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From shame...@apache.org
Subject [26/39] 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 18:14:43 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
new file mode 100644
index 0000000..11fb4ce
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
@@ -0,0 +1,190 @@
+/*
+ *
+ * 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.api.job;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class SlurmOutputParser implements OutputParser {
+    private static final Logger log = LoggerFactory.getLogger(SlurmOutputParser.class);
+    public static final int JOB_NAME_OUTPUT_LENGTH = 8;
+    public static final String STATUS = "status";
+
+    public void parseSingleJob(JobDescriptor descriptor, String rawOutput) throws SSHApiException {
+        log.info(rawOutput);
+        String[] info = rawOutput.split("\n");
+        String lastString = info[info.length - 1];
+        if (lastString.contains("JOB ID")) {
+            // because there's no state
+            descriptor.setStatus("U");
+        } else {
+            int column = 0;
+            System.out.println(lastString);
+            for (String each : lastString.split(" ")) {
+                if (each.trim().isEmpty()) {
+                    continue;
+                } else {
+                    switch (column) {
+                        case 0:
+                            descriptor.setJobID(each);
+                            column++;
+                            break;
+                        case 1:
+                            descriptor.setPartition(each);
+                            column++;
+                            break;
+                        case 2:
+                            descriptor.setJobName(each);
+                            column++;
+                            break;
+                        case 3:
+                            descriptor.setUserName(each);
+                            column++;
+                            break;
+                        case 4:
+                            descriptor.setStatus(each);
+                            column++;
+                            break;
+                        case 5:
+                            descriptor.setUsedCPUTime(each);
+                            column++;
+                            break;
+                        case 6:
+                            try {
+                                int nodes = Integer.parseInt(each);
+                                descriptor.setNodes(nodes);
+                            }catch (Exception e){
+                                log.error("Node count read from command output is not an integer !!!");
+                            }
+                            column++;
+                            break;
+                        case 7:
+                            descriptor.setNodeList(each);
+                            column++;
+                            break;
+                    }
+                }
+            }
+        }
+
+    }
+
+    /**
+     * This can be used to parseSingleJob the outpu of sbatch and extrac the jobID from the content
+     *
+     * @param rawOutput
+     * @return
+     */
+    public String parseJobSubmission(String rawOutput) throws SSHApiException {
+        // FIXME : use regex to match correct jobId;
+        log.info(rawOutput);
+        String[] info = rawOutput.split("\n");
+        for (String anInfo : info) {
+            if (anInfo.contains("Submitted batch job")) {
+                String[] split = anInfo.split("Submitted batch job");
+                return split[1].trim();
+            }
+        }
+        return "";
+//        throw new SSHApiException(rawOutput);  //todo//To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public JobStatus parseJobStatus(String jobID, String rawOutput) throws SSHApiException {
+        log.info(rawOutput);
+        Pattern pattern = Pattern.compile(jobID + "(?=\\s+\\S+\\s+\\S+\\s+\\S+\\s+(?<" + STATUS + ">\\w+))");
+        Matcher matcher = pattern.matcher(rawOutput);
+        if (matcher.find()) {
+            return JobStatus.valueOf(matcher.group(STATUS));
+        }
+        return null;
+    }
+
+    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
+        log.debug(rawOutput);
+        String[] info = rawOutput.split("\n");
+        String lastString = info[info.length - 1];
+        if (lastString.contains("JOBID") || lastString.contains("PARTITION")) {
+            log.info("There are no jobs with this username ... ");
+            return;
+        }
+//        int lastStop = 0;
+        for (String jobID : statusMap.keySet()) {
+            String jobId = jobID.split(",")[0];
+            String jobName = jobID.split(",")[1];
+            boolean found = false;
+            for (int i = 0; i < info.length; i++) {
+                if (info[i].contains(jobName.substring(0, 8))) {
+                    // now starts processing this line
+                    log.info(info[i]);
+                    String correctLine = info[i];
+                    String[] columns = correctLine.split(" ");
+                    List<String> columnList = new ArrayList<String>();
+                    for (String s : columns) {
+                        if (!"".equals(s)) {
+                            columnList.add(s);
+                        }
+                    }
+                    try {
+                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
+                    } catch (IndexOutOfBoundsException e) {
+                        statusMap.put(jobID, JobStatus.valueOf("U"));
+                    }
+                    found = true;
+                    break;
+                }
+            }
+            if (!found) {
+                log.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobId);
+            }
+        }
+    }
+
+    @Override
+    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+        String regJobId = "jobId";
+        if (jobName == null) {
+            return null;
+        } else if(jobName.length() > JOB_NAME_OUTPUT_LENGTH) {
+            jobName = jobName.substring(0, JOB_NAME_OUTPUT_LENGTH);
+        }
+        Pattern pattern = Pattern.compile("(?=(?<" + regJobId + ">\\d+)\\s+\\w+\\s+" + jobName + ")"); // regex - look ahead and match
+        if (rawOutput != null) {
+            Matcher matcher = pattern.matcher(rawOutput);
+            if (matcher.find()) {
+                return matcher.group(regJobId);
+            } else {
+                log.error("No match is found for JobName");
+                return null;
+            }
+        } else {
+            log.error("Error: RawOutput shouldn't be null");
+            return null;
+        }
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
new file mode 100644
index 0000000..4fbbe30
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
@@ -0,0 +1,119 @@
+/*
+ *
+ * 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.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.File;
+
+public class UGEJobConfiguration implements JobManagerConfiguration {
+
+    private String jobDescriptionTemplateName;
+
+    private String scriptExtension;
+
+    private String installedPath;
+
+    private OutputParser parser;
+
+    public UGEJobConfiguration() {
+        // this can be used to construct and use setter methods to set all the params in order
+    }
+
+    public UGEJobConfiguration(String jobDescriptionTemplateName,
+                               String scriptExtension, String installedPath, OutputParser parser) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+        this.scriptExtension = scriptExtension;
+        this.parser = parser;
+        if (installedPath.endsWith("/")) {
+            this.installedPath = installedPath;
+        } else {
+            this.installedPath = installedPath + "/";
+        }
+    }
+
+    public RawCommandInfo getCancelCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "qdel " + jobID);
+    }
+
+    public String getJobDescriptionTemplateName() {
+        return jobDescriptionTemplateName;
+    }
+
+    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+    }
+
+    public RawCommandInfo getMonitorCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "qstat -j " + jobID);
+    }
+
+    public String getScriptExtension() {
+        return scriptExtension;
+    }
+
+    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+        return new RawCommandInfo(this.installedPath + "qsub " +
+                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+    }
+
+    public String getInstalledPath() {
+        return installedPath;
+    }
+
+    public void setInstalledPath(String installedPath) {
+        this.installedPath = installedPath;
+    }
+
+    public OutputParser getParser() {
+        return parser;
+    }
+
+    public void setParser(OutputParser parser) {
+        this.parser = parser;
+    }
+
+    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+    }
+
+    @Override
+    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+        // For PBS there is no option to get jobDetails by JobName, so we search with userName
+        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+    }
+
+    @Override
+    public String  getBaseCancelCommand() {
+        return "qdel";
+    }
+
+    @Override
+    public String  getBaseMonitorCommand() {
+        return "qstat";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "qsub ";
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
new file mode 100644
index 0000000..a6cc3ed
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
@@ -0,0 +1,188 @@
+/*
+ *
+ * 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.api.job;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class UGEOutputParser implements OutputParser{
+    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
+    public static final String JOB_ID = "jobId";
+
+    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
+        log.debug(rawOutput);
+        String[] info = rawOutput.split("\n");
+        String[] line;
+        for (int i = 0; i < info.length; i++) {
+            if (info[i].contains("=")) {
+                line = info[i].split("=", 2);
+            } else {
+                line = info[i].split(":", 2);
+            }
+            if (line.length >= 2) {
+                String header = line[0].trim();
+                log.debug("Header = " + header);
+                String value = line[1].trim();
+                log.debug("value = " + value);
+
+                if (header.equals("Variable_List")) {
+                    while (info[i + 1].startsWith("\t")) {
+                        value += info[i + 1];
+                        i++;
+                    }
+                    value = value.replaceAll("\t", "");
+                    jobDescriptor.setVariableList(value);
+                } else if ("Job Id".equals(header)) {
+                    jobDescriptor.setJobID(value);
+                } else if ("Job_Name".equals(header)) {
+                    jobDescriptor.setJobName(value);
+                } else if ("Account_Name".equals(header)) {
+                    jobDescriptor.setAcountString(value);
+                } else if ("job_state".equals(header)) {
+                    jobDescriptor.setStatus(value);
+                } else if ("Job_Owner".equals(header)) {
+                    jobDescriptor.setOwner(value);
+                } else if ("resources_used.cput".equals(header)) {
+                    jobDescriptor.setUsedCPUTime(value);
+                } else if ("resources_used.mem".equals(header)) {
+                    jobDescriptor.setUsedMemory(value);
+                } else if ("resources_used.walltime".equals(header)) {
+                    jobDescriptor.setEllapsedTime(value);
+                } else if ("job_state".equals(header)) {
+                    jobDescriptor.setStatus(value);
+                } else if ("queue".equals(header))
+                    jobDescriptor.setQueueName(value);
+                else if ("ctime".equals(header)) {
+                    jobDescriptor.setCTime(value);
+                } else if ("qtime".equals(header)) {
+                    jobDescriptor.setQTime(value);
+                } else if ("mtime".equals(header)) {
+                    jobDescriptor.setMTime(value);
+                } else if ("start_time".equals(header)) {
+                    jobDescriptor.setSTime(value);
+                } else if ("comp_time".equals(header)) {
+                    jobDescriptor.setCompTime(value);
+                } else if ("exec_host".equals(header)) {
+                    jobDescriptor.setExecuteNode(value);
+                } else if ("Output_Path".equals(header)) {
+                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+                        jobDescriptor.setStandardOutFile(value);
+                    else {
+                        jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
+                        i++;
+                    }
+                } else if ("Error_Path".equals(header)) {
+                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+                        jobDescriptor.setStandardErrorFile(value);
+                    else {
+                        String st = info[i + 1].trim();
+                        jobDescriptor.setStandardErrorFile(value + st);
+                        i++;
+                    }
+
+                } else if ("submit_args".equals(header)) {
+                    while (i + 1 < info.length) {
+                        if (info[i + 1].startsWith("\t")) {
+                            value += info[i + 1];
+                            i++;
+                        } else
+                            break;
+                    }
+                    value = value.replaceAll("\t", "");
+                    jobDescriptor.setSubmitArgs(value);
+                }
+            }
+        }
+    }
+
+	public String parseJobSubmission(String rawOutput) {
+		log.debug(rawOutput);
+		if (rawOutput != null && !rawOutput.isEmpty()) {
+			String[] info = rawOutput.split("\n");
+			String lastLine = info[info.length - 1];
+			return lastLine.split(" ")[2]; // In PBS stdout is going to be directly the jobID
+		} else {
+			return "";
+		}
+	}
+
+    public JobStatus parseJobStatus(String jobID, String rawOutput) {
+        Pattern pattern = Pattern.compile("job_number:[\\s]+" + jobID);
+        Matcher matcher = pattern.matcher(rawOutput);
+        if (matcher.find()) {
+            return JobStatus.Q; // fixme; return correct status.
+        }
+        return JobStatus.U;
+    }
+
+    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) {
+        log.debug(rawOutput);
+        String[] info = rawOutput.split("\n");
+        int lastStop = 0;
+        for (String jobID : statusMap.keySet()) {
+            for(int i=lastStop;i<info.length;i++){
+               if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){
+                   // now starts processing this line
+                   log.info(info[i]);
+                   String correctLine = info[i];
+                   String[] columns = correctLine.split(" ");
+                   List<String> columnList = new ArrayList<String>();
+                   for (String s : columns) {
+                       if (!"".equals(s)) {
+                           columnList.add(s);
+                       }
+                   }
+                   lastStop = i+1;
+                   if ("E".equals(columnList.get(4))) {
+                       // There is another status with the same letter E other than error status
+                       // to avoid that we make a small tweek to the job status
+                       columnList.set(4, "Er");
+                   }
+                   statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
+                   break;
+               }
+            }
+        }
+    }
+
+    @Override
+    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+        if (jobName.length() > 10) {
+            jobName = jobName.substring(0, 10);
+        }
+        Pattern pattern = Pattern.compile("(?<" + JOB_ID + ">\\S+)\\s+\\S+\\s+(" + jobName + ")");
+        Matcher matcher = pattern.matcher(rawOutput);
+        if (matcher.find()) {
+            return matcher.group(JOB_ID);
+        }
+        return null;
+    }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
new file mode 100644
index 0000000..9658fba
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
@@ -0,0 +1,76 @@
+/*
+ *
+ * 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.config;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+/**
+ * Reads basic configurations.
+ */
+public class ConfigReader {
+
+    private static final String CONFIGURATION_FILE = "gsissh.properties";
+
+
+    private Properties properties;
+
+    /**
+     * Reads configurations from the class path configuration file.
+     * @throws IOException If an error occurred while reading configurations.
+     */
+    public ConfigReader() throws IOException {
+        this.properties = getPropertiesFromClasspath(CONFIGURATION_FILE);
+    }
+
+    private Properties getPropertiesFromClasspath(String propFileName) throws IOException {
+        Properties props = new Properties();
+        InputStream inputStream = this.getClass().getClassLoader()
+                .getResourceAsStream(propFileName);
+
+        if (inputStream == null) {
+            throw new FileNotFoundException("System configuration file '" + propFileName
+                    + "' not found in the classpath");
+        }
+
+        props.load(inputStream);
+
+        return props;
+    }
+
+    public String getConfiguration(String key) {
+        return this.properties.getProperty(key);
+    }
+
+
+    /**
+     * Gets all the SSH related properties used by JSch.
+     * @return All properties.
+     */
+    public Properties getProperties() {
+        return this.properties;
+    }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/DefaultJobSubmissionListener.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/DefaultJobSubmissionListener.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/DefaultJobSubmissionListener.java
new file mode 100644
index 0000000..d60ea32
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/DefaultJobSubmissionListener.java
@@ -0,0 +1,42 @@
+/*
+ *
+ * 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.impl;
+
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.listener.JobSubmissionListener;
+
+public class DefaultJobSubmissionListener extends JobSubmissionListener {
+
+    public void statusChanged(JobDescriptor jobDescriptor) throws SSHApiException {
+        System.out.println("Job status has changed to : " + jobDescriptor.getStatus());
+    }
+
+    @Override
+    public void statusChanged(JobStatus jobStatus) throws SSHApiException {
+        System.out.println("Job status has changed to : " + jobStatus.toString());
+    }
+
+    @Override
+    public boolean isJobDone() throws SSHApiException {
+        return getJobStatus().equals(JobStatus.C);
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/GSISSHAbstractCluster.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/GSISSHAbstractCluster.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/GSISSHAbstractCluster.java
new file mode 100644
index 0000000..814a7e1
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/GSISSHAbstractCluster.java
@@ -0,0 +1,767 @@
+/*
+ *
+ * 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.impl;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.net.URL;
+import java.security.SecureRandom;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import org.apache.airavata.gfac.ssh.api.Cluster;
+import org.apache.airavata.gfac.ssh.api.CommandExecutor;
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.api.ServerInfo;
+import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
+import org.apache.airavata.gfac.core.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gfac.core.authentication.SSHKeyAuthentication;
+import org.apache.airavata.gfac.core.authentication.SSHPasswordAuthentication;
+import org.apache.airavata.gfac.core.authentication.SSHPublicKeyAuthentication;
+import org.apache.airavata.gfac.core.authentication.SSHPublicKeyFileAuthentication;
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.api.job.JobManagerConfiguration;
+import org.apache.airavata.gfac.ssh.api.job.OutputParser;
+import org.apache.airavata.gfac.ssh.config.ConfigReader;
+import org.apache.airavata.gfac.ssh.jsch.ExtendedJSch;
+import org.apache.airavata.gfac.ssh.util.SSHAPIUIKeyboardInteractive;
+import org.apache.airavata.gfac.ssh.util.SSHKeyPasswordHandler;
+import org.apache.airavata.gfac.ssh.util.SSHUtils;
+import org.apache.commons.io.FileUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.jcraft.jsch.ExtendedSession;
+import com.jcraft.jsch.GSISSHIdentityFile;
+import com.jcraft.jsch.GSISSHIdentityRepository;
+import com.jcraft.jsch.Identity;
+import com.jcraft.jsch.JSch;
+import com.jcraft.jsch.JSchException;
+import com.jcraft.jsch.Session;
+
+public class GSISSHAbstractCluster implements Cluster {
+
+    private static final Logger log = LoggerFactory.getLogger(GSISSHAbstractCluster.class);
+    public static final String X509_CERT_DIR = "X509_CERT_DIR";
+    public static final String SSH_SESSION_TIMEOUT = "ssh.session.timeout";
+
+    public JobManagerConfiguration jobManagerConfiguration;
+
+    private ServerInfo serverInfo;
+
+    private AuthenticationInfo authenticationInfo;
+
+    private Session session;
+
+    private ConfigReader configReader;
+	
+    private JSch defaultJSch;
+
+    private static Identity identityFile = null;
+
+    public GSISSHAbstractCluster(ServerInfo serverInfo, AuthenticationInfo authenticationInfo, JobManagerConfiguration config) throws SSHApiException {
+        this(serverInfo, authenticationInfo);
+        this.jobManagerConfiguration = config;
+    }
+
+    public  GSISSHAbstractCluster(ServerInfo serverInfo, AuthenticationInfo authenticationInfo) throws SSHApiException {
+
+        reconnect(serverInfo, authenticationInfo);
+    }
+
+    public GSISSHAbstractCluster(JobManagerConfiguration config) {
+        this.jobManagerConfiguration = config;
+    }
+    private synchronized void reconnect(ServerInfo serverInfo, AuthenticationInfo authenticationInfo) throws SSHApiException {
+        this.serverInfo = serverInfo;
+
+        this.authenticationInfo = authenticationInfo;
+
+        if (authenticationInfo instanceof GSIAuthenticationInfo) {
+            JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
+            JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
+            System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo) authenticationInfo).getProperties().
+                    get("X509_CERT_DIR"));
+        }
+
+
+        try {
+            this.configReader = new ConfigReader();
+        } catch (IOException e) {
+            throw new SSHApiException("Unable to load system configurations.", e);
+        }
+        try {
+        	 if(defaultJSch == null){
+             	defaultJSch = createJSch(authenticationInfo);
+             }
+     	        log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
+                     + serverInfo.getUserName());
+
+        	session = createSession(defaultJSch,serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
+        	}
+        	catch (Exception e) {
+            throw new SSHApiException("An exception occurred while creating SSH session." +
+                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                    " connecting user name - "
+                    + serverInfo.getUserName(), e);
+        }
+
+        //=============================================================
+        // Handling vanilla SSH pieces
+        //=============================================================
+        if (authenticationInfo instanceof SSHPasswordAuthentication) {
+            String password = ((SSHPasswordAuthentication) authenticationInfo).
+                    getPassword(serverInfo.getUserName(), serverInfo.getHost());
+
+            session.setUserInfo(new SSHAPIUIKeyboardInteractive(password));
+
+            // TODO figure out why we need to set password to session
+            session.setPassword(password);
+
+        } else if (authenticationInfo instanceof SSHPublicKeyFileAuthentication) {
+
+            SSHPublicKeyFileAuthentication sshPublicKeyFileAuthentication
+                    = (SSHPublicKeyFileAuthentication) authenticationInfo;
+            String privateKeyFile = sshPublicKeyFileAuthentication.
+                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
+
+            logDebug("The private key file for vanilla SSH " + privateKeyFile);
+
+            String publicKeyFile = sshPublicKeyFileAuthentication.
+                    getPublicKeyFile(serverInfo.getUserName(), serverInfo.getHost());
+
+            logDebug("The public key file for vanilla SSH " + publicKeyFile);
+
+            try {
+                identityFile = GSISSHIdentityFile.newInstance(privateKeyFile, null, defaultJSch);
+            } catch (JSchException e) {
+                throw new SSHApiException("An exception occurred while initializing keys using files. " +
+                        "(private key and public key)." +
+                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                        " connecting user name - "
+                        + serverInfo.getUserName() + " private key file - " + privateKeyFile + ", public key file - " +
+                        publicKeyFile, e);
+            }
+
+            // Add identity to identity repository
+            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(defaultJSch);
+            identityRepository.add(identityFile);
+
+            // Set repository to session
+            session.setIdentityRepository(identityRepository);
+
+            // Set the user info
+            SSHKeyPasswordHandler sshKeyPasswordHandler
+                    = new SSHKeyPasswordHandler((SSHKeyAuthentication) authenticationInfo);
+
+            session.setUserInfo(sshKeyPasswordHandler);
+
+        } else if (authenticationInfo instanceof SSHPublicKeyAuthentication) {
+
+            SSHPublicKeyAuthentication sshPublicKeyAuthentication
+                    = (SSHPublicKeyAuthentication) authenticationInfo;
+            try {
+                String name = serverInfo.getUserName() + "_" + serverInfo.getHost();
+                identityFile = GSISSHIdentityFile.newInstance(name,
+                        sshPublicKeyAuthentication.getPrivateKey(serverInfo.getUserName(), serverInfo.getHost()),
+                        sshPublicKeyAuthentication.getPublicKey(serverInfo.getUserName(), serverInfo.getHost()), defaultJSch);
+            } catch (JSchException e) {
+                throw new SSHApiException("An exception occurred while initializing keys using byte arrays. " +
+                        "(private key and public key)." +
+                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                        " connecting user name - "
+                        + serverInfo.getUserName(), e);
+            }
+
+            // Add identity to identity repository
+            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(defaultJSch);
+            identityRepository.add(identityFile);
+
+            // Set repository to session
+            session.setIdentityRepository(identityRepository);
+
+            // Set the user info
+            SSHKeyPasswordHandler sshKeyPasswordHandler
+                    = new SSHKeyPasswordHandler((SSHKeyAuthentication) authenticationInfo);
+
+            session.setUserInfo(sshKeyPasswordHandler);
+
+        }
+
+        // Not a good way, but we dont have any choice
+        if (session instanceof ExtendedSession) {
+            if (authenticationInfo instanceof GSIAuthenticationInfo) {
+                ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo) authenticationInfo);
+            }
+        }
+
+        try {
+            session.connect(Integer.parseInt(configReader.getConfiguration(SSH_SESSION_TIMEOUT)));
+        } catch (Exception e) {
+            throw new SSHApiException("An exception occurred while connecting to server." +
+                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                    " connecting user name - "
+                    + serverInfo.getUserName(), e);
+        }
+    }
+
+    public synchronized JobDescriptor cancelJob(String jobID) throws SSHApiException {
+        JobStatus jobStatus = getJobStatus(jobID);
+        if (jobStatus == null || jobStatus == JobStatus.U) {
+            log.info("Validation before cancel is failed, couldn't found job in remote host to cancel. Job may be already completed|failed|canceled");
+            return null;
+        }
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getCancelCommand(jobID);
+
+        StandardOutReader stdOutReader = new StandardOutReader();
+        log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+        CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
+        String outputifAvailable = getOutputifAvailable(stdOutReader, "Error reading output of job submission", jobManagerConfiguration.getBaseCancelCommand());
+        // this might not be the case for all teh resources, if so Cluster implementation can override this method
+        // because here after cancelling we try to get the job description and return it back
+        try {
+            return this.getJobDescriptorById(jobID);
+        } catch (Exception e) {
+            //its ok to fail to get status when the job is gone
+            return null;
+        }
+    }
+
+    public synchronized String submitBatchJobWithScript(String scriptPath, String workingDirectory) throws SSHApiException {
+        this.scpTo(workingDirectory, scriptPath);
+
+        // since this is a constant we do not ask users to fill this
+
+//        RawCommandInfo rawCommandInfo = new RawCommandInfo(this.installedPath + this.jobManagerConfiguration.getSubmitCommand() + " " +
+//                workingDirectory + File.separator + FilenameUtils.getName(scriptPath));
+
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getSubmitCommand(workingDirectory,scriptPath);
+        StandardOutReader standardOutReader = new StandardOutReader();
+        log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+        CommandExecutor.executeCommand(rawCommandInfo, this.session, standardOutReader);
+
+        //Check whether pbs submission is successful or not, if it failed throw and exception in submitJob method
+        // with the error thrown in qsub command
+        //
+        String outputifAvailable = getOutputifAvailable(standardOutReader,"Error reading output of job submission",jobManagerConfiguration.getBaseSubmitCommand());
+        OutputParser outputParser = jobManagerConfiguration.getParser();
+        return  outputParser.parseJobSubmission(outputifAvailable);
+    }
+
+    public synchronized String submitBatchJob(JobDescriptor jobDescriptor) throws SSHApiException {
+        TransformerFactory factory = TransformerFactory.newInstance();
+        URL resource = this.getClass().getClassLoader().getResource(jobManagerConfiguration.getJobDescriptionTemplateName());
+
+        if (resource == null) {
+            String error = "System configuration file '" + jobManagerConfiguration.getJobDescriptionTemplateName()
+                    + "' not found in the classpath";
+            throw new SSHApiException(error);
+        }
+
+        Source xslt = new StreamSource(new File(resource.getPath()));
+        Transformer transformer;
+        StringWriter results = new StringWriter();
+        File tempPBSFile = null;
+        try {
+            // generate the pbs script using xslt
+            transformer = factory.newTransformer(xslt);
+            Source text = new StreamSource(new ByteArrayInputStream(jobDescriptor.toXML().getBytes()));
+            transformer.transform(text, new StreamResult(results));
+            String scriptContent = results.toString().replaceAll("^[ |\t]*\n$", "");
+            if (scriptContent.startsWith("\n")) {
+                scriptContent = scriptContent.substring(1);
+            }
+//            log.debug("generated PBS:" + results.toString());
+
+            // creating a temporary file using pbs script generated above
+            int number = new SecureRandom().nextInt();
+            number = (number < 0 ? -number : number);
+
+            tempPBSFile = new File(Integer.toString(number) + jobManagerConfiguration.getScriptExtension());
+            FileUtils.writeStringToFile(tempPBSFile, scriptContent);
+
+            //reusing submitBatchJobWithScript method to submit a job
+            String jobID = null;
+            int retry = 3;
+            while(retry>0) {
+                try {
+                    jobID = this.submitBatchJobWithScript(tempPBSFile.getAbsolutePath(),
+                            jobDescriptor.getWorkingDirectory());
+                    retry=0;
+                } catch (SSHApiException e) {
+                    retry--;
+                    if(retry==0) {
+                        throw e;
+                    }else{
+                        try {
+                            Thread.sleep(5000);
+                        } catch (InterruptedException e1) {
+                            log.error(e1.getMessage(), e1);
+                        }
+                        log.error("Error occured during job submission but doing a retry");
+                    }
+                }
+            }
+            log.debug("Job has successfully submitted, JobID : " + jobID);
+            if (jobID != null) {
+                return jobID.replace("\n", "");
+            } else {
+                return null;
+            }
+            } catch (TransformerConfigurationException e) {
+            throw new SSHApiException("Error parsing PBS transformation", e);
+        } catch (TransformerException e) {
+            throw new SSHApiException("Error generating PBS script", e);
+        } catch (IOException e) {
+            throw new SSHApiException("An exception occurred while connecting to server." +
+                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                    " connecting user name - "
+                    + serverInfo.getUserName(), e);
+        } finally {
+            if (tempPBSFile != null) {
+                tempPBSFile.delete();
+            }
+        }
+    }
+
+
+    public void generateJobScript(JobDescriptor jobDescriptor) throws SSHApiException {
+        TransformerFactory factory = TransformerFactory.newInstance();
+        URL resource = this.getClass().getClassLoader().getResource(jobManagerConfiguration.getJobDescriptionTemplateName());
+
+        if (resource == null) {
+            String error = "System configuration file '" + jobManagerConfiguration.getJobDescriptionTemplateName()
+                    + "' not found in the classpath";
+            throw new SSHApiException(error);
+        }
+
+        Source xslt = new StreamSource(new File(resource.getPath()));
+        Transformer transformer;
+        StringWriter results = new StringWriter();
+        File tempPBSFile = null;
+        try {
+            // generate the pbs script using xslt
+            transformer = factory.newTransformer(xslt);
+            Source text = new StreamSource(new ByteArrayInputStream(jobDescriptor.toXML().getBytes()));
+            transformer.transform(text, new StreamResult(results));
+            String scriptContent = results.toString().replaceAll("^[ |\t]*\n$", "");
+            if (scriptContent.startsWith("\n")) {
+                scriptContent = scriptContent.substring(1);
+            }
+//            log.debug("generated PBS:" + results.toString());
+
+            // creating a temporary file using pbs script generated above
+            int number = new SecureRandom().nextInt();
+            number = (number < 0 ? -number : number);
+
+            tempPBSFile = new File(Integer.toString(number) + jobManagerConfiguration.getScriptExtension());
+            log.info("File Path: " + tempPBSFile.getAbsolutePath());
+            log.info("File Content: " + scriptContent);
+            FileUtils.writeStringToFile(tempPBSFile, scriptContent);
+        } catch (TransformerConfigurationException e) {
+            throw new SSHApiException("Error parsing PBS transformation", e);
+        } catch (TransformerException e) {
+            throw new SSHApiException("Error generating PBS script", e);
+        } catch (IOException e) {
+            throw new SSHApiException("An exception occurred while connecting to server." +
+                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
+                    " connecting user name - "
+                    + serverInfo.getUserName(), e);
+        } finally {
+            if (tempPBSFile != null) {
+                tempPBSFile.delete();
+            }
+        }
+    }
+
+
+
+    public synchronized JobDescriptor getJobDescriptorById(String jobID) throws SSHApiException {
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getMonitorCommand(jobID);
+        StandardOutReader stdOutReader = new StandardOutReader();
+        log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+        CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !",jobManagerConfiguration.getBaseMonitorCommand());
+        JobDescriptor jobDescriptor = new JobDescriptor();
+        jobManagerConfiguration.getParser().parseSingleJob(jobDescriptor, result);
+        return jobDescriptor;
+    }
+
+    public synchronized JobStatus getJobStatus(String jobID) throws SSHApiException {
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getMonitorCommand(jobID);
+        StandardOutReader stdOutReader = new StandardOutReader();
+        log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+        CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", jobManagerConfiguration.getBaseMonitorCommand());
+        return jobManagerConfiguration.getParser().parseJobStatus(jobID, result);
+    }
+
+    @Override
+    public String getJobIdByJobName(String jobName, String userName) throws SSHApiException {
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getJobIdMonitorCommand(jobName, userName);
+        StandardOutReader stdOutReader = new StandardOutReader();
+        log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+        CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !",
+                jobManagerConfiguration.getJobIdMonitorCommand(jobName,userName).getCommand());
+        return jobManagerConfiguration.getParser().parseJobId(jobName, result);
+    }
+
+    private static void logDebug(String message) {
+        if (log.isDebugEnabled()) {
+            log.debug(message);
+        }
+    }
+
+    public JobManagerConfiguration getJobManagerConfiguration() {
+        return jobManagerConfiguration;
+    }
+
+    public void setJobManagerConfiguration(JobManagerConfiguration jobManagerConfiguration) {
+        this.jobManagerConfiguration = jobManagerConfiguration;
+    }
+
+    public synchronized void scpTo(String remoteFile, String localFile) throws SSHApiException {
+        int retry = 3;
+        while (retry > 0) {
+            try {
+                if (!session.isConnected()) {
+                    session.connect();
+                }
+                log.info("Transfering file:/" + localFile + " To:" + serverInfo.getHost() + ":" + remoteFile);
+                SSHUtils.scpTo(remoteFile, localFile, session);
+                retry = 0;
+            } catch (IOException e) {
+                retry--;
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during scping local file:" + localFile + " to remote file "
+                            + serverInfo.getHost() + ":rFile : " + remoteFile, e);
+                }
+            } catch (JSchException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during scping local file:" + localFile + " to remote file "
+                            + serverInfo.getHost() + ":rFile : " + remoteFile, e);
+                }
+            }
+        }
+    }
+
+    public synchronized void scpFrom(String remoteFile, String localFile) throws SSHApiException {
+        int retry = 3;
+        while(retry>0) {
+            try {
+                if (!session.isConnected()) {
+                    session.connect();
+                }
+                log.info("Transfering from:" + serverInfo.getHost() + ":" + remoteFile + " To:" + "file:/" + localFile);
+                SSHUtils.scpFrom(remoteFile, localFile, session);
+                retry=0;
+            } catch (IOException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during scping local file:" + localFile + " to remote file "
+                            + serverInfo.getHost() + ":rFile", e);
+                }else{
+                    log.error("Error performing scp but doing a retry");
+                }
+            } catch (JSchException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if(retry==0) {
+                    throw new SSHApiException("Failed during scping local file:" + localFile + " to remote file "
+                            + serverInfo.getHost() + ":rFile", e);
+                }else{
+                    log.error("Error performing scp but doing a retry");
+                }
+            }
+        }
+    }
+    
+    public synchronized void scpThirdParty(String remoteFileSource, String remoteFileTarget) throws SSHApiException {
+        try {
+            if(!session.isConnected()){
+                session.connect();
+            }
+            log.info("Transfering from:" + remoteFileSource + " To: " + remoteFileTarget);
+            SSHUtils.scpThirdParty(remoteFileSource, remoteFileTarget, session);
+        } catch (IOException e) {
+            throw new SSHApiException("Failed during scping  file:" + remoteFileSource + " to remote file "
+                    +remoteFileTarget , e);
+        } catch (JSchException e) {
+            throw new SSHApiException("Failed during scping  file:" + remoteFileSource + " to remote file "
+                    +remoteFileTarget, e);
+        }
+    }
+
+    public synchronized void makeDirectory(String directoryPath) throws SSHApiException {
+        int retry = 3;
+        while (retry > 0) {
+            try {
+                if (!session.isConnected()) {
+                    session.connect();
+                }
+                log.info("Creating directory: " + serverInfo.getHost() + ":" + directoryPath);
+                SSHUtils.makeDirectory(directoryPath, session);
+                retry = 0;
+            } catch (IOException e) {
+                throw new SSHApiException("Failed during creating directory:" + directoryPath + " to remote file "
+                        + serverInfo.getHost() + ":rFile", e);
+            } catch (JSchException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during creating directory :" + directoryPath + " to remote file "
+                            + serverInfo.getHost() + ":rFile", e);
+                }
+            } catch (SSHApiException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during creating directory :" + directoryPath + " to remote file "
+                            + serverInfo.getHost() + ":rFile", e);
+                }
+            }
+        }
+    }
+
+    public synchronized List<String> listDirectory(String directoryPath) throws SSHApiException {
+        int retry = 3;
+        List<String> files = null;
+        while (retry > 0) {
+            try {
+                if (!session.isConnected()) {
+                    session.connect();
+                }
+                log.info("Listing directory: " + serverInfo.getHost() + ":" + directoryPath);
+                files = SSHUtils.listDirectory(directoryPath, session);
+                retry=0;
+            } catch (IOException e) {
+                log.error(e.getMessage(), e);
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during listing directory:" + directoryPath + " to remote file ", e);
+                }
+            } catch (JSchException e) {
+                retry--;
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during listing directory :" + directoryPath + " to remote file ", e);
+                }
+            }catch (SSHApiException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed during listing directory :" + directoryPath + " to remote file "
+                            + serverInfo.getHost() + ":rFile", e);
+                }
+            }
+        }
+        return files;
+    }
+
+    public synchronized void getJobStatuses(String userName, Map<String,JobStatus> jobIDs)throws SSHApiException {
+        int retry = 3;
+        RawCommandInfo rawCommandInfo = jobManagerConfiguration.getUserBasedMonitorCommand(userName);
+        StandardOutReader stdOutReader = new StandardOutReader();
+        while (retry > 0){
+            try {
+                log.info("Executing RawCommand : " + rawCommandInfo.getCommand());
+                CommandExecutor.executeCommand(rawCommandInfo, this.getSession(), stdOutReader);
+                retry=0;
+            } catch (SSHApiException e) {
+                retry--;
+                try {
+                    Thread.sleep(5000);
+                } catch (InterruptedException e1) {
+                    log.error(e1.getMessage(), e1);
+                }
+                reconnect(serverInfo, authenticationInfo);
+                if (retry == 0) {
+                    throw new SSHApiException("Failed Getting statuses  to remote file", e);
+                }
+            }
+        }
+        String result = getOutputifAvailable(stdOutReader, "Error getting job information from the resource !", jobManagerConfiguration.getBaseMonitorCommand());
+        jobManagerConfiguration.getParser().parseJobStatuses(userName, jobIDs, result);
+    }
+
+    public ServerInfo getServerInfo() {
+        return serverInfo;
+    }
+
+    public AuthenticationInfo getAuthenticationInfo() {
+        return authenticationInfo;
+    }
+
+    /**
+     * This gaurantee to return a valid session
+     *
+     * @return
+     */
+    public Session getSession() {
+        return this.session;
+    }
+
+    /**
+     * This method will read standard output and if there's any it will be parsed
+     *
+     * @param jobIDReaderCommandOutput
+     * @param errorMsg
+     * @return
+     * @throws SSHApiException
+     */
+    private String getOutputifAvailable(StandardOutReader jobIDReaderCommandOutput, String errorMsg, String command) throws SSHApiException {
+        String stdOutputString = jobIDReaderCommandOutput.getStdOutputString();
+        String stdErrorString = jobIDReaderCommandOutput.getStdErrorString();
+        log.info("StandardOutput Returned:" + stdOutputString);
+        log.info("StandardError  Returned:" +stdErrorString);
+        String[] list = command.split(File.separator);
+        command = list[list.length - 1];
+        // We are checking for stderr containing the command issued. Thus ignores the verbose logs in stderr.
+        if (stdErrorString != null && stdErrorString.contains(command.trim()) && !stdErrorString.contains("Warning")) {
+            log.error("Standard Error output : " + stdErrorString);
+            throw new SSHApiException(errorMsg + "\n\r StandardOutput: "+ stdOutputString + "\n\r StandardError: "+ stdErrorString);
+        }else if(stdOutputString.contains("error")){
+            throw new SSHApiException(errorMsg + "\n\r StandardOutput: "+ stdOutputString + "\n\r StandardError: "+ stdErrorString);
+        }
+        return stdOutputString;
+    }
+
+    public void disconnect() throws SSHApiException {
+    	if(getSession().isConnected()){
+    		getSession().disconnect();
+    	}
+    }
+    /**
+	
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
+	 * @return the new default JSch implementation.
+	 * @throws JSchException
+	 *             known host keys cannot be loaded.
+	 */
+	protected JSch createJSch(AuthenticationInfo authenticationInfo) throws JSchException {
+//		final File fs = new File(System.getProperty("user.home"));
+		if(authenticationInfo instanceof GSIAuthenticationInfo){
+			final JSch jsch = new ExtendedJSch();
+//			knownHosts(jsch, fs);
+			return jsch;
+		}else{
+		final JSch jsch = new JSch();
+//		knownHosts(jsch, fs);
+		return jsch;
+		}
+		
+	}
+	/**
+	 * Create a new remote session for the requested address.
+	 *
+	 * @param user
+	 *            login to authenticate as.
+	 * @param host
+	 *            server name to connect to.
+	 * @param port
+	 *            port number of the SSH daemon (typically 22).
+	 * @return new session instance, but otherwise unconfigured.
+	 * @throws JSchException
+	 *             the session could not be created.
+	 */
+	private Session createSession(JSch jsch, String user, String host, int port) throws JSchException {
+		final Session session = jsch.getSession(user, host, port);
+		// We retry already in getSession() method. JSch must not retry
+		// on its own.
+		session.setConfig("MaxAuthTries", "1"); //$NON-NLS-1$ //$NON-NLS-2$
+		session.setTimeout(Integer.parseInt(configReader.getConfiguration(SSH_SESSION_TIMEOUT)));
+	    java.util.Properties config = this.configReader.getProperties();
+	    session.setConfig(config);
+	    
+    	return session;
+	}
+	private static void knownHosts(final JSch sch,final File home) throws JSchException {
+		if (home == null)
+			return;
+		final File known_hosts = new File(new File(home, ".ssh"), "known_hosts"); //$NON-NLS-1$ //$NON-NLS-2$
+		try {
+			final FileInputStream in = new FileInputStream(known_hosts);
+			try {
+				sch.setKnownHosts(in);
+			} finally {
+				in.close();
+			}
+		} catch (FileNotFoundException none) {
+			// Oh well. They don't have a known hosts in home.
+		} catch (IOException err) {
+			// Oh well. They don't have a known hosts in home.
+		}
+	}
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/JobStatus.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/JobStatus.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/JobStatus.java
new file mode 100644
index 0000000..648d955
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/JobStatus.java
@@ -0,0 +1,110 @@
+ /*
+ *
+ * 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.impl;
+
+ /**
+  * This will contains all the PBS specific job statuses.
+  * C -  Job is completed after having run/
+  * E -  Job is exiting after having run.
+  * H -  Job is held.
+  * Q -  job is queued, eligible to run or routed.
+  * R -  job is running.
+  * T -  job is being moved to new location.
+  * W -  job is waiting for its execution time
+  * (-a option) to be reached.
+  * S -  (Unicos only) job is suspend.
+  */
+ public enum JobStatus {
+     C, E, H, Q, R, T, W, S,U,F,CA,CD,CF,CG,NF,PD,PR,TO,qw,t,r,h,Er,Eqw,PEND,RUN,PSUSP,USUSP,SSUSP,DONE,EXIT,UNKWN,ZOMBI;
+
+     public static JobStatus fromString(String status){
+        if(status != null){
+            if("C".equals(status)){
+                return JobStatus.C;
+            }else if("E".equals(status)){
+                return JobStatus.E;
+            }else if("H".equals(status)){
+                return JobStatus.H;
+            }else if("Q".equals(status)){
+                return JobStatus.Q;
+            }else if("R".equals(status)){
+                return JobStatus.R;
+            }else if("T".equals(status)){
+                return JobStatus.T;
+            }else if("W".equals(status)){
+                return JobStatus.W;
+            }else if("S".equals(status)){
+                return JobStatus.S;
+            }else if("F".equals(status)){
+                return JobStatus.F;
+            }else if("S".equals(status)){
+                return JobStatus.S;
+            }else if("CA".equals(status)){
+                return JobStatus.CA;
+            }else if("CF".equals(status)){
+                return JobStatus.CF;
+            }else if("CD".equals(status)){
+                return JobStatus.CD;
+            }else if("CG".equals(status)){
+                return JobStatus.CG;
+            }else if("NF".equals(status)){
+                return JobStatus.NF;
+            }else if("PD".equals(status)){
+                return JobStatus.PD;
+            }else if("PR".equals(status)){
+                return JobStatus.PR;
+            }else if("TO".equals(status)){
+                return JobStatus.TO;
+            }else if("U".equals(status)){
+                return JobStatus.U;
+            }else if("qw".equals(status)){
+                return JobStatus.qw;
+            }else if("t".equals(status)){
+                return JobStatus.t;
+            }else if("r".equals(status)){
+                return JobStatus.r;
+            }else if("h".equals(status)){
+                return JobStatus.h;
+            }else if("Er".equals(status)){
+                return JobStatus.Er;
+            }else if("Eqw".equals(status)){
+                return JobStatus.Er;
+            }else if("RUN".equals(status)){      // LSF starts here
+                return JobStatus.RUN;
+            }else if("PEND".equals(status)){
+                return JobStatus.PEND;
+            }else if("DONE".equals(status)){
+                return JobStatus.DONE;
+            }else if("PSUSP".equals(status)){
+                return JobStatus.PSUSP;
+            }else if("USUSP".equals(status)){
+                return JobStatus.USUSP;
+            }else if("SSUSP".equals(status)){
+                return JobStatus.SSUSP;
+            }else if("EXIT".equals(status)){
+                return JobStatus.EXIT;
+            }else if("ZOMBI".equals(status)){
+                return JobStatus.ZOMBI;
+            }
+        }
+         return JobStatus.U;
+     }
+ }

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/PBSCluster.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/PBSCluster.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/PBSCluster.java
new file mode 100644
index 0000000..def84d5
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/PBSCluster.java
@@ -0,0 +1,45 @@
+/*
+ *
+ * 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.impl;
+
+import org.apache.airavata.gfac.ssh.api.*;
+import org.apache.airavata.gfac.ssh.api.authentication.*;
+import org.apache.airavata.gfac.ssh.api.job.JobManagerConfiguration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+/**
+ * This is the default implementation of a cluster.
+ * this has most of the methods to be used by the end user of the
+ * library.
+ */
+public class PBSCluster extends GSISSHAbstractCluster {
+    private static final Logger log = LoggerFactory.getLogger(PBSCluster.class);
+
+
+    public PBSCluster(JobManagerConfiguration jobManagerConfiguration) {
+        super(jobManagerConfiguration);
+    }
+    public PBSCluster(ServerInfo serverInfo, AuthenticationInfo authenticationInfo, JobManagerConfiguration config) throws SSHApiException {
+        super(serverInfo, authenticationInfo,config);
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/RawCommandInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/RawCommandInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/RawCommandInfo.java
new file mode 100644
index 0000000..9ac2ba0
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/RawCommandInfo.java
@@ -0,0 +1,55 @@
+/*
+ *
+ * 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.impl;
+
+import org.apache.airavata.gfac.ssh.api.CommandInfo;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 8/14/13
+ * Time: 5:18 PM
+ */
+
+/**
+ * The raw command information. String returned by getCommand is directly executed in SSH
+ * shell. E.g :- getCommand return string set for rawCommand - "/opt/torque/bin/qsub /home/ogce/test.pbs".
+ */
+public class RawCommandInfo implements CommandInfo {
+
+    private String rawCommand;
+
+    public RawCommandInfo(String cmd) {
+        this.rawCommand = cmd;
+    }
+
+    public String getCommand() {
+        return this.rawCommand;
+    }
+
+    public String getRawCommand() {
+        return rawCommand;
+    }
+
+    public void setRawCommand(String rawCommand) {
+        this.rawCommand = rawCommand;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SSHUserInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SSHUserInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SSHUserInfo.java
new file mode 100644
index 0000000..e878dff
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SSHUserInfo.java
@@ -0,0 +1,63 @@
+/*
+ *
+ * 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.impl;
+
+import com.jcraft.jsch.UserInfo;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 9/20/13
+ * Time: 2:31 PM
+ */
+
+public class SSHUserInfo implements UserInfo {
+
+    private String password;
+
+    public SSHUserInfo(String pwd) {
+        this.password = pwd;
+    }
+
+    public String getPassphrase() {
+        return this.password;
+    }
+
+    public String getPassword() {
+        return this.password;
+    }
+
+    public boolean promptPassword(String message) {
+        return false;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public boolean promptPassphrase(String message) {
+        return false;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public boolean promptYesNo(String message) {
+        return false;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public void showMessage(String message) {
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/StandardOutReader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/StandardOutReader.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/StandardOutReader.java
new file mode 100644
index 0000000..265a57d
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/StandardOutReader.java
@@ -0,0 +1,79 @@
+/*
+ *
+ * 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.impl;
+
+import com.jcraft.jsch.Channel;
+
+import org.apache.airavata.gfac.ssh.api.CommandOutput;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+public class StandardOutReader implements CommandOutput {
+
+    private static final Logger logger = LoggerFactory.getLogger(StandardOutReader.class);
+    String stdOutputString = null;
+    ByteArrayOutputStream errorStream = new ByteArrayOutputStream();
+    public void onOutput(Channel channel) {
+        try {
+            StringBuffer pbsOutput = new StringBuffer("");
+            InputStream inputStream =  channel.getInputStream();
+            byte[] tmp = new byte[1024];
+            do {
+                while (inputStream.available() > 0) {
+                    int i = inputStream.read(tmp, 0, 1024);
+                    if (i < 0) break;
+                    pbsOutput.append(new String(tmp, 0, i));
+                }
+            } while (!channel.isClosed()) ;
+            String output = pbsOutput.toString();
+            this.setStdOutputString(output);
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+        }
+
+    }
+
+
+    public void exitCode(int code) {
+        System.out.println("Program exit code - " + code);
+    }
+
+    public String getStdOutputString() {
+        return stdOutputString;
+    }
+
+    public void setStdOutputString(String stdOutputString) {
+        this.stdOutputString = stdOutputString;
+    }
+
+    public String getStdErrorString() {
+        return errorStream.toString();
+    }
+
+    public OutputStream getStandardError() {
+        return errorStream;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SystemCommandOutput.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SystemCommandOutput.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SystemCommandOutput.java
new file mode 100644
index 0000000..24d218b
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/SystemCommandOutput.java
@@ -0,0 +1,78 @@
+/*
+ *
+ * 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.impl;
+
+import com.jcraft.jsch.Channel;
+import org.apache.airavata.gfac.ssh.api.CommandOutput;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 8/15/13
+ * Time: 10:44 AM
+ */
+
+public class SystemCommandOutput implements CommandOutput {
+
+    private static final Logger logger = LoggerFactory.getLogger(SystemCommandOutput.class);
+    public void onOutput(Channel channel) {
+        try {
+            InputStream inputStream = channel.getInputStream();
+
+            byte[] tmp = new byte[1024];
+            while (true) {
+                while (inputStream.available() > 0) {
+                    int i = inputStream.read(tmp, 0, 1024);
+                    if (i < 0) break;
+                    System.out.print(new String(tmp, 0, i));
+                }
+                if (channel.isClosed()) {
+                    System.out.println("exit-status: " + channel.getExitStatus());
+                    break;
+                }
+                try {
+                    Thread.sleep(1000);
+                } catch (Exception ignored) {
+                }
+            }
+
+        } catch (IOException e) {
+            logger.error(e.getMessage(), e);
+        }
+
+    }
+
+    public OutputStream getStandardError() {
+        return System.err;
+    }
+
+    public void exitCode(int code) {
+        System.out.println("Program exit code - " + code);
+    }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPasswordAuthenticationInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPasswordAuthenticationInfo.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPasswordAuthenticationInfo.java
new file mode 100644
index 0000000..29cd154
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPasswordAuthenticationInfo.java
@@ -0,0 +1,48 @@
+/*
+ *
+ * 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.impl.authentication;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 9/20/13
+ * Time: 12:15 PM
+ */
+
+import org.apache.airavata.gfac.core.authentication.SSHPasswordAuthentication;
+
+/**
+ * An authenticator used for raw SSH sessions. Gives SSH user name, password
+ * directly.
+ * This is only an example implementation.
+ */
+public class DefaultPasswordAuthenticationInfo implements SSHPasswordAuthentication {
+
+    private String password;
+
+    public DefaultPasswordAuthenticationInfo(String pwd) {
+        this.password = pwd;
+    }
+
+    public String getPassword(String userName, String hostName) {
+        return password;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyAuthentication.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyAuthentication.java
new file mode 100644
index 0000000..35595ed
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyAuthentication.java
@@ -0,0 +1,68 @@
+/*
+ *
+ * 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.impl.authentication;
+
+import org.apache.airavata.gfac.core.authentication.SSHPublicKeyAuthentication;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 11:44 AM
+ */
+
+/**
+ * Default public key authentication.
+ * Note : This is only a sample implementation.
+ */
+public class DefaultPublicKeyAuthentication implements SSHPublicKeyAuthentication {
+
+    private byte[] privateKey;
+    private byte[] publicKey;
+    private String passPhrase = null;
+
+    public DefaultPublicKeyAuthentication(byte[] priv, byte[] pub) {
+        this.privateKey = priv;
+        this.publicKey = pub;
+    }
+
+    public DefaultPublicKeyAuthentication(byte[] priv, byte[] pub, String pass) {
+        this.privateKey = priv;
+        this.publicKey = pub;
+        this.passPhrase = pass;
+    }
+
+    public String getPassPhrase() {
+        return passPhrase;
+    }
+
+    public void bannerMessage(String message) {
+        System.out.println(message);
+    }
+
+    public byte[] getPrivateKey(String userName, String hostName) {
+        return privateKey;
+    }
+
+    public byte[] getPublicKey(String userName, String hostName) {
+        return publicKey;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyFileAuthentication.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyFileAuthentication.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyFileAuthentication.java
new file mode 100644
index 0000000..480213c
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/impl/authentication/DefaultPublicKeyFileAuthentication.java
@@ -0,0 +1,70 @@
+/*
+ *
+ * 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.impl.authentication;
+
+import org.apache.airavata.gfac.core.authentication.SSHPublicKeyFileAuthentication;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 11:40 AM
+ */
+
+/**
+ * Default public key authentication using files.
+ * Note : This is only a sample implementation.
+ */
+public class DefaultPublicKeyFileAuthentication implements SSHPublicKeyFileAuthentication {
+
+    private String publicKeyFile;
+    private String privateKeyFile;
+    private String passPhrase = null;
+
+    public DefaultPublicKeyFileAuthentication(String pubFile, String privFile) {
+        this.publicKeyFile = pubFile;
+        this.privateKeyFile = privFile;
+
+    }
+
+    public DefaultPublicKeyFileAuthentication(String pubFile, String privFile, String pass) {
+        this.publicKeyFile = pubFile;
+        this.privateKeyFile = privFile;
+        this.passPhrase = pass;
+
+    }
+
+    public String getPassPhrase() {
+        return passPhrase;
+    }
+
+    public void bannerMessage(String message) {
+        System.out.println(message);
+    }
+
+    public String getPublicKeyFile(String userName, String hostName) {
+        return publicKeyFile;
+    }
+
+    public String getPrivateKeyFile(String userName, String hostName) {
+        return privateKeyFile;
+    }
+}


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