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From shame...@apache.org
Subject [29/39] airavata git commit: Refactored gfac sub modules, merged gfac-ssh, gfac-gsissh, gfac-local, gfac-monitor and gsissh modules and create gface-impl, removed implementation from gfac-core to gfac-impl
Date Wed, 03 Jun 2015 18:14:46 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutHandlerWorker.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutHandlerWorker.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutHandlerWorker.java
deleted file mode 100644
index f027ccb..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutHandlerWorker.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- *
- * 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.core.utils;
-
-import org.apache.airavata.common.utils.MonitorPublisher;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.cpi.GFac;
-import org.apache.airavata.gfac.core.monitor.MonitorID;
-import org.apache.airavata.model.messaging.event.TaskIdentifier;
-import org.apache.airavata.model.messaging.event.TaskStatusChangeRequestEvent;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TaskState;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.PrintWriter;
-import java.io.StringWriter;
-
-public class OutHandlerWorker implements Runnable {
-    private final static Logger logger = LoggerFactory.getLogger(OutHandlerWorker.class);
-
-    private GFac gfac;
-
-    private MonitorID monitorID;
-
-    private MonitorPublisher monitorPublisher;
-    private JobExecutionContext jEC;
-
-    public OutHandlerWorker(GFac gfac, MonitorID monitorID,MonitorPublisher monitorPublisher) {
-        this.gfac = gfac;
-        this.monitorID = monitorID;
-        this.monitorPublisher = monitorPublisher;
-        this.jEC = monitorID.getJobExecutionContext();
-    }
-
-    public OutHandlerWorker(JobExecutionContext jEC) {
-        this.jEC = jEC;
-        this.gfac = jEC.getGfac();
-        this.monitorPublisher = jEC.getMonitorPublisher();
-    }
-
-    @Override
-    public void run() {
-        try {
-//            gfac.invokeOutFlowHandlers(monitorID.getJobExecutionContext());
-            gfac.invokeOutFlowHandlers(jEC);
-        } catch (Exception e) {
-            logger.error(e.getMessage(),e);
-            TaskIdentifier taskIdentifier = new TaskIdentifier(monitorID.getTaskID(), monitorID.getWorkflowNodeID(),monitorID.getExperimentID(), monitorID.getJobExecutionContext().getGatewayID());
-            //FIXME this is a case where the output retrieving fails even if the job execution was a success. Thus updating the task status
-            monitorPublisher.publish(new TaskStatusChangeRequestEvent(TaskState.FAILED, taskIdentifier));
-            try {
-                StringWriter errors = new StringWriter();
-                e.printStackTrace(new PrintWriter(errors));
-                GFacUtils.saveErrorDetails(monitorID.getJobExecutionContext(),  errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            } catch (GFacException e1) {
-                logger.error("Error while persisting error details", e);
-            }
-            logger.info(e.getLocalizedMessage(), e);
-            // Save error details to registry
-
-        }
-//        monitorPublisher.publish(monitorID.getStatus());
-        monitorPublisher.publish(jEC.getJobDetails().getJobStatus());
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutputUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutputUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutputUtils.java
deleted file mode 100644
index 3c8bbf0..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/OutputUtils.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- *
- * 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.core.utils;
-
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class OutputUtils {
-    private static String regexPattern = "\\s*=\\s*(.*)\\r?\\n";
-
-	public static void fillOutputFromStdout(Map<String, Object> output, String stdout, String stderr, List<OutputDataObjectType> outputArray) throws Exception {
-        // this is no longer correct
-//		if (stdout == null || stdout.equals("")) {
-//			throw new GFacHandlerException("Standard output is empty.");
-//		}
-
-		Set<String> keys = output.keySet();
-        OutputDataObjectType actual = null;
-        OutputDataObjectType resultOutput = null;
-		for (String paramName : keys) {
-			actual = (OutputDataObjectType) output.get(paramName);
-			// if parameter value is not already set, we let it go
-
-			if (actual == null) {
-				continue;
-			}
-            resultOutput = new OutputDataObjectType();
-            if (DataType.STDOUT == actual.getType()) {
-                actual.setValue(stdout);
-                resultOutput.setName(paramName);
-                resultOutput.setType(DataType.STDOUT);
-                resultOutput.setValue(stdout);
-                outputArray.add(resultOutput);
-			} else if (DataType.STDERR == actual.getType()) {
-                actual.setValue(stderr);
-                resultOutput.setName(paramName);
-                resultOutput.setType(DataType.STDERR);
-                resultOutput.setValue(stderr);
-                outputArray.add(resultOutput);
-            }
-//			else if ("URI".equals(actual.getType().getType().toString())) {
-//				continue;
-//			} 
-            else {
-                String parseStdout = parseStdout(stdout, paramName);
-                if (parseStdout != null) {
-                    actual.setValue(parseStdout);
-                    resultOutput.setName(paramName);
-                    resultOutput.setType(DataType.STRING);
-                    resultOutput.setValue(parseStdout);
-                    outputArray.add(resultOutput);
-                }
-            }
-        }
-	}
-
-    private static String parseStdout(String stdout, String outParam) throws Exception {
-        String regex = Pattern.quote(outParam) + regexPattern;
-        String match = null;
-        Pattern pattern = Pattern.compile(regex);
-        Matcher matcher = pattern.matcher(stdout);
-        while (matcher.find()) {
-            match = matcher.group(1);
-        }
-        if (match != null) {
-            match = match.trim();
-            return match;
-        } 
-        return null;
-    }
-
-    public static String[] parseStdoutArray(String stdout, String outParam) throws Exception {
-        String regex = Pattern.quote(outParam) + regexPattern;
-        StringBuffer match = new StringBuffer();
-        Pattern pattern = Pattern.compile(regex);
-        Matcher matcher = pattern.matcher(stdout);
-        while (matcher.find()) {
-            match.append(matcher.group(1) + StringUtil.DELIMETER);
-        }
-        if (match != null && match.length() >0) {
-        	return StringUtil.getElementsFromString(match.toString());
-        } 
-        return null;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/pom.xml b/modules/gfac/gfac-gsissh/pom.xml
deleted file mode 100644
index 81c3ec9..0000000
--- a/modules/gfac/gfac-gsissh/pom.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--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 (theƏ "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. -->
-
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <parent>
-        <groupId>org.apache.airavata</groupId>
-        <artifactId>gfac</artifactId>
-        <version>0.16-SNAPSHOT</version>
-        <relativePath>../pom.xml</relativePath>
-    </parent>
-
-    <modelVersion>4.0.0</modelVersion>
-    <artifactId>airavata-gfac-gsissh</artifactId>
-    <name>Airavata GFac GSI-SSH implementation</name>
-    <description>This is the extension of </description>
-    <url>http://airavata.apache.org/</url>
-
-    <dependencies>
-
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-email-monitor</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <!-- Logging -->
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-
-        <!-- GFAC dependencies -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-ssh</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <!-- Credential Store -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-credential-store</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-server-configuration</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-client-configuration</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-
-        <!-- Test -->
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.testng</groupId>
-            <artifactId>testng</artifactId>
-            <version>6.1.1</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>jcl-over-slf4j</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-log4j12</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-        <!-- gsi-ssh api dependencies -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>gsissh</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-data-models</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>com.jcraft</groupId>
-            <artifactId>jsch</artifactId>
-            <version>0.1.50</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.xmlbeans</groupId>
-            <artifactId>xmlbeans</artifactId>
-            <version>${xmlbeans.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>net.schmizz</groupId>
-            <artifactId>sshj</artifactId>
-            <version>0.6.1</version>
-        </dependency>
-    </dependencies>
-</project>

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
deleted file mode 100644
index b4790c7..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- *
- * 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.gsissh.handler;
-
-import org.apache.airavata.gfac.GFacException;
-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.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.model.workspace.experiment.*;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.Properties;
-
-public class GSISSHDirectorySetupHandler extends AbstractHandler {
-      private static final Logger log = LoggerFactory.getLogger(GSISSHDirectorySetupHandler.class);
-
-	public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        try {
-            String hostAddress = jobExecutionContext.getHostName();
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-        } catch (Exception e) {
-        	 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 creating SSHSecurityContext", e, e.getLocalizedMessage());
-        }
-
-        log.info("Setup SSH job directorties");
-        super.invoke(jobExecutionContext);
-        makeDirectory(jobExecutionContext);
-	}
-	private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        Cluster cluster = null;
-        try {
-            String hostAddress = jobExecutionContext.getHostName();
-            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
-            if (cluster == null) {
-                try {
-                    GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-                } catch (GFacException e1) {
-                    log.error(e1.getLocalizedMessage());
-                }
-                throw new GFacHandlerException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-
-            String workingDirectory = jobExecutionContext.getWorkingDir();
-            cluster.makeDirectory(workingDirectory);
-            if(!jobExecutionContext.getInputDir().equals(workingDirectory))
-                cluster.makeDirectory(jobExecutionContext.getInputDir());
-            if(!jobExecutionContext.getOutputDir().equals(workingDirectory))
-            	cluster.makeDirectory(jobExecutionContext.getOutputDir());
-            
-            DataTransferDetails detail = new DataTransferDetails();
-            TransferStatus status = new TransferStatus();
-            status.setTransferState(TransferState.DIRECTORY_SETUP);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("Working directory = " + workingDirectory);
-
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-
-		} catch (Exception e) {
-			DataTransferDetails detail = new DataTransferDetails();
-			TransferStatus status = new TransferStatus();
-			detail.setTransferDescription("Working directory = " + jobExecutionContext.getWorkingDir());
-			status.setTransferState(TransferState.FAILED);
-			detail.setTransferStatus(status);
-			try {
-				registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-				GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
-			} catch (Exception e1) {
-				throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-			}
-			throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
-		}
-	}
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-         this.invoke(jobExecutionContext);
-    }
-
-    public void initProperties(Properties properties) throws GFacHandlerException {
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
deleted file mode 100644
index 3b36e86..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
+++ /dev/null
@@ -1,213 +0,0 @@
-/*
- *
- * 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.gsissh.handler;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.gfac.GFacException;
-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.utils.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Properties;
-import java.util.Set;
-
-/**
- * Recoverability for this handler assumes the same input values will come in the second
- * run, and assume nobody is changing registry during the original submission and re-submission
- */
-public class GSISSHInputHandler extends AbstractHandler {
-    private static final Logger log = LoggerFactory.getLogger(GSISSHInputHandler.class);
-
-
-    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();
-        DataTransferDetails detail = new DataTransferDetails();
-        TransferStatus status = new TransferStatus();
-        StringBuffer data = new StringBuffer("|");
-        Cluster cluster = null;
-
-        try {
-            String hostAddress = jobExecutionContext.getHostName();
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-
-            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
-            if (cluster == null) {
-                throw new GFacException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-
-            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");
-                }
-            }
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                try {
-                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-                } catch (ApplicationSettingsException e) {
-                    log.error(e.getMessage());
-                    try {
-                        GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-                    } catch (GFacException e1) {
-                        log.error(e1.getLocalizedMessage());
-                    }
-                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-                }
-            }
-            log.info("Invoking SCPInputHandler");
-
-            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) {
-                    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(cluster, jobExecutionContext, paramValue);
-                        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);
-                        registry.add(ChildDataType.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(inputParamType.getType().getType().toString())) {
-//                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
-//                    List<String> newFiles = new ArrayList<String>();
-//                    for (String paramValueEach : split) {
-//                        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(cluster, jobExecutionContext, paramValueEach);
-//                            status.setTransferState(TransferState.UPLOAD);
-//                            detail.setTransferStatus(status);
-//                            detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
-//                            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-//                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
-//                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-//                            newFiles.add(stageInputFiles);
-//                        }
-//
-//                    }
-//                    ((URIArrayType) inputParamType.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
-//                }
-                inputNew.getParameters().put(paramName, inputParamType);
-            }
-        } catch (Exception e) {
-            log.error(e.getMessage());
-            status.setTransferState(TransferState.FAILED);
-            detail.setTransferDescription(e.getLocalizedMessage());
-            detail.setTransferStatus(status);
-            try {
-                GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
-                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-            } catch (Exception e1) {
-                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-            }
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-        jobExecutionContext.setInMessageContext(inputNew);
-    }
-
-    private static String stageInputFiles(Cluster cluster, JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
-        int i = paramValue.lastIndexOf(File.separator);
-        String substring = paramValue.substring(i + 1);
-        try {
-            String targetFile = jobExecutionContext.getInputDir() + File.separator + substring;
-            if (paramValue.startsWith("file")) {
-                paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
-            }
-            boolean success = false;
-            int j = 1;
-            while(!success){
-            try {
-				cluster.scpTo(targetFile, paramValue);
-				success = true;
-			} catch (Exception e) {
-				log.info(e.getLocalizedMessage());
-				Thread.sleep(2000);
-				 if(j==3) {
-					throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-				 }
-            }
-            j++;
-            }
-            return targetFile;
-        } catch (Exception e) {
-            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
-        }
-    }
-
-    public void initProperties(Properties properties) throws GFacHandlerException {
-
-    }
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        this.invoke(jobExecutionContext);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
deleted file mode 100644
index 18dcb97..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
+++ /dev/null
@@ -1,323 +0,0 @@
-/*
- *
- * 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.gsissh.handler;
-
-//import org.apache.airavata.commons.gfac.type.ActualParameter;
-//import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.gfac.GFacException;
-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.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.core.utils.OutputUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
-
-public class GSISSHOutputHandler extends AbstractHandler {
-    private static final Logger log = LoggerFactory.getLogger(GSISSHOutputHandler.class);
-
-    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        super.invoke(jobExecutionContext);
-        int index = 0;
-        int oldIndex = 0;
-        List<String> oldFiles = new ArrayList<String>();
-        StringBuffer data = new StringBuffer("|");
-        String hostAddress = jobExecutionContext.getHostName();
-        try {
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-        }  catch (Exception e) {
-        	 try {
-  				GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-  			} catch (GFacException e1) {
-  				 log.error(e1.getLocalizedMessage());
-  			}  
-            log.error(e.getMessage());
-            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-        }
-        DataTransferDetails detail = new DataTransferDetails();
-        TransferStatus status = new TransferStatus();
-
-        Cluster cluster = null;
-        
-        try {
-            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
-            if (cluster == null) {
-                GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
-                
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-
-            // Get the Stdouts and StdErrs
-            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");
-                }
-            }
-
-            String timeStampedExperimentID = GFacUtils.createUniqueNameWithDate(jobExecutionContext.getExperimentID());
-
-            TaskDetails taskData = jobExecutionContext.getTaskData();
-            String outputDataDir = null;
-            File localStdOutFile;
-            File localStdErrFile;
-            //FIXME: AdvancedOutput is remote location and third party transfer should work to make this work 
-//            if (taskData.getAdvancedOutputDataHandling() != null) {
-//                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
-//            }
-            if (outputDataDir == null) {
-                outputDataDir = File.separator + "tmp";
-            }
-            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
-            (new File(outputDataDir)).mkdirs();
-         	
-            String stdOutStr = "";
-            if (index < oldIndex) {
-                localStdOutFile = new File(oldFiles.get(index));
-                data.append(oldFiles.get(index++)).append(",");
-            } else {
-            	int i = 0;
-                localStdOutFile = new File(outputDataDir + File.separator + jobExecutionContext.getApplicationName() + ".stdout");
-                while(stdOutStr.isEmpty()){
-                try {
-                	cluster.scpFrom(jobExecutionContext.getStandardOutput(), localStdOutFile.getAbsolutePath());
-                	stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
-				} catch (Exception e) {
-					log.error(e.getLocalizedMessage());
-					  Thread.sleep(2000);
-		        }
-                i++;
-                if(i==3)break;
-                }
-                
-                StringBuffer temp = new StringBuffer(data.append(localStdOutFile.getAbsolutePath()).append(",").toString());
-                GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-            }
-            if (index < oldIndex) {
-                localStdErrFile = new File(oldFiles.get(index));
-                data.append(oldFiles.get(index++)).append(",");
-            } else {
-                localStdErrFile = new File(outputDataDir + File.separator + jobExecutionContext.getApplicationName() + ".stderr");
-                cluster.scpFrom(jobExecutionContext.getStandardError(), localStdErrFile.getAbsolutePath());
-                StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
-                GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-            }
-
-            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
-            status.setTransferState(TransferState.STDOUT_DOWNLOAD);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("STDOUT:" + localStdOutFile.getAbsolutePath());
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-
-            status.setTransferState(TransferState.STDERROR_DOWNLOAD);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription("STDERR:" + localStdErrFile.getAbsolutePath());
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-
-            //todo this is a mess we have to fix this
-            List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>();
-            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
-            Set<String> keys = output.keySet();
-            for (String paramName : keys) {
-                OutputDataObjectType outputDataObjectType = (OutputDataObjectType) output.get(paramName);
-                if (DataType.URI == outputDataObjectType.getType()) {
-
-                    List<String> outputList = null;
-                    int retry=3;
-                    while(retry>0){
-                    	 outputList = cluster.listDirectory(jobExecutionContext.getOutputDir());
-                        if (outputList.size() == 1 && outputList.get(0).isEmpty()) {
-                            Thread.sleep(10000);
-                        } else if (outputList.size() > 0) {
-                            break;
-                        }else{
-                            Thread.sleep(10000);
-                        }
-                        retry--;
-                        if(retry==0){
-                        }
-                    	 Thread.sleep(10000);
-                    }
-                    if (outputList.size() == 0 || outputList.get(0).isEmpty() || outputList.size() > 1) {
-                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
-                        Set<String> strings = output.keySet();
-                        outputArray.clear();
-                        for (String key : strings) {
-                            OutputDataObjectType outputDataObjectType1 = (OutputDataObjectType) output.get(key);
-                            if (DataType.URI == outputDataObjectType1.getType()) {
-                                String downloadFile = outputDataObjectType1.getValue();
-                                String localFile;
-                                if (index < oldIndex) {
-                                    localFile = oldFiles.get(index);
-                                    data.append(oldFiles.get(index++)).append(",");
-                                } else {
-                                    cluster.scpFrom(downloadFile, outputDataDir);
-                                    String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
-                                    localFile = outputDataDir + File.separator + fileName;
-                                    StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
-                                    GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                                }
-                                jobExecutionContext.addOutputFile(localFile);
-                                outputDataObjectType1.setValue(localFile);
-                                OutputDataObjectType dataObjectType = new OutputDataObjectType();
-                                dataObjectType.setValue(localFile);
-                                dataObjectType.setName(key);
-                                dataObjectType.setType(DataType.URI);
-                                outputArray.add(dataObjectType);
-                            }else if (DataType.STDOUT == outputDataObjectType1.getType()) {
-                                String localFile;
-                                if (index < oldIndex) {
-                                    localFile = oldFiles.get(index);
-                                    data.append(oldFiles.get(index++)).append(",");
-                                } else {
-                                    String fileName = localStdOutFile.getName();
-                                    localFile = outputDataDir + File.separator + fileName;
-                                    StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
-                                    GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                                }
-                                jobExecutionContext.addOutputFile(localFile);
-                                outputDataObjectType1.setValue(localFile);
-                                OutputDataObjectType dataObjectType = new OutputDataObjectType();
-                                dataObjectType.setValue(localFile);
-                                dataObjectType.setName(key);
-                                dataObjectType.setType(DataType.STDOUT);
-                                outputArray.add(dataObjectType);
-                            }else if (DataType.STDERR == outputDataObjectType1.getType()) {
-                                String localFile;
-                                if (index < oldIndex) {
-                                    localFile = oldFiles.get(index);
-                                    data.append(oldFiles.get(index++)).append(",");
-                                } else {
-                                    String fileName = localStdErrFile.getName();
-                                    localFile = outputDataDir + File.separator + fileName;
-                                    StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
-                                    GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                                }
-                                jobExecutionContext.addOutputFile(localFile);
-                                outputDataObjectType1.setValue(localFile);
-                                OutputDataObjectType dataObjectType = new OutputDataObjectType();
-                                dataObjectType.setValue(localFile);
-                                dataObjectType.setName(key);
-                                dataObjectType.setType(DataType.STDERR);
-                                outputArray.add(dataObjectType);
-                            }
-                        }
-                        break;
-                    } else if(outputList.size() == 1) { //FIXME: this is ultrascan specific
-                        String valueList = outputList.get(0);
-                        String outputFile;
-                        if (index < oldIndex) {
-                            outputFile = oldFiles.get(index);
-                            data.append(oldFiles.get(index++)).append(",");
-                        } else {
-                            cluster.scpFrom(jobExecutionContext.getOutputDir() + File.separator + valueList, outputDataDir);
-                            outputFile = outputDataDir + File.separator + valueList;
-                            jobExecutionContext.addOutputFile(outputFile);
-                            StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
-                            GFacUtils.saveHandlerData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                        }
-                        jobExecutionContext.addOutputFile(outputFile);
-                        outputDataObjectType.setValue(outputFile);
-                        OutputDataObjectType dataObjectType  = new OutputDataObjectType();
-                        dataObjectType.setValue(valueList);
-                        dataObjectType.setName(paramName);
-                        dataObjectType.setType(DataType.URI);
-                        outputArray.add(dataObjectType);
-                    }
-                } else {
-                    OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
-//                    break;
-                }
-            }
-            if (outputArray == null || outputArray.isEmpty()) {
-                if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() == null){
-                throw new GFacHandlerException(
-                        "Empty Output returned from the Application, Double check the application"
-                                + "and ApplicationDescriptor output Parameter Names"
-                );
-                }
-            }
-            // Why we set following?
-            jobExecutionContext.setStandardError(localStdErrFile.getAbsolutePath());
-            jobExecutionContext.setStandardOutput(localStdOutFile.getAbsolutePath());
-            jobExecutionContext.setOutputDir(outputDataDir);
-            status.setTransferState(TransferState.DOWNLOAD);
-            detail.setTransferStatus(status);
-            detail.setTransferDescription(outputDataDir);
-            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-            registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
-            fireTaskOutputChangeEvent(jobExecutionContext, outputArray);
-        } catch (Exception e) {
-            try {
-                status.setTransferState(TransferState.FAILED);
-                detail.setTransferStatus(status);
-                detail.setTransferDescription(e.getLocalizedMessage());
-                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
-                GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
-            } catch (Exception e1) {
-                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
-            }
-            throw new GFacHandlerException("Error in retrieving results", e);
-        }
-     }
-
-    public void initProperties(Properties properties) throws GFacHandlerException {
-
-    }
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        this.invoke(jobExecutionContext);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/NewGSISSHOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/NewGSISSHOutputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/NewGSISSHOutputHandler.java
deleted file mode 100644
index ed94312..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/NewGSISSHOutputHandler.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package org.apache.airavata.gfac.gsissh.handler;
-
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.airavata.gfac.GFacException;
-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.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gfac.ssh.util.HandleOutputs;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.registry.cpi.RegistryException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class NewGSISSHOutputHandler extends AbstractHandler{
-	 private static final Logger log = LoggerFactory.getLogger(NewGSISSHOutputHandler.class);
-	  public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-	        super.invoke(jobExecutionContext);
-	        String hostAddress = jobExecutionContext.getHostName();
-	        try {
-	            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-	                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-	            }
-	        }  catch (Exception e) {
-	        	 try {
-	  				GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-	  			} catch (GFacException e1) {
-	  				 log.error(e1.getLocalizedMessage());
-	  			}  
-	            log.error(e.getMessage());
-	            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-	        }
-	        Cluster cluster = null;
-	        
-	        try {
-	            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
-	            if (cluster == null) {
-	                GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
-	                
-	                throw new GFacProviderException("Security context is not set properly");
-	            } else {
-	                log.info("Successfully retrieved the Security Context");
-	            }
-	        } catch (Exception e) {
-	            log.error(e.getMessage());
-	            try {
-	                GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-	            } catch (GFacException e1) {
-	                log.error(e1.getLocalizedMessage());
-	            }
-	            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-	        }
-
-	        super.invoke(jobExecutionContext);
-	        List<OutputDataObjectType> outputArray =  HandleOutputs.handleOutputs(jobExecutionContext, cluster);
-            try {
-				registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
-			} catch (RegistryException e) {
-				throw new GFacHandlerException(e);
-			}
-	    }
-
-    @Override
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        // TODO: Auto generated method body.
-    }
-
-    @Override
-	public void initProperties(Properties properties) throws GFacHandlerException {
-		// TODO Auto-generated method stub
-		
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
deleted file mode 100644
index 36aac4c..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
+++ /dev/null
@@ -1,351 +0,0 @@
-/*
- *
- * 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.gsissh.provider.impl;
-
-import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.airavata.common.exception.AiravataException;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.gfac.ExecutionMode;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.handler.ThreadedHandler;
-import org.apache.airavata.gfac.core.notification.events.StartExecutionEvent;
-import org.apache.airavata.gfac.core.provider.AbstractProvider;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
-import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
-import org.apache.airavata.gfac.monitor.email.EmailBasedMonitor;
-import org.apache.airavata.gfac.monitor.email.EmailMonitorFactory;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
-import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
-import org.apache.airavata.model.appcatalog.computeresource.MonitorMode;
-import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.JobDetails;
-import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.zookeeper.KeeperException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.List;
-import java.util.Map;
-
-//import org.apache.airavata.schemas.gfac.GsisshHostType;
-
-public class GSISSHProvider extends AbstractProvider {
-    private static final Logger log = LoggerFactory.getLogger(GSISSHProvider.class);
-
-    public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-
-    }
-
-    public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        super.initialize(jobExecutionContext);
-        try {
-            String hostAddress = jobExecutionContext.getHostName();
-            if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-        } catch (ApplicationSettingsException e) {
-            log.error(e.getMessage());
-            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-        } catch (GFacException e) {
-            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-        }
-    }
-
-    public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        log.info("Invoking GSISSH Provider Invoke ...");
-        StringBuffer data = new StringBuffer();
-        jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
-        ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
-                .getComputeResourceDescription();
-        ApplicationDeploymentDescription appDeployDesc = jobExecutionContext.getApplicationContext()
-                .getApplicationDeploymentDescription();
-        JobDetails jobDetails = new JobDetails();
-        Cluster cluster = null;
-
-        try {
-            if (jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName()) != null) {
-                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName())).getPbsCluster();
-            }
-            if (cluster == null) {
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-            // This installed path is a mandetory field, because this could change based on the computing resource
-            JobDescriptor jobDescriptor = GFACGSISSHUtils.createJobDescriptor(jobExecutionContext, cluster);
-            jobDetails.setJobName(jobDescriptor.getJobName());
-
-            log.info(jobDescriptor.toXML());
-            data.append("jobDesc=").append(jobDescriptor.toXML());
-            jobDetails.setJobDescription(jobDescriptor.toXML());
-            String jobID = cluster.submitBatchJob(jobDescriptor);
-            jobExecutionContext.setJobDetails(jobDetails);
-            if (jobID == null) {
-                jobDetails.setJobID("none");
-                GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            } else {
-                jobDetails.setJobID(jobID.split("\\.")[0]);
-                GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SUBMITTED);
-            }
-            data.append(",jobId=").append(jobDetails.getJobID());
-
-            // Now job has submitted to the resource, its up to the Provider to parse the information to daemon handler
-            // to perform monitoring, daemon handlers can be accessed from anywhere
-            monitor(jobExecutionContext);
-            // we know this host is type GsiSSHHostType
-        } catch (Exception e) {
-		    String error = "Error submitting the job to host " + computeResourceDescription.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            StringWriter errors = new StringWriter();
-            e.printStackTrace(new PrintWriter(errors));
-            GFacUtils.saveErrorDetails(jobExecutionContext,  errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        } finally {
-            log.info("Saving data for future recovery: ");
-            log.info(data.toString());
-            GFacUtils.saveHandlerData(jobExecutionContext, data, this.getClass().getName());
-        } 
-          
-    }
-
-    public void removeFromMonitorHandlers(JobExecutionContext jobExecutionContext, SSHJobSubmission sshJobSubmission, String jobID) throws GFacHandlerException {
-/*        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        if (daemonHandlers == null) {
-            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        }
-        ThreadedHandler pullMonitorHandler = null;
-        ThreadedHandler pushMonitorHandler = null;
-        MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-        for (ThreadedHandler threadedHandler : daemonHandlers) {
-            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pullMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.POLL_JOB_MANAGER) {
-                    jobExecutionContext.setProperty("cancel","true");
-                    pullMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
-                            " to handle by the GridPullMonitorHandler");
-                }
-            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pushMonitorHandler = threadedHandler;
-                if ( monitorMode == null || monitorMode == MonitorMode.XSEDE_AMQP_SUBSCRIBE) {
-                    pushMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
-                            " to handle by the GridPushMonitorHandler");
-                }
-            }
-            // have to handle the GridPushMonitorHandler logic
-        }
-        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
-            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
-                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
-        }*/
-    }
-
-    public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        //To change body of implemented methods use File | Settings | File Templates.
-    }
-
-    public boolean cancelJob(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
-        //To change body of implemented methods use File | Settings | File Templates.
-        log.info("canceling the job status in GSISSHProvider!!!!!");
-        JobDetails jobDetails = jobExecutionContext.getJobDetails();
-        String hostName = jobExecutionContext.getHostName();
-        try {
-            Cluster cluster = null;
-            if (jobExecutionContext.getSecurityContext(hostName) == null) {
-                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-            }
-            cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostName)).getPbsCluster();
-            if (cluster == null) {
-                throw new GFacProviderException("Security context is not set properly");
-            } else {
-                log.info("Successfully retrieved the Security Context");
-            }
-            // This installed path is a mandetory field, because this could change based on the computing resource
-            if(jobDetails == null) {
-                log.error("There is not JobDetails so cancelations cannot perform !!!");
-                return false;
-            }
-            if (jobDetails.getJobID() != null) {
-                // if this operation success without any exceptions, we can assume cancel operation succeeded.
-                cluster.cancelJob(jobDetails.getJobID());
-            } else {
-                log.error("No Job Id is set, so cannot perform the cancel operation !!!");
-                return false;
-            }
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.CANCELED);
-            return true;
-            // we know this host is type GsiSSHHostType
-        } catch (SSHApiException e) {
-            String error = "Error submitting the job to host " + jobExecutionContext.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        } catch (Exception e) {
-            String error = "Error submitting the job to host " + jobExecutionContext.getHostName() + " message: " + e.getMessage();
-            log.error(error);
-            jobDetails.setJobID("none");
-            GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
-            GFacUtils.saveErrorDetails(jobExecutionContext,  e.getCause().toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            throw new GFacProviderException(error, e);
-        }
-    }
-
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
-        // have to implement the logic to recover a gfac failure
-        log.info("Invoking Recovering for the Experiment: " + jobExecutionContext.getExperimentID());
-        ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
-                .getComputeResourceDescription();
-        String hostName = jobExecutionContext.getHostName();
-        String jobId = "";
-        String jobDesc = "";
-        try {
-            String pluginData = GFacUtils.getHandlerData(jobExecutionContext, this.getClass().getName());
-            String[] split = pluginData.split(",");
-            if (split.length < 2) {
-                try {
-                    this.execute(jobExecutionContext);
-                } catch (GFacException e) {
-                    log.error("Error while  recovering provider", e);
-                    throw new GFacProviderException("Error recovering provider", e);
-                }
-                return;
-            }
-            jobDesc = split[0].substring(7);
-            jobId = split[1].substring(6);
-
-            log.info("Following data have recovered: ");
-            log.info("Job Description: " + jobDesc);
-            log.info("Job Id: " + jobId);
-            if (jobId == null || "none".equals(jobId) ||
-                    "".equals(jobId)) {
-                try {
-                    this.execute(jobExecutionContext);
-                } catch (GFacException e) {
-                    log.error("Error while  recovering provider", e);
-                    throw new GFacProviderException("Error recovering provider", e);
-                }
-                return;
-            }
-        } catch (Exception e) {
-            log.error("Error while  recovering provider", e);
-        }
-        try {
-            // Now we are we have enough data to recover
-            JobDetails jobDetails = new JobDetails();
-            jobDetails.setJobDescription(jobDesc);
-            jobDetails.setJobID(jobId);
-            jobExecutionContext.setJobDetails(jobDetails);
-            if (jobExecutionContext.getSecurityContext(hostName) == null) {
-                try {
-                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
-                } catch (ApplicationSettingsException e) {
-                    log.error(e.getMessage());
-                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
-                }
-            }
-            monitor(jobExecutionContext);
-        } catch (Exception e) {
-            log.error("Error while recover the job", e);
-            throw new GFacProviderException("Error delegating already ran job to Monitoring", e);
-        }
-    }
-
-    @Override
-    public void monitor(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
-        String jobSubmissionInterfaceId = jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionInterfaceId();
-        SSHJobSubmission sshJobSubmission = null;
-        try {
-            sshJobSubmission = jobExecutionContext.getAppCatalog().getComputeResource().getSSHJobSubmission(jobSubmissionInterfaceId);
-        } catch (AppCatalogException e) {
-            throw new GFacException("Error while reading compute resource", e);
-        }
-        if (jobExecutionContext.getPreferredJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
-            MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-            if (monitorMode != null && monitorMode == MonitorMode.JOB_EMAIL_NOTIFICATION_MONITOR) {
-                try {
-                    EmailBasedMonitor emailBasedMonitor = EmailMonitorFactory.getEmailBasedMonitor(
-                            sshJobSubmission.getResourceJobManager().getResourceJobManagerType());
-                    emailBasedMonitor.addToJobMonitorMap(jobExecutionContext);
-                } catch (AiravataException e) {
-                    throw new GFacHandlerException("Error while activating email job monitoring ", e);
-                }
-                return;
-            }
-        }
-/*
-        // if email monitor is not activeated or not configure we use pull or push monitor
-        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        if (daemonHandlers == null) {
-            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        }
-        ThreadedHandler pullMonitorHandler = null;
-        ThreadedHandler pushMonitorHandler = null;
-        MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
-        String jobID = jobExecutionContext.getJobDetails().getJobID();
-        for (ThreadedHandler threadedHandler : daemonHandlers) {
-            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pullMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.POLL_JOB_MANAGER) {
-                    log.info("Job is launched successfully now parsing it to monitoring in pull mode, JobID Returned:  " + jobID);
-                    pullMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
-                            " to handle by the GridPullMonitorHandler");
-                }
-            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pushMonitorHandler = threadedHandler;
-                if (monitorMode == null || monitorMode == MonitorMode.XSEDE_AMQP_SUBSCRIBE) {
-                    log.info("Job is launched successfully now parsing it to monitoring in push mode, JobID Returned:  " + jobID);
-                    pushMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
-                            " to handle by the GridPushMonitorHandler");
-                }
-            }
-            // have to handle the GridPushMonitorHandler logic
-        }
-        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
-            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
-                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
-
-        }*/
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
deleted file mode 100644
index 46e7acd..0000000
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- *
- * 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.gsissh.security;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.credential.store.credential.Credential;
-import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
-import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.AbstractSecurityContext;
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.RequestData;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.globus.gsi.X509Credential;
-import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
-import org.globus.gsi.provider.GlobusProvider;
-import org.globus.myproxy.GetParams;
-import org.globus.myproxy.MyProxy;
-import org.globus.myproxy.MyProxyException;
-import org.gridforum.jgss.ExtendedGSSCredential;
-import org.ietf.jgss.GSSCredential;
-import org.ietf.jgss.GSSException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.security.Security;
-import java.security.cert.X509Certificate;
-
-/**
- * Handles GRID related security.
- */
-public class GSISecurityContext extends AbstractSecurityContext {
-
-    protected static final Logger log = LoggerFactory.getLogger(GSISecurityContext.class);
-    /*
-     * context name
-     */
-
-    private Cluster pbsCluster = null;
-
-
-    public GSISecurityContext(CredentialReader credentialReader, RequestData requestData, Cluster pbsCluster) {
-        super(credentialReader, requestData);
-        this.pbsCluster = pbsCluster;
-    }
-
-
-    public GSISecurityContext(CredentialReader credentialReader, RequestData requestData) {
-        super(credentialReader, requestData);
-    }
-
-
-    public GSISecurityContext(Cluster pbsCluster) {
-        this.setPbsCluster(pbsCluster);
-    }
-
-
-
-    public Cluster getPbsCluster() {
-        return pbsCluster;
-    }
-
-    public void setPbsCluster(Cluster pbsCluster) {
-        this.pbsCluster = pbsCluster;
-    }
-}


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