil.xmlElementToString(workflowObj
-//                    .toXML());
-//			List<WSComponentPort> ports = getWSComponentPortInputs(workflowObj);
-//			for (WorkflowInput input : inputs) {
-//				WSComponentPort port = getWSComponentPort(input.getName(),
-//						ports);
-//				if (port != null) {
-//					port.setValue(input.getValue());
-//				}
-//			}
-//			List<NameValue> inputValues = new ArrayList<NameValue>();
-//			for (WSComponentPort port : ports) {
-//				NameValue nameValue = new NameValue();
-//				nameValue.setName(port.getName());
-//				if (port.getValue() == null) {
-//					nameValue.setValue(port.getDefaultValue());
-//				} else {
-//					nameValue.setValue(port.getValue().toString());
-//				}
-//				inputValues.add(nameValue);
-//			}
-//			workflow = workflowString;
-//			String topic = workflowObj.getName() + "_" + UUID.randomUUID();
-//            getRegistryClient().setWorkflowInstanceTemplateName(topic,
-//                    workflowObj.getName());
-//			return runWorkflow(topic, inputValues.toArray(new NameValue[] {}),
-//					user, metadata, workflowInstanceName, builder);
-//		} catch (GraphException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (ComponentException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (Exception e) {
-//            throw new AiravataAPIInvocationException(e);
-//        }
-//	}
-//
-////	public String runWorkflow(String workflowName, List<WorkflowInput> inputs,
-//			String user, String metadata, String workflowInstanceName,
-//			String experimentID) throws AiravataAPIInvocationException {
-//		try {
-//            Workflow workflowObj = extractWorkflow(workflowName);
-//			String workflowString = XMLUtil.xmlElementToString(workflowObj
-//                    .toXML());
-//			List<WSComponentPort> ports;
-//			ports = getWSComponentPortInputs(workflowObj);
-//			for (WorkflowInput input : inputs) {
-//				WSComponentPort port = getWSComponentPort(input.getName(),
-//						ports);
-//				if (port != null) {
-//					port.setValue(input.getValue());
-//				}
-//			}
-//			List<NameValue> inputValues = new ArrayList<NameValue>();
-//			for (WSComponentPort port : ports) {
-//				NameValue nameValue = new NameValue();
-//				nameValue.setName(port.getName());
-//				if (port.getValue() == null) {
-//					nameValue.setValue(port.getDefaultValue());
-//				} else {
-//					nameValue.setValue(port.getValue().toString());
-//				}
-//				inputValues.add(nameValue);
-//			}
-//			workflow = workflowString;
-//			if (experimentID == null || experimentID.isEmpty()) {
-//				experimentID = workflowObj.getName() + "_" + UUID.randomUUID();
-//			}
-//            getRegistryClient().setWorkflowInstanceTemplateName(experimentID,
-//                    workflowObj.getName());
-//			return runWorkflow(experimentID,
-//					inputValues.toArray(new NameValue[] {}), user, metadata,
-//					workflowInstanceName, this.builder);
-//		}  catch (GraphException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (ComponentException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (Exception e) {
-//            throw new AiravataAPIInvocationException(
-//                    "Error working with Airavata Registry: "
-//                            + e.getLocalizedMessage(), e);
-//        }
-//	}
-//
-//    private Workflow extractWorkflow(String workflowName) throws AiravataAPIInvocationException {
-//        Workflow workflowObj = null;
-//        if(!workflowName.contains("http://airavata.apache.org/xbaya/xwf")){//(getClient().getWorkflowManager().isWorkflowExists(workflowName)) {
-//            workflowObj = getWorkflow(workflowName);
-//        }else {
-//            try{
-//                workflowObj = getWorkflowManager().getWorkflowFromString(workflowName);
-//            }catch (AiravataAPIInvocationException e){
-//                getWorkflowManager().getWorkflow(workflowName);
-//            }
-//
-//        }
-//        return workflowObj;
-//    }
-//
-//    public List<WorkflowInput> getWorkflowInputs(String workflowTemplateId)
-//			throws AiravataAPIInvocationException {
-//		try {
-//			Workflow workflowTemplate = getWorkflow(workflowTemplateId);
-//			List<WSComponentPort> inputs = getWSComponentPortInputs(workflowTemplate);
-//			List<InputNode> inputNodes = getInputNodes(workflowTemplate);
-//			List<WorkflowInput> results = new ArrayList<WorkflowInput>();
-//			for (InputNode port : inputNodes) {
-//				Object value = null;
-//				WSComponentPort wsComponentPort = getWSComponentPort(
-//						port.getName(), inputs);
-//				if (wsComponentPort != null) {
-//					value = wsComponentPort.getValue();
-//				}
-//				results.add(new WorkflowInput(port.getName(), port
-//						.getParameterType().getLocalPart(), port
-//						.getDefaultValue(), value, !port.isVisibility()));
-//			}
-//			return results;
-//		} catch (AiravataAPIInvocationException e) {
-//			throw e;
-//		}catch (Exception e) {
-//			throw new AiravataAPIInvocationException(e);
-//		}
-//	}
-//
-//	public String getWorkflowAsString(String workflowTemplateId)
-//			throws AiravataAPIInvocationException {
-//		try {
-//			Map<String, String> workflows = getRegistryClient().getWorkflows();
-//			for (String name : workflows.keySet()) {
-//				if (name.equals(workflowTemplateId)) {
-//					return workflows.get(name);
-//				}
-//			}
-//			return null;
-//		} catch (Exception e) {
-//			throw new AiravataAPIInvocationException(e);
-//		}
-//
-//	}
-//
-//	private List<WSComponentPort> getWSComponentPortInputs(
-//			String workflowTemplateId) throws AiravataAPIInvocationException{
-//		Workflow workflow = getWorkflow(workflowTemplateId);
-//		try {
-//			return getWSComponentPortInputs(workflow);
-//		} catch (GraphException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (ComponentException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		}
-//	}
-//
-//	private Workflow getWorkflow(String workflowTemplateId)
-//			throws AiravataAPIInvocationException {
-//		try {
-//			Workflow workflow = new Workflow(
-//					getWorkflowAsString(workflowTemplateId));
-//			return workflow;
-//		} catch (GraphException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (ComponentException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		}
-//
-//	}
-//
-//	private List<WSComponentPort> getWSComponentPortInputs(Workflow workflow)
-//			throws GraphException, ComponentException {
-//		workflow.createScript();
-//		List<WSComponentPort> inputs = workflow.getInputs();
-//		return inputs;
-//	}
-//
-//	private List<InputNode> getInputNodes(String workflowTemplateId)
-//			throws AiravataAPIInvocationException {
-//		Workflow workflow = getWorkflow(workflowTemplateId);
-//		return getInputNodes(workflow);
-//	}
-//
-//	private List<InputNode> getInputNodes(Workflow workflow) {
-//		List<InputNode> inputNodes = GraphUtil.getInputNodes(workflow
-//				.getGraph());
-//		return inputNodes;
-//	}
-//
-//	private WSComponentPort getWSComponentPort(String name,
-//			List<WSComponentPort> ports) {
-//		for (WSComponentPort port : ports) {
-//			if (port.getName().equals(name)) {
-//				return port;
-//			}
-//		}
-//		return null;
-//	}
-
-	public static WorkflowContextHeaderBuilder getBuilder() {
-		return builder;
-	}
-//
-//	private static void addNode(Node parentNode, Node childNode)
-//			throws RepositoryException {
-//		Node node;
-//		String childNodeName = childNode.getName();
-//		if (!parentNode.hasNode(childNodeName)) {
-//			node = parentNode.addNode(childNodeName);
-//		} else {
-//			node = parentNode.getNode(childNodeName);
-//		}
-//		System.out.println(node.getPath());
-//		PropertyIterator childProperties = childNode.getProperties();
-//		while (childProperties.hasNext()) {
-//			Property childProperty = childProperties.nextProperty();
-//			if (!(childProperty.getName().startsWith("jcr:") || childProperty
-//					.getName().startsWith("rep:"))) {
-//				if (childProperty.isMultiple()) {
-//					node.setProperty(childProperty.getName(),
-//							childProperty.getValues());
-//				} else {
-//					node.setProperty(childProperty.getName(),
-//							childProperty.getValue());
-//				}
-//
-//			}
-//		}
-//		NodeIterator children = childNode.getNodes();
-//		while (children.hasNext()) {
-//			Node c = children.nextNode();
-//			addNode(node, c);
-//		}
-//	}
-
-	// private static void migrateRespositoryData(
-	// AiravataJCRRegistry sourceRegistry,
-	// AiravataJCRRegistry targetRegistry) throws Exception {
-	// Session session1 = null;
-	// Session session2 = null;
-	// try {
-	// session1 = sourceRegistry.getRepository().login(new
-	// SimpleCredentials(sourceRegistry.getUsername(), new
-	// String(sourceRegistry.getPassword()).toCharArray()));
-	// session2 = targetRegistry.getRepository().login(new
-	// SimpleCredentials(targetRegistry.getUsername(), new
-	// String(targetRegistry.getPassword()).toCharArray()));
-	// } catch (Exception e) {
-	// // TODO Auto-generated catch block
-	// e.printStackTrace();
-	// throw e;
-	// }
-	//
-	//
-	// NodeIterator nodes = session1.getRootNode().getNodes();
-	// Node rootNode = session2.getRootNode();
-	// List<String> ignoreRoots=Arrays.asList(new
-	// String[]{"/AIRAVATA_CONFIGURATION_DATA"});
-	// while(nodes.hasNext()){
-	// Node nextNode = nodes.nextNode();
-	// String path = nextNode.getPath();
-	// if (!(path.equals("/jcr:system")||path.equals("/rep:policy") ||
-	// ignoreRoots.contains(path))) {
-	// addNode(rootNode,nextNode);
-	// System.out.println();
-	// }
-	// }
-	// System.out.print("Saving session.");
-	// session1.logout();
-	// System.out.print(".");
-	// session2.save();
-	// System.out.print(".");
-	// session2.logout();
-	// System.out.println(".done");
-	// }
-
 	public AiravataManager getAiravataManager() {
 		if (airavataManagerImpl == null) {
 			airavataManagerImpl = new AiravataManagerImpl(this);
@@ -982,77 +269,43 @@ public class AiravataClient extends Obse
 	public String getCurrentUser() {
 		return currentUser;
 	}
-//
-//	public List<String> getWorkflowServiceNodeIDs(String templateID) throws AiravataAPIInvocationException {
-//		try {
-//			Workflow workflow = new Workflow(getWorkflowAsString(templateID));
-//			return workflow.getWorkflowServiceNodeIDs();
-//		}  catch (GraphException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (ComponentException e) {
-//			throw new AiravataAPIInvocationException(e);
-//		} catch (AiravataAPIInvocationException e) {
-//			throw e;
-//		}
-//	}
 
 	public Version getVersion() {
 		return API_VERSION;
 	}
 
-    @Override
-    public DescriptorBuilder getDescriptorBuilder() {
-        return new DescriptorBuilder();
-    }
+	@Override
+	public DescriptorBuilder getDescriptorBuilder() {
+		return new DescriptorBuilder();
+	}
 
-    public void setCurrentUser(String currentUser) {
+	public void setCurrentUser(String currentUser) {
 		this.currentUser = currentUser;
 	}
-//
-//	private void launchWorkflow(final String topic, final NameValue[] inputs,
-//			final WorkflowContextHeaderBuilder builder) {
-//		try {
-//			builder.getWorkflowMonitoringContext().setExperimentId(topic);
-//			WorkflowInterpretorStub stub = new WorkflowInterpretorStub(
-//					getClientConfiguration().getXbayaServiceURL().toString());
-//			stub._getServiceClient().addHeader(
-//					AXIOMUtil.stringToOM(XMLUtil.xmlElementToString(builder
-//							.getXml())));
-//			stub.launchWorkflow(workflow, topic, inputs);
-//			// log.info("Workflow output : " + worflowoutput);
-//		} catch (AxisFault e) {
-//			e.printStackTrace();
-//		} catch (XMLStreamException e) {
-//			e.printStackTrace();
-//		} catch (RemoteException e) {
-//			e.printStackTrace();
-//		}
-//	}
-
-    public void setRegitryURI(URI regitryURI) {
-        this.regitryURI = regitryURI;
-    }
-
-    public String getPassword() {
-        if(getCallBack() != null){
-            return getCallBack().getPassword(getCurrentUser());
-        }
-        return null;
-
-    }
-
-    public URI getRegitryURI() {
-        return regitryURI;
-    }
-
-    public PasswordCallback getCallBack() {
-        return callBack;
-    }
-
-    public void setCallBack(PasswordCallback callBack) {
-        this.callBack = callBack;
-    }
-    
+
+	public void setRegitryURI(URI regitryURI) {
+		this.regitryURI = regitryURI;
+	}
+
+	public String getPassword() {
+		if (getCallBack() != null) {
+			return getCallBack().getPassword(getCurrentUser());
+		}
+		return null;
+
+	}
+
+	public URI getRegitryURI() {
+		return regitryURI;
+	}
+
+	public PasswordCallback getCallBack() {
+		return callBack;
+	}
+
+	public void setCallBack(PasswordCallback callBack) {
+		this.callBack = callBack;
+	}
 
 	public String getGateway() {
 		return gateway;

Added: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java?rev=1430653&view=auto
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java (added)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java Wed Jan  9 01:52:13 2013
@@ -0,0 +1,38 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.client.api;
+
+public interface AmazonWebServicesSettings {
+	public String getAccessKeyId();
+	public String getAMIId();
+	public String getInstanceId();
+	public String getInstanceType();
+	public String getSecretAccessKey();
+	public String getUsername();
+	
+	public void setAccessKeyId(String accessKeyId);
+	public void setAMIId(String amiId);
+	public void setInstanceId(String instanceId);
+	public void setInstanceType(String instanceType);
+	public void setSecretAccessKey(String secretAccessKey);
+	public void setUsername(String username);
+}

Propchange: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/AmazonWebServicesSettings.java
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java?rev=1430653&view=auto
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java (added)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java Wed Jan  9 01:52:13 2013
@@ -0,0 +1,33 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.client.api;
+
+public interface CredentialManagementServiceSettings {
+	public String getExecutionSessionId();
+	public String getScmsURL();
+	
+	public void setExecutionSessionId(String executionSessionId);
+	public void setScmsURL(String scmsURL);
+	
+	public void resetExecutionSessionId();
+	public void resetScmsURL();
+}

Propchange: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/CredentialManagementServiceSettings.java
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/ExperimentAdvanceOptions.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/ExperimentAdvanceOptions.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/ExperimentAdvanceOptions.java (original)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/ExperimentAdvanceOptions.java Wed Jan  9 01:52:13 2013
@@ -26,6 +26,8 @@ import java.util.UUID;
 import org.apache.airavata.client.impl.WorkflowOutputDataSettingsImpl;
 import org.apache.airavata.client.impl.WorkflowSchedulingSettingsImpl;
 
+import sun.reflect.generics.reflectiveObjects.NotImplementedException;
+
 
 public class ExperimentAdvanceOptions {
 	private String executionUser;
@@ -143,4 +145,13 @@ public class ExperimentAdvanceOptions {
 		}
 		return outputDataSettings;
 	}
+	
+	/**
+	 * Get the custom security settings for running the experiment
+	 * @return
+	 * @throws AiravataAPIInvocationException
+	 */
+	public SecuritySettings getCustomSecuritySettings() throws AiravataAPIInvocationException{
+		throw new AiravataAPIInvocationException(new NotImplementedException());
+	}
 }

Added: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java?rev=1430653&view=auto
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java (added)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java Wed Jan  9 01:52:13 2013
@@ -0,0 +1,39 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.client.api;
+
+public interface GridMyProxyRepositorySettings {
+	public String getUsername();
+	public String getPassword();
+	public String getMyProxyServer();
+	public int getLifeTime();
+	
+	public void setUsername(String username);
+	public void setPassword(String password);
+	public void setMyProxyServer(String myproxyServer);
+	public void setLifeTime(int lifeTime);
+	
+	public void resetUsername();
+	public void resetPassword();
+	public void resetMyProxyServer();
+	public void resetLifeTime();
+}

Propchange: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/GridMyProxyRepositorySettings.java
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java?rev=1430653&view=auto
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java (added)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java Wed Jan  9 01:52:13 2013
@@ -0,0 +1,30 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.client.api;
+
+public interface SSHAuthenticationSettings {
+	public String getAccessKeyId();
+	public String getSecretAccessKey();
+	
+	public void setAccessKeyId(String accessKeyId);
+	public void setSecretAccessKey(String secretAccessKey);
+}

Propchange: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SSHAuthenticationSettings.java
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java?rev=1430653&view=auto
==============================================================================
--- airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java (added)
+++ airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java Wed Jan  9 01:52:13 2013
@@ -0,0 +1,29 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.client.api;
+
+public interface SecuritySettings {
+	public AmazonWebServicesSettings getAmazonWSSettings();
+	public CredentialManagementServiceSettings getCMServiceSettings();
+	public GridMyProxyRepositorySettings getGridMyProxyRepositorySettings();
+	public SSHAuthenticationSettings getSSHAuthenticationSettings();
+}

Propchange: airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/api/SecuritySettings.java
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: airavata/trunk/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/XMLUtil.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/XMLUtil.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/XMLUtil.java (original)
+++ airavata/trunk/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/XMLUtil.java Wed Jan  9 01:52:13 2013
@@ -22,6 +22,7 @@
 package org.apache.airavata.common.utils;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
@@ -43,7 +44,9 @@ import org.apache.xmlbeans.XmlObject;
 import org.apache.xmlbeans.XmlOptions;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.w3c.dom.*;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Text;
 import org.xml.sax.SAXException;
 import org.xmlpull.infoset.XmlDocument;
 import org.xmlpull.infoset.XmlElement;
@@ -283,11 +286,20 @@ public class XMLUtil {
      * @return The XmlElement in the document.
      * @throws IOException
      */
-    public static org.xmlpull.infoset.XmlElement loadXML(File file) throws IOException {
-        String xmlText = IOUtil.readFileToString(file);
+    public static org.xmlpull.infoset.XmlElement loadXML(InputStream stream) throws IOException {
+        String xmlText = IOUtil.readToString(stream);
         XmlDocument document = BUILDER.parseString(xmlText);
         return document.getDocumentElement();
     }
+    
+    /**
+     * @param file
+     * @return The XmlElement in the document.
+     * @throws IOException
+     */
+    public static org.xmlpull.infoset.XmlElement loadXML(File file) throws IOException {
+        return loadXML(new FileInputStream(file));
+    }
 
     /**
      * @param string

Modified: airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java (original)
+++ airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java Wed Jan  9 01:52:13 2013
@@ -22,15 +22,23 @@ import org.apache.airavata.commons.gfac.
 import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.commons.gfac.type.ServiceDescription;
 import org.apache.airavata.registry.api.PasswordCallback;
-import org.apache.airavata.schemas.gfac.*;
+import org.apache.airavata.registry.api.impl.WorkflowExecutionDataImpl;
+import org.apache.airavata.registry.api.workflow.ExperimentData;
+import org.apache.airavata.registry.api.workflow.NodeExecutionData;
+import org.apache.airavata.schemas.gfac.DataType;
+import org.apache.airavata.schemas.gfac.HostDescriptionType;
+import org.apache.airavata.schemas.gfac.InputParameterType;
+import org.apache.airavata.schemas.gfac.OutputParameterType;
 import org.apache.airavata.workflow.model.component.ComponentException;
 import org.apache.airavata.workflow.model.graph.GraphException;
 import org.apache.airavata.workflow.model.wf.Workflow;
 import org.apache.airavata.workflow.model.wf.WorkflowInput;
+import org.apache.airavata.ws.monitor.EventData;
+import org.apache.airavata.ws.monitor.EventDataListenerAdapter;
+import org.apache.airavata.ws.monitor.EventDataRepository;
 import org.apache.airavata.ws.monitor.Monitor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
@@ -359,7 +367,7 @@ public class BaseCaseIT {
         log("Workflow setting up completed ...");
 
         try {
-            runWorkFlow(workflow, Arrays.asList("echo_output=Airavata Test"));
+        	runWorkFlowWithoutMonitor(workflow, Arrays.asList("echo_output=Airavata_Test"));
         } catch (Exception e) {
             log.error("An error occurred while invoking workflow", e);
         }
@@ -369,16 +377,8 @@ public class BaseCaseIT {
 
         AiravataAPI airavataAPI = AiravataAPIFactory.getAPI(new URI(getRegistryURL()), getGatewayName(),
                 getUserName(), new PasswordCallbackImpl());
+        List<WorkflowInput> workflowInputs = setupInputs(workflow, inputValues);
         String workflowName = workflow.getName();
-        List<WorkflowInput> workflowInputs = airavataAPI.getWorkflowManager().getWorkflowInputs(workflowName);
-
-        Assert.assertEquals(workflowInputs.size(), inputValues.size());
-
-        int i = 0;
-        for (String valueString : inputValues) {
-            workflowInputs.get(i).setValue(valueString);
-            ++i;
-        }
         ExperimentAdvanceOptions options = airavataAPI.getExecutionManager().createExperimentAdvanceOptions(workflowName,getUserName(),null);
         String experimentId = airavataAPI.getExecutionManager().runExperiment(workflowName, workflowInputs, options);
         
@@ -388,11 +388,69 @@ public class BaseCaseIT {
         log.info("Starting monitoring ....");
 
         monitor(experimentId);
+    }
+    
+    protected void runWorkFlowWithoutMonitor(Workflow workflow, List<String> inputValues) throws Exception {
+
+        AiravataAPI airavataAPI = AiravataAPIFactory.getAPI(new URI(getRegistryURL()), getGatewayName(),
+                getUserName(), new PasswordCallbackImpl());
+        List<WorkflowInput> workflowInputs = setupInputs(workflow, inputValues);
+        String workflowName = workflow.getName();
+        ExperimentAdvanceOptions options = airavataAPI.getExecutionManager().createExperimentAdvanceOptions(workflowName,getUserName(),null);
+        String experimentId = airavataAPI.getExecutionManager().runExperiment(workflowName, workflowInputs, options, new EventDataListenerAdapter() {
+			@Override
+			public void notify(EventDataRepository eventDataRepo, EventData eventData) {
+				//do nothing
+			}
+		});
+        
+        Assert.assertNotNull(experimentId);
+        airavataAPI.getExecutionManager().waitForExperimentTermination(experimentId);
+        
+        log.info("Run workflow completed ....");
+        log.info("Starting monitoring ....");
 
+        verifyOutput(experimentId, "echo_output=Airavata_Test");
     }
 
-    protected String getWorkflowComposeContent(String fileName) throws IOException {
+    protected void verifyOutput(String experimentId, String outputVerifyingString) throws Exception {
+    	AiravataAPI airavataAPI = AiravataAPIFactory.getAPI(new URI(getRegistryURL()), getGatewayName(),
+                getUserName(), new PasswordCallbackImpl());
+        log.info("Workflow Experiment ID Returned : " + experimentId);
+
+        ExperimentData experimentData = airavataAPI.getProvenanceManager().getExperimentData(experimentId);
+
+        log.info("Verifying output ...");
+
+        List<WorkflowExecutionDataImpl> workflowInstanceData = experimentData.getWorkflowExecutionDataList();
+
+        for(WorkflowExecutionDataImpl data:workflowInstanceData){
+            List<NodeExecutionData> nodeDataList = data.getNodeDataList();
+            for(NodeExecutionData nodeData:nodeDataList){
+            	System.out.print("******************************");
+            	System.out.println(nodeData.getOutputData().get(0).getValue());
+                Assert.assertEquals("Airavata_Test", nodeData.getOutputData().get(0).getValue());
+                Assert.assertEquals(outputVerifyingString, nodeData.getInputData().get(0).getValue());
+            }
+        }
+    }
+    
+	private List<WorkflowInput> setupInputs(Workflow workflow,List<String> inputValues)	throws Exception {
+		AiravataAPI airavataAPI = AiravataAPIFactory.getAPI(new URI(getRegistryURL()), getGatewayName(),
+                getUserName(), new PasswordCallbackImpl());
+		List<WorkflowInput> workflowInputs = airavataAPI.getWorkflowManager().getWorkflowInputs(workflow.getName());
 
+        Assert.assertEquals(workflowInputs.size(), inputValues.size());
+
+        int i = 0;
+        for (String valueString : inputValues) {
+            workflowInputs.get(i).setValue(valueString);
+            ++i;
+        }
+		return workflowInputs;
+	}
+
+    protected String getWorkflowComposeContent(String fileName) throws IOException {
         File f = new File(".");
         log.info(f.getAbsolutePath());
 

Modified: airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/TestMonitorListener.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/TestMonitorListener.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/TestMonitorListener.java (original)
+++ airavata/trunk/modules/integration-tests/src/test/java/org/apache/airavata/integration/TestMonitorListener.java Wed Jan  9 01:52:13 2013
@@ -39,7 +39,7 @@ public class TestMonitorListener impleme
         Assert.assertNotNull(event);
         if (MonitorUtil.EventType.WORKFLOW_TERMINATED.equals(event.getType())) {
             try {
-                verifyOutput("echo_output=Airavata Test");
+                verifyOutput("echo_output=Airavata_Test");
             } catch (Exception e) {
                 log.error("Error verifying output", e);
                 throw new RuntimeException(e);
@@ -65,7 +65,7 @@ public class TestMonitorListener impleme
         for(WorkflowExecutionDataImpl data:workflowInstanceData){
             List<NodeExecutionData> nodeDataList = data.getNodeDataList();
             for(NodeExecutionData nodeData:nodeDataList){
-                Assert.assertEquals("Airavata Test", nodeData.getOutputData().get(0).getValue());
+                Assert.assertEquals("Airavata_Test", nodeData.getOutputData().get(0).getValue());
                 Assert.assertEquals(outputVerifyingString, nodeData.getInputData().get(0).getValue());
             }
         }

Modified: airavata/trunk/modules/integration-tests/src/test/resources/registry.properties
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/integration-tests/src/test/resources/registry.properties?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/integration-tests/src/test/resources/registry.properties (original)
+++ airavata/trunk/modules/integration-tests/src/test/resources/registry.properties Wed Jan  9 01:52:13 2013
@@ -53,11 +53,3 @@ default.registry.gateway=default
 #for rest [RegistryClient]
 #registry.jdbc.url=http://localhost:9080/airavata-services
 
-#user defined registry accessor classes
-#class.provenance.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-#class.configuration.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-#class.descriptor.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-#class.project.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-#class.user.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-#class.published.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
-

Modified: airavata/trunk/modules/registry/registry-api/src/main/java/org/apache/airavata/registry/api/util/RegistrySettings.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/registry/registry-api/src/main/java/org/apache/airavata/registry/api/util/RegistrySettings.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/registry/registry-api/src/main/java/org/apache/airavata/registry/api/util/RegistrySettings.java (original)
+++ airavata/trunk/modules/registry/registry-api/src/main/java/org/apache/airavata/registry/api/util/RegistrySettings.java Wed Jan  9 01:52:13 2013
@@ -21,7 +21,6 @@
 
 package org.apache.airavata.registry.api.util;
 
-import java.io.File;
 import java.net.URL;
 import java.util.Properties;
 
@@ -40,17 +39,15 @@ public class RegistrySettings {
     private static final String REGISTRY_ACCESSOR_CLASS = "class.registry.accessor";
     
     static{
-    	String propertyFileName = REPOSITORY_PROPERTIES;
-    	if (RegistrySettings.class.getClassLoader()
-				.getResource(propertyFileName) == null) {
+    	URL url = RegistrySettings.class.getClassLoader()
+				.getResource(REPOSITORY_PROPERTIES);
+		if (url == null) {
     		if (AiravataUtils.isServer()){
-        		propertyFileName=SERVER_REPOSITORY_PROPERTIES;
+    			 url=RegistrySettings.class.getClassLoader().getResource(SERVER_REPOSITORY_PROPERTIES);
         	}else{
-        		propertyFileName=CLIENT_REPOSITORY_PROPERTIES;
+        		url=RegistrySettings.class.getClassLoader().getResource(CLIENT_REPOSITORY_PROPERTIES);
         	}
 		}
-		URL url = RegistrySettings.class.getClassLoader()
-				.getResource(propertyFileName);
         try {
             properties.load(url.openStream());
         } catch (Exception e) {

Modified: airavata/trunk/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/wf/Workflow.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/wf/Workflow.java?rev=1430653&r1=1430652&r2=1430653&view=diff
==============================================================================
--- airavata/trunk/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/wf/Workflow.java (original)
+++ airavata/trunk/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/wf/Workflow.java Wed Jan  9 01:52:13 2013
@@ -24,7 +24,6 @@ package org.apache.airavata.workflow.mod
 import java.awt.image.BufferedImage;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -145,8 +144,6 @@ public class Workflow implements Cloneab
 
     private XmlElement odeDeploymentDiscriptor;
 
-    private QName qname;
-
     private volatile WorkflowExecutionState executionState = WorkflowExecutionState.NONE;
 
     private WsdlDefinitions tridentWSDL;
@@ -190,8 +187,7 @@ public class Workflow implements Cloneab
     public Workflow(URI workflowFilePath) throws GraphException, ComponentException {
         this();
         try {
-            File filePath = new File(workflowFilePath);
-            XmlElement workflowElement = XMLUtil.loadXML(filePath);
+            XmlElement workflowElement = XMLUtil.loadXML(workflowFilePath.toURL().openStream());
             parse(workflowElement);
         } catch (RuntimeException e) {
             throw new GraphException(e);
@@ -853,11 +849,6 @@ public class Workflow implements Cloneab
     private void generateODEScripts(URI dscUrl, String odeEprEndingWithPort) throws GraphException, ComponentException {
         this.getGraph().setID(this.getName());
 
-        // find whether its Streaming
-        List<NodeImpl> nodes = this.graph.getNodes();
-        Node activeNode = null;
-        String operationName = null;
-
         BPELScript script = null;
 
         script = new BPELScript(this);
@@ -910,7 +901,7 @@ public class Workflow implements Cloneab
      */
     public QName getQname() {
 
-        return this.qname = new QName(WorkflowConstants.LEAD_NS, this.getName());
+        return new QName(WorkflowConstants.LEAD_NS, this.getName());
 
     }
 



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