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From chath...@apache.org
Subject [4/5] airavata git commit: fixing compilation issues
Date Wed, 24 Jun 2015 14:15:05 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/df3fbe6a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
index 884ccd5..21991fd 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
@@ -1,92 +1,92 @@
-/*
- *
- * 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.gfac.local.handler;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.AbstractHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.commons.io.FileUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Map;
-import java.util.Properties;
-
-
-public class LocalInputHandler extends AbstractHandler {
-    private static final Logger logger = LoggerFactory.getLogger(LocalInputHandler.class);
-    @Override
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        super.invoke(jobExecutionContext);
-        Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
-        for (Map.Entry<String, Object> inputParamEntry : inputParameters.entrySet()) {
-            if (inputParamEntry.getValue() instanceof InputDataObjectType) {
-                InputDataObjectType inputDataObject = (InputDataObjectType) inputParamEntry.getValue();
-                if (inputDataObject.getType() == DataType.URI
-                        && inputDataObject != null
-                        && !inputDataObject.getValue().equals("")) {
-                    try {
-                        inputDataObject.setValue(stageFile(jobExecutionContext.getInputDir(), inputDataObject.getValue()));
-                    } catch (IOException e) {
-                        throw new GFacHandlerException("Error while data staging sourceFile= " + inputDataObject.getValue());
-                    }
-                }
-            }
-        }
-    }
-
-    private String stageFile(String inputDir, String sourceFilePath) throws IOException {
-        int i = sourceFilePath.lastIndexOf(File.separator);
-        String substring = sourceFilePath.substring(i + 1);
-        if (inputDir.endsWith("/")) {
-            inputDir = inputDir.substring(0, inputDir.length() - 1);
-        }
-        String targetFilePath = inputDir + File.separator + substring;
-
-        if (sourceFilePath.startsWith("file")) {
-            sourceFilePath = sourceFilePath.substring(sourceFilePath.indexOf(":") + 1, sourceFilePath.length());
-        }
-
-        File sourceFile = new File(sourceFilePath);
-        File targetFile = new File(targetFilePath);
-        if (targetFile.exists()) {
-            targetFile.delete();
-        }
-        logger.info("staging source file : " + sourceFilePath + " to target file : " + targetFilePath);
-        FileUtils.copyFile(sourceFile, targetFile);
-
-        return targetFilePath;
-    }
-
-    @Override
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-
-    }
-
-    @Override
-    public void initProperties(Properties properties) throws GFacHandlerException {
-
-    }
-}
+///*
+// *
+// * 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.gfac.local.handler;
+//
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.handler.AbstractHandler;
+//import org.apache.airavata.gfac.core.handler.GFacHandlerException;
+//import org.apache.airavata.model.appcatalog.appinterface.DataType;
+//import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+//import org.apache.commons.io.FileUtils;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+//import java.io.File;
+//import java.io.IOException;
+//import java.util.Map;
+//import java.util.Properties;
+//
+//
+//public class LocalInputHandler extends AbstractHandler {
+//    private static final Logger logger = LoggerFactory.getLogger(LocalInputHandler.class);
+//    @Override
+//    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
+//        super.invoke(jobExecutionContext);
+//        Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
+//        for (Map.Entry<String, Object> inputParamEntry : inputParameters.entrySet()) {
+//            if (inputParamEntry.getValue() instanceof InputDataObjectType) {
+//                InputDataObjectType inputDataObject = (InputDataObjectType) inputParamEntry.getValue();
+//                if (inputDataObject.getType() == DataType.URI
+//                        && inputDataObject != null
+//                        && !inputDataObject.getValue().equals("")) {
+//                    try {
+//                        inputDataObject.setValue(stageFile(jobExecutionContext.getInputDir(), inputDataObject.getValue()));
+//                    } catch (IOException e) {
+//                        throw new GFacHandlerException("Error while data staging sourceFile= " + inputDataObject.getValue());
+//                    }
+//                }
+//            }
+//        }
+//    }
+//
+//    private String stageFile(String inputDir, String sourceFilePath) throws IOException {
+//        int i = sourceFilePath.lastIndexOf(File.separator);
+//        String substring = sourceFilePath.substring(i + 1);
+//        if (inputDir.endsWith("/")) {
+//            inputDir = inputDir.substring(0, inputDir.length() - 1);
+//        }
+//        String targetFilePath = inputDir + File.separator + substring;
+//
+//        if (sourceFilePath.startsWith("file")) {
+//            sourceFilePath = sourceFilePath.substring(sourceFilePath.indexOf(":") + 1, sourceFilePath.length());
+//        }
+//
+//        File sourceFile = new File(sourceFilePath);
+//        File targetFile = new File(targetFilePath);
+//        if (targetFile.exists()) {
+//            targetFile.delete();
+//        }
+//        logger.info("staging source file : " + sourceFilePath + " to target file : " + targetFilePath);
+//        FileUtils.copyFile(sourceFile, targetFile);
+//
+//        return targetFilePath;
+//    }
+//
+//    @Override
+//    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
+//
+//    }
+//
+//    @Override
+//    public void initProperties(Properties properties) throws GFacHandlerException {
+//
+//    }
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/df3fbe6a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
index 5bd75e5..2ea6518 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
@@ -1,309 +1,309 @@
-/*
- *
- * 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.gfac.local.provider.impl;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.apache.airavata.gfac.core.GFacConstants;
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.provider.AbstractProvider;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.gfac.impl.OutputUtils;
-import org.apache.airavata.gfac.local.utils.InputStreamToFileWriter;
-import org.apache.airavata.gfac.local.utils.InputUtils;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.appdeployment.SetEnvPaths;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.messaging.event.JobIdentifier;
-import org.apache.airavata.model.messaging.event.JobStatusChangeEvent;
-import org.apache.airavata.model.messaging.event.TaskIdentifier;
-import org.apache.airavata.model.messaging.event.TaskOutputChangeEvent;
-import org.apache.airavata.model.experiment.JobDetails;
-import org.apache.airavata.model.experiment.JobState;
-import org.apache.airavata.model.experiment.TaskDetails;
-import org.apache.airavata.registry.cpi.ExpCatChildDataType;
-import org.apache.airavata.registry.cpi.ExperimentCatalogModelType;
-import org.apache.xmlbeans.XmlException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
-
-public class LocalProvider extends AbstractProvider {
-    private static final Logger log = LoggerFactory.getLogger(LocalProvider.class);
-    private ProcessBuilder builder;
-    private List<String> cmdList;
-    private String jobId;
-    
-    public static class LocalProviderJobData{
-    	private String applicationName;
-    	private List<String> inputParameters;
-    	private String workingDir;
-    	private String inputDir;
-    	private String outputDir;
-		public String getApplicationName() {
-			return applicationName;
-		}
-		public void setApplicationName(String applicationName) {
-			this.applicationName = applicationName;
-		}
-		public List<String> getInputParameters() {
-			return inputParameters;
-		}
-		public void setInputParameters(List<String> inputParameters) {
-			this.inputParameters = inputParameters;
-		}
-		public String getWorkingDir() {
-			return workingDir;
-		}
-		public void setWorkingDir(String workingDir) {
-			this.workingDir = workingDir;
-		}
-		public String getInputDir() {
-			return inputDir;
-		}
-		public void setInputDir(String inputDir) {
-			this.inputDir = inputDir;
-		}
-		public String getOutputDir() {
-			return outputDir;
-		}
-		public void setOutputDir(String outputDir) {
-			this.outputDir = outputDir;
-		}
-    }
-    public LocalProvider(){
-        cmdList = new ArrayList<String>();
-    }
-
-    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
-    	super.initialize(jobExecutionContext);
-
-        // build command with all inputs
-        buildCommand();
-        initProcessBuilder(jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription());
-
-        // extra environment variables
-        builder.environment().put(GFacConstants.INPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getInputDir());
-        builder.environment().put(GFacConstants.OUTPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getOutputDir());
-
-        // set working directory
-        builder.directory(new File(jobExecutionContext.getWorkingDir()));
-
-        // log info
-        log.info("Command = " + InputUtils.buildCommand(cmdList));
-        log.info("Working dir = " + builder.directory());
-        /*for (String key : builder.environment().keySet()) {
-            log.info("Env[" + key + "] = " + builder.environment().get(key));
-        }*/
-    }
-
-    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        JobDetails jobDetails = new JobDetails();
-        try {
-        	jobId = jobExecutionContext.getTaskData().getTaskID();
-            jobDetails.setJobID(jobId);
-            jobDetails.setJobDescription(jobExecutionContext.getApplicationContext()
-                    .getApplicationDeploymentDescription().getAppDeploymentDescription());
-            jobExecutionContext.setJobDetails(jobDetails);
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SETUP);
-            // running cmd
-            Process process = builder.start();
-
-            Thread standardOutWriter = new InputStreamToFileWriter(process.getInputStream(), jobExecutionContext.getStandardOutput());
-            Thread standardErrorWriter = new InputStreamToFileWriter(process.getErrorStream(), jobExecutionContext.getStandardError());
-
-            // start output threads
-            standardOutWriter.setDaemon(true);
-            standardErrorWriter.setDaemon(true);
-            standardOutWriter.start();
-            standardErrorWriter.start();
-
-            int returnValue = process.waitFor();
-
-            // make sure other two threads are done
-            standardOutWriter.join();
-            standardErrorWriter.join();
-
-            /*
-             * check return value. usually not very helpful to draw conclusions based on return values so don't bother.
-             * just provide warning in the log messages
-             */
-            if (returnValue != 0) {
-                log.error("Process finished with non zero return value. Process may have failed");
-            } else {
-                log.info("Process finished with return value of zero.");
-            }
-
-            StringBuffer buf = new StringBuffer();
-            buf.append("Executed ").append(InputUtils.buildCommand(cmdList))
-                    .append(" on the localHost, working directory = ").append(jobExecutionContext.getWorkingDir())
-                    .append(" tempDirectory = ").append(jobExecutionContext.getScratchLocation()).append(" With the status ")
-                    .append(String.valueOf(returnValue));
-
-            log.info(buf.toString());
-
-            // updating the job status to complete because there's nothing to monitor in local jobs
-//            MonitorID monitorID = createMonitorID(jobExecutionContext);
-            JobIdentifier jobIdentity = new JobIdentifier(jobExecutionContext.getJobDetails().getJobID(),
-                    jobExecutionContext.getTaskData().getTaskID(),
-                    jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
-                    jobExecutionContext.getExperimentID(),
-                    jobExecutionContext.getGatewayID());
-            jobExecutionContext.getLocalEventPublisher().publish(new JobStatusChangeEvent(JobState.COMPLETE, jobIdentity));
-        } catch (IOException io) {
-            throw new GFacProviderException(io.getMessage(), io);
-        } catch (InterruptedException e) {
-            throw new GFacProviderException(e.getMessage(), e);
-        }catch (GFacException e) {
-            throw new GFacProviderException(e.getMessage(), e);
-        }
-    }
-
-//	private MonitorID createMonitorID(JobExecutionContext jobExecutionContext) {
-//		MonitorID monitorID = new MonitorID(jobExecutionContext.getApplicationContext().getHostDescription(), jobId,
-//		        jobExecutionContext.getTaskData().getTaskID(),
-//		        jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(), jobExecutionContext.getExperimentID(),
-//		        jobExecutionContext.getExperiment().getUserName(),jobId);
-//		return monitorID;
-//	}
-
-//	private void saveApplicationJob(JobExecutionContext jobExecutionContext)
-//			throws GFacProviderException {
-//		ApplicationDeploymentDescriptionType app = jobExecutionContext.
-//                getApplicationContext().getApplicationDeploymentDescription().getType();
-//		ApplicationJob appJob = GFacUtils.createApplicationJob(jobExecutionContext);
-//		appJob.setJobId(jobId);
-//		LocalProviderJobData data = new LocalProviderJobData();
-//		data.setApplicationName(app.getExecutableLocation());
-//		data.setInputDir(app.getInputDataDirectory());
-//		data.setOutputDir(app.getOutputDataDirectory());
-//		data.setWorkingDir(builder.directory().toString());
-//		data.setInputParameters(ProviderUtils.getInputParameters(jobExecutionContext));
-//		ByteArrayOutputStream stream = new ByteArrayOutputStream();
-//		JAXB.marshal(data, stream);
-//		appJob.setJobData(stream.toString());
-//		appJob.setSubmittedTime(Calendar.getInstance().getTime());
-//		appJob.setStatus(ApplicationJobStatus.SUBMITTED);
-//		appJob.setStatusUpdateTime(appJob.getSubmittedTime());
-//		GFacUtils.recordApplicationJob(jobExecutionContext, appJob);
-//	}
-
-    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        try {
-        	List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>();
-            String stdOutStr = GFacUtils.readFileToString(jobExecutionContext.getStandardOutput());
-            String stdErrStr = GFacUtils.readFileToString(jobExecutionContext.getStandardError());
-			Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
-            OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
-            TaskDetails taskDetails = (TaskDetails) experimentCatalog.get(ExperimentCatalogModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
-            if (taskDetails != null){
-                taskDetails.setApplicationOutputs(outputArray);
-                experimentCatalog.update(ExperimentCatalogModelType.TASK_DETAIL, taskDetails, taskDetails.getTaskID());
-            }
-            experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
-            TaskIdentifier taskIdentity = new TaskIdentifier(jobExecutionContext.getTaskData().getTaskID(),
-                    jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
-                    jobExecutionContext.getExperimentID(),
-                    jobExecutionContext.getGatewayID());
-            jobExecutionContext.getLocalEventPublisher().publish(new TaskOutputChangeEvent(outputArray, taskIdentity));
-        } catch (XmlException e) {
-            throw new GFacProviderException("Cannot read output:" + e.getMessage(), e);
-        } catch (IOException io) {
-            throw new GFacProviderException(io.getMessage(), io);
-        } catch (Exception e){
-        	throw new GFacProviderException("Error in retrieving results",e);
-        }
-    }
-
-    public boolean cancelJob(JobExecutionContext jobExecutionContext) throws GFacException {
-        throw new NotImplementedException();
-    }
-
-    @Override
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        // TODO: Auto generated method body.
-    }
-
-    @Override
-    public void monitor(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        // TODO: Auto generated method body.
-    }
-
-
-    private void buildCommand() {
-        cmdList.add(jobExecutionContext.getExecutablePath());
-        Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
-
-        // sort the inputs first and then build the command List
-        Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
-            @Override
-            public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType t1) {
-                return inputDataObjectType.getInputOrder() - t1.getInputOrder();
-            }
-        };
-        Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
-        for (Object object : inputParameters.values()) {
-            if (object instanceof InputDataObjectType) {
-                InputDataObjectType inputDOT = (InputDataObjectType) object;
-                sortedInputSet.add(inputDOT);
-            }
-        }
-        for (InputDataObjectType inputDataObjectType : sortedInputSet) {
-            if (inputDataObjectType.getApplicationArgument() != null
-                    && !inputDataObjectType.getApplicationArgument().equals("")) {
-                cmdList.add(inputDataObjectType.getApplicationArgument());
-            }
-
-            if (inputDataObjectType.getValue() != null
-                    && !inputDataObjectType.getValue().equals("")) {
-                cmdList.add(inputDataObjectType.getValue());
-            }
-        }
-
-    }
-
-    private void initProcessBuilder(ApplicationDeploymentDescription app){
-        builder = new ProcessBuilder(cmdList);
-
-        List<SetEnvPaths> setEnvironment = app.getSetEnvironment();
-        if (setEnvironment != null) {
-            for (SetEnvPaths envPath : setEnvironment) {
-                Map<String,String> builderEnv = builder.environment();
-                builderEnv.put(envPath.getName(), envPath.getValue());
-            }
-        }
-    }
-
-    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-
-    }
-}
+///*
+// *
+// * 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.gfac.local.provider.impl;
+//
+//import java.io.File;
+//import java.io.IOException;
+//import java.util.ArrayList;
+//import java.util.Comparator;
+//import java.util.List;
+//import java.util.Map;
+//import java.util.Set;
+//import java.util.TreeSet;
+//
+//import org.apache.airavata.gfac.core.GFacConstants;
+//import org.apache.airavata.gfac.core.GFacException;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.provider.AbstractProvider;
+//import org.apache.airavata.gfac.core.provider.GFacProviderException;
+//import org.apache.airavata.gfac.core.GFacUtils;
+//import org.apache.airavata.gfac.impl.OutputUtils;
+//import org.apache.airavata.gfac.local.utils.InputStreamToFileWriter;
+//import org.apache.airavata.gfac.local.utils.InputUtils;
+//import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
+//import org.apache.airavata.model.appcatalog.appdeployment.SetEnvPaths;
+//import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+//import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
+//import org.apache.airavata.model.messaging.event.JobIdentifier;
+//import org.apache.airavata.model.messaging.event.JobStatusChangeEvent;
+//import org.apache.airavata.model.messaging.event.TaskIdentifier;
+//import org.apache.airavata.model.messaging.event.TaskOutputChangeEvent;
+//import org.apache.airavata.model.experiment.JobDetails;
+//import org.apache.airavata.model.experiment.JobState;
+//import org.apache.airavata.model.experiment.TaskDetails;
+//import org.apache.airavata.registry.cpi.ExpCatChildDataType;
+//import org.apache.airavata.registry.cpi.ExperimentCatalogModelType;
+//import org.apache.xmlbeans.XmlException;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+//import sun.reflect.generics.reflectiveObjects.NotImplementedException;
+//
+//public class LocalProvider extends AbstractProvider {
+//    private static final Logger log = LoggerFactory.getLogger(LocalProvider.class);
+//    private ProcessBuilder builder;
+//    private List<String> cmdList;
+//    private String jobId;
+//
+//    public static class LocalProviderJobData{
+//    	private String applicationName;
+//    	private List<String> inputParameters;
+//    	private String workingDir;
+//    	private String inputDir;
+//    	private String outputDir;
+//		public String getApplicationName() {
+//			return applicationName;
+//		}
+//		public void setApplicationName(String applicationName) {
+//			this.applicationName = applicationName;
+//		}
+//		public List<String> getInputParameters() {
+//			return inputParameters;
+//		}
+//		public void setInputParameters(List<String> inputParameters) {
+//			this.inputParameters = inputParameters;
+//		}
+//		public String getWorkingDir() {
+//			return workingDir;
+//		}
+//		public void setWorkingDir(String workingDir) {
+//			this.workingDir = workingDir;
+//		}
+//		public String getInputDir() {
+//			return inputDir;
+//		}
+//		public void setInputDir(String inputDir) {
+//			this.inputDir = inputDir;
+//		}
+//		public String getOutputDir() {
+//			return outputDir;
+//		}
+//		public void setOutputDir(String outputDir) {
+//			this.outputDir = outputDir;
+//		}
+//    }
+//    public LocalProvider(){
+//        cmdList = new ArrayList<String>();
+//    }
+//
+//    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
+//    	super.initialize(jobExecutionContext);
+//
+//        // build command with all inputs
+//        buildCommand();
+//        initProcessBuilder(jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription());
+//
+//        // extra environment variables
+//        builder.environment().put(GFacConstants.INPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getInputDir());
+//        builder.environment().put(GFacConstants.OUTPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getOutputDir());
+//
+//        // set working directory
+//        builder.directory(new File(jobExecutionContext.getWorkingDir()));
+//
+//        // log info
+//        log.info("Command = " + InputUtils.buildCommand(cmdList));
+//        log.info("Working dir = " + builder.directory());
+//        /*for (String key : builder.environment().keySet()) {
+//            log.info("Env[" + key + "] = " + builder.environment().get(key));
+//        }*/
+//    }
+//
+//    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException {
+//        JobDetails jobDetails = new JobDetails();
+//        try {
+//        	jobId = jobExecutionContext.getTaskData().getTaskID();
+//            jobDetails.setJobID(jobId);
+//            jobDetails.setJobDescription(jobExecutionContext.getApplicationContext()
+//                    .getApplicationDeploymentDescription().getAppDeploymentDescription());
+//            jobExecutionContext.setJobDetails(jobDetails);
+//            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SETUP);
+//            // running cmd
+//            Process process = builder.start();
+//
+//            Thread standardOutWriter = new InputStreamToFileWriter(process.getInputStream(), jobExecutionContext.getStandardOutput());
+//            Thread standardErrorWriter = new InputStreamToFileWriter(process.getErrorStream(), jobExecutionContext.getStandardError());
+//
+//            // start output threads
+//            standardOutWriter.setDaemon(true);
+//            standardErrorWriter.setDaemon(true);
+//            standardOutWriter.start();
+//            standardErrorWriter.start();
+//
+//            int returnValue = process.waitFor();
+//
+//            // make sure other two threads are done
+//            standardOutWriter.join();
+//            standardErrorWriter.join();
+//
+//            /*
+//             * check return value. usually not very helpful to draw conclusions based on return values so don't bother.
+//             * just provide warning in the log messages
+//             */
+//            if (returnValue != 0) {
+//                log.error("Process finished with non zero return value. Process may have failed");
+//            } else {
+//                log.info("Process finished with return value of zero.");
+//            }
+//
+//            StringBuffer buf = new StringBuffer();
+//            buf.append("Executed ").append(InputUtils.buildCommand(cmdList))
+//                    .append(" on the localHost, working directory = ").append(jobExecutionContext.getWorkingDir())
+//                    .append(" tempDirectory = ").append(jobExecutionContext.getScratchLocation()).append(" With the status ")
+//                    .append(String.valueOf(returnValue));
+//
+//            log.info(buf.toString());
+//
+//            // updating the job status to complete because there's nothing to monitor in local jobs
+////            MonitorID monitorID = createMonitorID(jobExecutionContext);
+//            JobIdentifier jobIdentity = new JobIdentifier(jobExecutionContext.getJobDetails().getJobID(),
+//                    jobExecutionContext.getTaskData().getTaskID(),
+//                    jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
+//                    jobExecutionContext.getExperimentID(),
+//                    jobExecutionContext.getGatewayID());
+//            jobExecutionContext.getLocalEventPublisher().publish(new JobStatusChangeEvent(JobState.COMPLETE, jobIdentity));
+//        } catch (IOException io) {
+//            throw new GFacProviderException(io.getMessage(), io);
+//        } catch (InterruptedException e) {
+//            throw new GFacProviderException(e.getMessage(), e);
+//        }catch (GFacException e) {
+//            throw new GFacProviderException(e.getMessage(), e);
+//        }
+//    }
+//
+////	private MonitorID createMonitorID(JobExecutionContext jobExecutionContext) {
+////		MonitorID monitorID = new MonitorID(jobExecutionContext.getApplicationContext().getHostDescription(), jobId,
+////		        jobExecutionContext.getTaskData().getTaskID(),
+////		        jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(), jobExecutionContext.getExperimentID(),
+////		        jobExecutionContext.getExperiment().getUserName(),jobId);
+////		return monitorID;
+////	}
+//
+////	private void saveApplicationJob(JobExecutionContext jobExecutionContext)
+////			throws GFacProviderException {
+////		ApplicationDeploymentDescriptionType app = jobExecutionContext.
+////                getApplicationContext().getApplicationDeploymentDescription().getType();
+////		ApplicationJob appJob = GFacUtils.createApplicationJob(jobExecutionContext);
+////		appJob.setJobId(jobId);
+////		LocalProviderJobData data = new LocalProviderJobData();
+////		data.setApplicationName(app.getExecutableLocation());
+////		data.setInputDir(app.getInputDataDirectory());
+////		data.setOutputDir(app.getOutputDataDirectory());
+////		data.setWorkingDir(builder.directory().toString());
+////		data.setInputParameters(ProviderUtils.getInputParameters(jobExecutionContext));
+////		ByteArrayOutputStream stream = new ByteArrayOutputStream();
+////		JAXB.marshal(data, stream);
+////		appJob.setJobData(stream.toString());
+////		appJob.setSubmittedTime(Calendar.getInstance().getTime());
+////		appJob.setStatus(ApplicationJobStatus.SUBMITTED);
+////		appJob.setStatusUpdateTime(appJob.getSubmittedTime());
+////		GFacUtils.recordApplicationJob(jobExecutionContext, appJob);
+////	}
+//
+//    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
+//        try {
+//        	List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>();
+//            String stdOutStr = GFacUtils.readFileToString(jobExecutionContext.getStandardOutput());
+//            String stdErrStr = GFacUtils.readFileToString(jobExecutionContext.getStandardError());
+//			Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
+//            OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
+//            TaskDetails taskDetails = (TaskDetails) experimentCatalog.get(ExperimentCatalogModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
+//            if (taskDetails != null){
+//                taskDetails.setApplicationOutputs(outputArray);
+//                experimentCatalog.update(ExperimentCatalogModelType.TASK_DETAIL, taskDetails, taskDetails.getTaskID());
+//            }
+//            experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
+//            TaskIdentifier taskIdentity = new TaskIdentifier(jobExecutionContext.getTaskData().getTaskID(),
+//                    jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
+//                    jobExecutionContext.getExperimentID(),
+//                    jobExecutionContext.getGatewayID());
+//            jobExecutionContext.getLocalEventPublisher().publish(new TaskOutputChangeEvent(outputArray, taskIdentity));
+//        } catch (XmlException e) {
+//            throw new GFacProviderException("Cannot read output:" + e.getMessage(), e);
+//        } catch (IOException io) {
+//            throw new GFacProviderException(io.getMessage(), io);
+//        } catch (Exception e){
+//        	throw new GFacProviderException("Error in retrieving results",e);
+//        }
+//    }
+//
+//    public boolean cancelJob(JobExecutionContext jobExecutionContext) throws GFacException {
+//        throw new NotImplementedException();
+//    }
+//
+//    @Override
+//    public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+//        // TODO: Auto generated method body.
+//    }
+//
+//    @Override
+//    public void monitor(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+//        // TODO: Auto generated method body.
+//    }
+//
+//
+//    private void buildCommand() {
+//        cmdList.add(jobExecutionContext.getExecutablePath());
+//        Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
+//
+//        // sort the inputs first and then build the command List
+//        Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
+//            @Override
+//            public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType t1) {
+//                return inputDataObjectType.getInputOrder() - t1.getInputOrder();
+//            }
+//        };
+//        Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
+//        for (Object object : inputParameters.values()) {
+//            if (object instanceof InputDataObjectType) {
+//                InputDataObjectType inputDOT = (InputDataObjectType) object;
+//                sortedInputSet.add(inputDOT);
+//            }
+//        }
+//        for (InputDataObjectType inputDataObjectType : sortedInputSet) {
+//            if (inputDataObjectType.getApplicationArgument() != null
+//                    && !inputDataObjectType.getApplicationArgument().equals("")) {
+//                cmdList.add(inputDataObjectType.getApplicationArgument());
+//            }
+//
+//            if (inputDataObjectType.getValue() != null
+//                    && !inputDataObjectType.getValue().equals("")) {
+//                cmdList.add(inputDataObjectType.getValue());
+//            }
+//        }
+//
+//    }
+//
+//    private void initProcessBuilder(ApplicationDeploymentDescription app){
+//        builder = new ProcessBuilder(cmdList);
+//
+//        List<SetEnvPaths> setEnvironment = app.getSetEnvironment();
+//        if (setEnvironment != null) {
+//            for (SetEnvPaths envPath : setEnvironment) {
+//                Map<String,String> builderEnv = builder.environment();
+//                builderEnv.put(envPath.getName(), envPath.getValue());
+//            }
+//        }
+//    }
+//
+//    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
+//
+//    }
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/df3fbe6a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
index 2b45df7..8d7cd8d 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
@@ -1,51 +1,51 @@
-/*
- *
- * 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.gfac.local.utils;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class LocalProviderUtil {
-    private static final Logger log = LoggerFactory.getLogger(LocalProviderUtil.class);
-
-    private void makeFileSystemDir(String dir) throws GFacProviderException {
-        File f = new File(dir);
-        if (f.isDirectory() && f.exists()) {
-            return;
-        } else if (!new File(dir).mkdir()) {
-            throw new GFacProviderException("Cannot make directory " + dir);
-        }
-    }
-
-    public void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacProviderException {
-        log.info("working diectroy = " + jobExecutionContext.getWorkingDir());
-        log.info("temp directory = " + jobExecutionContext.getScratchLocation());
-        makeFileSystemDir(jobExecutionContext.getWorkingDir());
-        makeFileSystemDir(jobExecutionContext.getScratchLocation());
-        makeFileSystemDir(jobExecutionContext.getInputDir());
-        makeFileSystemDir(jobExecutionContext.getOutputDir());
-    }
-
-}
+///*
+// *
+// * 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.gfac.local.utils;
+//
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.provider.GFacProviderException;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+//import java.io.File;
+//
+//public class LocalProviderUtil {
+//    private static final Logger log = LoggerFactory.getLogger(LocalProviderUtil.class);
+//
+//    private void makeFileSystemDir(String dir) throws GFacProviderException {
+//        File f = new File(dir);
+//        if (f.isDirectory() && f.exists()) {
+//            return;
+//        } else if (!new File(dir).mkdir()) {
+//            throw new GFacProviderException("Cannot make directory " + dir);
+//        }
+//    }
+//
+//    public void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacProviderException {
+//        log.info("working diectroy = " + jobExecutionContext.getWorkingDir());
+//        log.info("temp directory = " + jobExecutionContext.getScratchLocation());
+//        makeFileSystemDir(jobExecutionContext.getWorkingDir());
+//        makeFileSystemDir(jobExecutionContext.getScratchLocation());
+//        makeFileSystemDir(jobExecutionContext.getInputDir());
+//        makeFileSystemDir(jobExecutionContext.getOutputDir());
+//    }
+//
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/df3fbe6a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
index 68fb39c..587bf46 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
@@ -1,229 +1,229 @@
-/*
- *
- * 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.gfac.ssh.handler;
-
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.apache.airavata.gfac.core.cluster.RemoteCluster;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.handler.AbstractHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
-import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
-import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
-import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.experiment.*;
-import org.apache.airavata.registry.cpi.ExpCatChildDataType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.*;
-
-/**
- * This handler will copy input data from gateway machine to airavata
- * installed machine, later running handlers can copy the input files to computing resource
- * <Handler class="AdvancedSCPOutputHandler">
- * <property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
- * <property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>
- * <property name="userName" value="airavata"/>
- * <property name="hostName" value="gw98.iu.xsede.org"/>
- * <property name="inputPath" value="/home/airavata/outputData"/>
- */
-public class AdvancedSCPInputHandler extends AbstractHandler {
-    private static final Logger log = LoggerFactory.getLogger(AdvancedSCPInputHandler.class);
-    public static final String ADVANCED_SSH_AUTH = "advanced.ssh.auth";
-    public static final int DEFAULT_SSH_PORT = 22;
-
-    private String password = null;
-
-    private String publicKeyPath;
-
-    private String passPhrase;
-
-    private String privateKeyPath;
-
-    private String userName;
-
-    private String hostName;
-
-    private String inputPath;
-
-    public void initProperties(Properties properties) throws GFacHandlerException {
-        password = (String) properties.get("password");
-        passPhrase = (String) properties.get("passPhrase");
-        privateKeyPath = (String) properties.get("privateKeyPath");
-        publicKeyPath = (String) properties.get("publicKeyPath");
-        userName = (String) properties.get("userName");
-        hostName = (String) properties.get("hostName");
-        inputPath = (String) properties.get("inputPath");
-    }
-
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        super.invoke(jobExecutionContext);
-        int index = 0;
-        int oldIndex = 0;
-        List<String> oldFiles = new ArrayList<String>();
-        MessageContext inputNew = new MessageContext();
-        StringBuffer data = new StringBuffer("|");
-        RemoteCluster remoteCluster = null;
-
-        try {
-            String pluginData = GFacUtils.getHandlerData(jobExecutionContext, this.getClass().getName());
-            if (pluginData != null) {
-                try {
-                    oldIndex = Integer.parseInt(pluginData.split("\\|")[0].trim());
-                    oldFiles = Arrays.asList(pluginData.split("\\|")[1].split(","));
-                    if (oldIndex == oldFiles.size()) {
-                        log.info("Old data looks good !!!!");
-                    } else {
-                        oldIndex = 0;
-                        oldFiles.clear();
-                    }
-                } catch (NumberFormatException e) {
-                    log.error("Previously stored data " + pluginData + " is wrong so we continue the operations");
-                }
-            }
-
-            AuthenticationInfo authenticationInfo = null;
-            if (password != null) {
-                authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
-            } else {
-                authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
-                        this.passPhrase);
-            }
-
-            // Server info
-            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
-            if (index < oldIndex) {
-                parentPath = oldFiles.get(index);
-                data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
-            } else {
-                (new File(parentPath)).mkdirs();
-                StringBuffer temp = new StringBuffer(data.append(parentPath).append(",").toString());
-                GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-            }
-            DataTransferDetails detail = new DataTransferDetails();
-            TransferStatus status = new TransferStatus();
-            // here doesn't matter what the job manager is because we are only doing some file handling
-            // not really dealing with monitoring or job submission, so we pa
-
-            MessageContext input = jobExecutionContext.getInMessageContext();
-            Set<String> parameters = input.getParameters().keySet();
-            for (String paramName : parameters) {
-                InputDataObjectType inputParamType = (InputDataObjectType) input.getParameters().get(paramName);
-                String paramValue = inputParamType.getValue();
-                // TODO: Review this with type
-                if (inputParamType.getType() == DataType.URI) {
-                    try {
-                        URL file = new URL(paramValue);
-                        String key = file.getUserInfo() + file.getHost() + DEFAULT_SSH_PORT;
-                        GFACSSHUtils.prepareSecurityContext(jobExecutionContext, authenticationInfo, file.getUserInfo(), file.getHost(), DEFAULT_SSH_PORT);
-                        remoteCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(key)).getRemoteCluster();
-                        paramValue = file.getPath();
-                    } catch (MalformedURLException e) {
-                        String key = this.userName + this.hostName + DEFAULT_SSH_PORT;
-                        GFACSSHUtils.prepareSecurityContext(jobExecutionContext, authenticationInfo, this.userName, this.hostName, DEFAULT_SSH_PORT);
-                        remoteCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(key)).getRemoteCluster();
-                        log.error(e.getLocalizedMessage(), e);
-                    }
-
-                    if (index < oldIndex) {
-                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
-                        inputParamType.setValue(oldFiles.get(index));
-                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
-                    } else {
-                        String stageInputFile = stageInputFiles(remoteCluster, paramValue, parentPath);
-                        inputParamType.setValue(stageInputFile);
-                        StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
-                        status.setTransferState(TransferState.UPLOAD);
-                        detail.setTransferStatus(status);
-                        detail.setTransferDescription("Input Data Staged: " + stageInputFile);
-                        experimentCatalog.add(ExpCatChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-
-                        GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                    }
-                }
-                // FIXME: what is the thrift model DataType equivalent for URIArray type?
-//                else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-//                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
-//                    List<String> newFiles = new ArrayList<String>();
-//                    for (String paramValueEach : split) {
-//                        try {
-//                            URL file = new URL(paramValue);
-//                            this.userName = file.getUserInfo();
-//                            this.hostName = file.getHost();
-//                            paramValueEach = file.getPath();
-//                        } catch (MalformedURLException e) {
-//                            log.error(e.getLocalizedMessage(), e);
-//                        }
-//                        if (index < oldIndex) {
-//                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
-//                            newFiles.add(oldFiles.get(index));
-//                            data.append(oldFiles.get(index++)).append(",");
-//                        } else {
-//                            String stageInputFiles = stageInputFiles(remoteCluster, paramValueEach, parentPath);
-//                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
-//                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-//                            newFiles.add(stageInputFiles);
-//                        }
+///*
+// *
+// * 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.gfac.ssh.handler;
+//
+//import org.apache.airavata.gfac.core.GFacException;
+//import org.apache.airavata.gfac.core.SSHApiException;
+//import org.apache.airavata.gfac.core.cluster.RemoteCluster;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.context.MessageContext;
+//import org.apache.airavata.gfac.core.handler.AbstractHandler;
+//import org.apache.airavata.gfac.core.handler.GFacHandlerException;
+//import org.apache.airavata.gfac.core.GFacUtils;
+//import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+//import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
+//import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
+//import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
+//import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
+//import org.apache.airavata.model.appcatalog.appinterface.DataType;
+//import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+//import org.apache.airavata.model.experiment.*;
+//import org.apache.airavata.registry.cpi.ExpCatChildDataType;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+//import java.io.File;
+//import java.io.PrintWriter;
+//import java.io.StringWriter;
+//import java.net.MalformedURLException;
+//import java.net.URL;
+//import java.util.*;
+//
+///**
+// * This handler will copy input data from gateway machine to airavata
+// * installed machine, later running handlers can copy the input files to computing resource
+// * <Handler class="AdvancedSCPOutputHandler">
+// * <property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
+// * <property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>
+// * <property name="userName" value="airavata"/>
+// * <property name="hostName" value="gw98.iu.xsede.org"/>
+// * <property name="inputPath" value="/home/airavata/outputData"/>
+// */
+//public class AdvancedSCPInputHandler extends AbstractHandler {
+//    private static final Logger log = LoggerFactory.getLogger(AdvancedSCPInputHandler.class);
+//    public static final String ADVANCED_SSH_AUTH = "advanced.ssh.auth";
+//    public static final int DEFAULT_SSH_PORT = 22;
+//
+//    private String password = null;
+//
+//    private String publicKeyPath;
+//
+//    private String passPhrase;
+//
+//    private String privateKeyPath;
+//
+//    private String userName;
+//
+//    private String hostName;
+//
+//    private String inputPath;
+//
+//    public void initProperties(Properties properties) throws GFacHandlerException {
+//        password = (String) properties.get("password");
+//        passPhrase = (String) properties.get("passPhrase");
+//        privateKeyPath = (String) properties.get("privateKeyPath");
+//        publicKeyPath = (String) properties.get("publicKeyPath");
+//        userName = (String) properties.get("userName");
+//        hostName = (String) properties.get("hostName");
+//        inputPath = (String) properties.get("inputPath");
+//    }
+//
+//    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
+//        super.invoke(jobExecutionContext);
+//        int index = 0;
+//        int oldIndex = 0;
+//        List<String> oldFiles = new ArrayList<String>();
+//        MessageContext inputNew = new MessageContext();
+//        StringBuffer data = new StringBuffer("|");
+//        RemoteCluster remoteCluster = null;
+//
+//        try {
+//            String pluginData = GFacUtils.getHandlerData(jobExecutionContext, this.getClass().getName());
+//            if (pluginData != null) {
+//                try {
+//                    oldIndex = Integer.parseInt(pluginData.split("\\|")[0].trim());
+//                    oldFiles = Arrays.asList(pluginData.split("\\|")[1].split(","));
+//                    if (oldIndex == oldFiles.size()) {
+//                        log.info("Old data looks good !!!!");
+//                    } else {
+//                        oldIndex = 0;
+//                        oldFiles.clear();
 //                    }
-//                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
+//                } catch (NumberFormatException e) {
+//                    log.error("Previously stored data " + pluginData + " is wrong so we continue the operations");
 //                }
-                inputNew.getParameters().put(paramName, inputParamType);
-            }
-        } catch (Exception e) {
-            log.error(e.getMessage());
-            try {
-                StringWriter errors = new StringWriter();
-                e.printStackTrace(new PrintWriter(errors));
-                GFacUtils.saveErrorDetails(jobExecutionContext,  errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            } catch (GFacException e1) {
-                log.error(e1.getLocalizedMessage());
-            }
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-        jobExecutionContext.setInMessageContext(inputNew);
-    }
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        this.invoke(jobExecutionContext);
-    }
-
-    private String stageInputFiles(RemoteCluster remoteCluster, String paramValue, String parentPath) throws GFacException {
-        try {
-            remoteCluster.scpFrom(paramValue, parentPath);
-            return "file://" + parentPath + File.separator + (new File(paramValue)).getName();
-        } catch (SSHApiException e) {
-            log.error("Error tranfering remote file to local file, remote path: " + paramValue);
-            throw new GFacException(e);
-        }
-    }
-}
+//            }
+//
+//            AuthenticationInfo authenticationInfo = null;
+//            if (password != null) {
+//                authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+//            } else {
+//                authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+//                        this.passPhrase);
+//            }
+//
+//            // Server info
+//            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
+//            if (index < oldIndex) {
+//                parentPath = oldFiles.get(index);
+//                data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
+//            } else {
+//                (new File(parentPath)).mkdirs();
+//                StringBuffer temp = new StringBuffer(data.append(parentPath).append(",").toString());
+//                GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+//            }
+//            DataTransferDetails detail = new DataTransferDetails();
+//            TransferStatus status = new TransferStatus();
+//            // here doesn't matter what the job manager is because we are only doing some file handling
+//            // not really dealing with monitoring or job submission, so we pa
+//
+//            MessageContext input = jobExecutionContext.getInMessageContext();
+//            Set<String> parameters = input.getParameters().keySet();
+//            for (String paramName : parameters) {
+//                InputDataObjectType inputParamType = (InputDataObjectType) input.getParameters().get(paramName);
+//                String paramValue = inputParamType.getValue();
+//                // TODO: Review this with type
+//                if (inputParamType.getType() == DataType.URI) {
+//                    try {
+//                        URL file = new URL(paramValue);
+//                        String key = file.getUserInfo() + file.getHost() + DEFAULT_SSH_PORT;
+//                        GFACSSHUtils.prepareSecurityContext(jobExecutionContext, authenticationInfo, file.getUserInfo(), file.getHost(), DEFAULT_SSH_PORT);
+//                        remoteCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(key)).getRemoteCluster();
+//                        paramValue = file.getPath();
+//                    } catch (MalformedURLException e) {
+//                        String key = this.userName + this.hostName + DEFAULT_SSH_PORT;
+//                        GFACSSHUtils.prepareSecurityContext(jobExecutionContext, authenticationInfo, this.userName, this.hostName, DEFAULT_SSH_PORT);
+//                        remoteCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(key)).getRemoteCluster();
+//                        log.error(e.getLocalizedMessage(), e);
+//                    }
+//
+//                    if (index < oldIndex) {
+//                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
+//                        inputParamType.setValue(oldFiles.get(index));
+//                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
+//                    } else {
+//                        String stageInputFile = stageInputFiles(remoteCluster, paramValue, parentPath);
+//                        inputParamType.setValue(stageInputFile);
+//                        StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
+//                        status.setTransferState(TransferState.UPLOAD);
+//                        detail.setTransferStatus(status);
+//                        detail.setTransferDescription("Input Data Staged: " + stageInputFile);
+//                        experimentCatalog.add(ExpCatChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+//
+//                        GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+//                    }
+//                }
+//                // FIXME: what is the thrift model DataType equivalent for URIArray type?
+////                else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
+////                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
+////                    List<String> newFiles = new ArrayList<String>();
+////                    for (String paramValueEach : split) {
+////                        try {
+////                            URL file = new URL(paramValue);
+////                            this.userName = file.getUserInfo();
+////                            this.hostName = file.getHost();
+////                            paramValueEach = file.getPath();
+////                        } catch (MalformedURLException e) {
+////                            log.error(e.getLocalizedMessage(), e);
+////                        }
+////                        if (index < oldIndex) {
+////                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
+////                            newFiles.add(oldFiles.get(index));
+////                            data.append(oldFiles.get(index++)).append(",");
+////                        } else {
+////                            String stageInputFiles = stageInputFiles(remoteCluster, paramValueEach, parentPath);
+////                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
+////                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+////                            newFiles.add(stageInputFiles);
+////                        }
+////                    }
+////                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
+////                }
+//                inputNew.getParameters().put(paramName, inputParamType);
+//            }
+//        } catch (Exception e) {
+//            log.error(e.getMessage());
+//            try {
+//                StringWriter errors = new StringWriter();
+//                e.printStackTrace(new PrintWriter(errors));
+//                GFacUtils.saveErrorDetails(jobExecutionContext,  errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
+//            } catch (GFacException e1) {
+//                log.error(e1.getLocalizedMessage());
+//            }
+//            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
+//        }
+//        jobExecutionContext.setInMessageContext(inputNew);
+//    }
+//
+//    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
+//        this.invoke(jobExecutionContext);
+//    }
+//
+//    private String stageInputFiles(RemoteCluster remoteCluster, String paramValue, String parentPath) throws GFacException {
+//        try {
+//            remoteCluster.scpFrom(paramValue, parentPath);
+//            return "file://" + parentPath + File.separator + (new File(paramValue)).getName();
+//        } catch (SSHApiException e) {
+//            log.error("Error tranfering remote file to local file, remote path: " + paramValue);
+//            throw new GFacException(e);
+//        }
+//    }
+//}


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