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From shame...@apache.org
Subject [03/81] [abbrv] 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 Thu, 04 Jun 2015 20:15:16 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
deleted file mode 100644
index 9a34a47..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
+++ /dev/null
@@ -1,473 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.CommandOutput;
-import org.apache.airavata.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.gsi.ssh.x2012.x12.*;
-import org.apache.xmlbeans.XmlException;
-
-import java.util.List;
-
-/**
- * This class define a job with required parameters, based on this configuration API is generating a Pbs script and
- * submit the job to the computing resource
- */
-public class JobDescriptor {
-
-    private JobDescriptorDocument jobDescriptionDocument;
-
-
-    public JobDescriptor() {
-        jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
-        jobDescriptionDocument.addNewJobDescriptor();
-    }
-
-    public JobDescriptor(JobDescriptorDocument jobDescriptorDocument) {
-        this.jobDescriptionDocument = jobDescriptorDocument;
-    }
-
-
-    public JobDescriptor(CommandOutput commandOutput) {
-        jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
-        jobDescriptionDocument.addNewJobDescriptor();
-    }
-
-
-    public String toXML() {
-        return jobDescriptionDocument.xmlText();
-    }
-
-    public JobDescriptorDocument getJobDescriptorDocument() {
-        return this.jobDescriptionDocument;
-    }
-
-    /**
-     * With new app catalog thrift object integration, we don't use this
-     * @param xml
-     * @return
-     * @throws XmlException
-     */
-    @Deprecated
-    public static JobDescriptor fromXML(String xml)
-            throws XmlException {
-        JobDescriptorDocument parse = JobDescriptorDocument.Factory
-                .parse(xml);
-        JobDescriptor jobDescriptor = new JobDescriptor(parse);
-        return jobDescriptor;
-    }
-
-
-    //todo write bunch of setter getters to set and get jobdescription parameters
-    public void setWorkingDirectory(String workingDirectory) {
-        this.getJobDescriptorDocument().getJobDescriptor().setWorkingDirectory(workingDirectory);
-    }
-
-    public String getWorkingDirectory() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory();
-    }
-
-    public void setShellName(String shellName) {
-        this.getJobDescriptorDocument().getJobDescriptor().setShellName(shellName);
-    }
-
-    public void setJobName(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setJobName(name);
-    }
-
-    public void setExecutablePath(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setExecutablePath(name);
-    }
-
-    public void setAllEnvExport(boolean name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setAllEnvExport(name);
-    }
-
-    public void setMailOptions(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMailOptions(name);
-    }
-
-    public void setStandardOutFile(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setStandardOutFile(name);
-    }
-
-    public void setStandardErrorFile(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setStandardErrorFile(name);
-    }
-
-    public void setNodes(int name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setNodes(name);
-    }
-
-    public void setProcessesPerNode(int name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setProcessesPerNode(name);
-    }
-
-    public String getOutputDirectory() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getOutputDirectory();
-    }
-
-    public String getInputDirectory() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getInputDirectory();
-    }
-    public void setOutputDirectory(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setOutputDirectory(name);
-    }
-
-    public void setInputDirectory(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setInputDirectory(name);
-    }
-
-    /**
-     * Users can pass the minute count for maxwalltime
-     * @param minutes
-     */
-    public void setMaxWallTime(String minutes) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
-                CommonUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
-
-    }
-
-
-    public void setMaxWallTimeForLSF(String minutes) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
-                CommonUtils.maxWallTimeCalculatorForLSF(Integer.parseInt(minutes)));
-
-    }
-    public void setAcountString(String name) {
-        this.getJobDescriptorDocument().getJobDescriptor().setAcountString(name);
-    }
-
-    public void setInputValues(List<String> inputValue) {
-        InputList inputList = this.getJobDescriptorDocument().getJobDescriptor().addNewInputs();
-        inputList.setInputArray(inputValue.toArray(new String[inputValue.size()]));
-    }
-
-    public void setJobID(String jobID) {
-        this.getJobDescriptorDocument().getJobDescriptor().setJobID(jobID);
-    }
-
-    public void setQueueName(String queueName) {
-        this.getJobDescriptorDocument().getJobDescriptor().setQueueName(queueName);
-    }
-
-    public void setStatus(String queueName) {
-        this.getJobDescriptorDocument().getJobDescriptor().setStatus(queueName);
-    }
-
-    public void setAfterAnyList(String[] afterAnyList) {
-        AfterAnyList afterAny = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterAny();
-        afterAny.setAfterAnyArray(afterAnyList);
-    }
-
-    public void setAfterOKList(String[] afterOKList) {
-        AfterOKList afterAnyList = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterOKList();
-        afterAnyList.setAfterOKListArray(afterOKList);
-    }
-    public void setCTime(String cTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setCTime(cTime);
-    }
-    public void setQTime(String qTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setQTime(qTime);
-    }
-    public void setMTime(String mTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMTime(mTime);
-    }
-    public void setSTime(String sTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setSTime(sTime);
-    }
-    public void setCompTime(String compTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setCompTime(compTime);
-    }
-    public void setOwner(String owner) {
-        this.getJobDescriptorDocument().getJobDescriptor().setOwner(owner);
-    }
-    public void setExecuteNode(String executeNode) {
-        this.getJobDescriptorDocument().getJobDescriptor().setExecuteNode(executeNode);
-    }
-    public void setEllapsedTime(String ellapsedTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setEllapsedTime(ellapsedTime);
-    }
-
-    public void setUsedCPUTime(String usedCPUTime) {
-        this.getJobDescriptorDocument().getJobDescriptor().setUsedCPUTime(usedCPUTime);
-    }
-    public void setCPUCount(int usedCPUTime) {
-            this.getJobDescriptorDocument().getJobDescriptor().setCpuCount(usedCPUTime);
-        }
-    public void setUsedMemory(String usedMemory) {
-        this.getJobDescriptorDocument().getJobDescriptor().setUsedMem(usedMemory);
-    }
-    public void setVariableList(String variableList) {
-        this.getJobDescriptorDocument().getJobDescriptor().setVariableList(variableList);
-    }
-    public void setSubmitArgs(String submitArgs) {
-        this.getJobDescriptorDocument().getJobDescriptor().setSubmitArgs(submitArgs);
-    }
-
-    public void setPreJobCommands(String[] commands){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
-            this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().setCommandArray(commands);
-    }
-
-     public void setPostJobCommands(String[] commands){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
-            this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().setCommandArray(commands);
-    }
-
-    public void setModuleLoadCommands(String[] commands) {
-        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
-            this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().setCommandArray(commands);
-    }
-
-    public void addModuleLoadCommands(String command) {
-        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
-            this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().addCommand(command);
-    }
-
-    public void addPreJobCommand(String command){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
-            this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().addCommand(command);
-    }
-
-     public void addPostJobCommand(String command){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
-            this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
-        }
-        this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().addCommand(command);
-    }
-
-    public void setPartition(String partition){
-        this.getJobDescriptorDocument().getJobDescriptor().setPartition(partition);
-    }
-
-     public void setUserName(String userName){
-        this.getJobDescriptorDocument().getJobDescriptor().setUserName(userName);
-    }
-     public void setNodeList(String nodeList){
-        this.getJobDescriptorDocument().getJobDescriptor().setNodeList(nodeList);
-    }
-    public void setJobSubmitter(String jobSubmitter){
-           this.getJobDescriptorDocument().getJobDescriptor().setJobSubmitterCommand(jobSubmitter);
-    }
-    public String getNodeList(){
-        return this.getJobDescriptorDocument().getJobDescriptor().getNodeList();
-    }
-    public String getExecutablePath() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getExecutablePath();
-    }
-
-    public boolean getAllEnvExport() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getAllEnvExport();
-    }
-
-    public String getMailOptions() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getMailOptions();
-    }
-
-    public String getStandardOutFile() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile();
-    }
-
-    public String getStandardErrorFile() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile();
-    }
-
-    public int getNodes(int name) {
-        return this.getJobDescriptorDocument().getJobDescriptor().getNodes();
-    }
-
-    public int getCPUCount(int name) {
-        return this.getJobDescriptorDocument().getJobDescriptor().getCpuCount();
-    }
-
-    public int getProcessesPerNode() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getProcessesPerNode();
-    }
-
-    public String getMaxWallTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getMaxWallTime();
-    }
-
-    public String getAcountString() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getAcountString();
-    }
-
-    public String[] getInputValues() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getInputs().getInputArray();
-    }
-
-    public String getJobID() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
-    }
-
-    public String getQueueName() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getQueueName();
-    }
-
-    public String getStatus() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getStatus();
-    }
-
-    public String[] getAfterAnyList() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getAfterAny().getAfterAnyArray();
-    }
-
-    public String[] getAfterOKList() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getAfterOKList().getAfterOKListArray();
-    }
-    public String getCTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getCTime();
-    }
-    public String getQTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getQTime();
-    }
-    public String getMTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getMTime();
-    }
-    public String getSTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getSTime();
-    }
-    public String getCompTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getCompTime();
-    }
-    public String getOwner() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getOwner();
-    }
-    public String getExecuteNode() {
-         return this.getJobDescriptorDocument().getJobDescriptor().getExecuteNode();
-    }
-    public String getEllapsedTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getEllapsedTime();
-    }
-
-    public String getUsedCPUTime() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getUsedCPUTime();
-    }
-
-    public String getUsedMemory() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getUsedMem();
-    }
-    public void getShellName() {
-        this.getJobDescriptorDocument().getJobDescriptor().getShellName();
-    }
-
-    public String getJobName() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getJobName();
-    }
-
-    public String getJobId() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
-    }
-
-
-    public String getVariableList() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
-    }
-    public String getSubmitArgs() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
-    }
-
-    public String[] getPostJobCommands(){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() != null) {
-            return this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().getCommandArray();
-        }
-        return null;
-    }
-
-    public String[] getModuleCommands() {
-        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() != null) {
-            return this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().getCommandArray();
-        }
-        return null;
-    }
-
-    public String[] getPreJobCommands(){
-        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() != null) {
-            return this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().getCommandArray();
-        }
-        return null;
-    }
-
-    public String getJobSubmitterCommand(){
-          return this.getJobDescriptorDocument().getJobDescriptor().getJobSubmitterCommand();
-    }
-
-    public String getPartition(){
-        return this.getJobDescriptorDocument().getJobDescriptor().getPartition();
-    }
-
-    public String getUserName(){
-        return this.getJobDescriptorDocument().getJobDescriptor().getUserName();
-    }
-
-    public void setCallBackIp(String ip){
-        this.jobDescriptionDocument.getJobDescriptor().setCallBackIp(ip);
-    }
-
-    public void setCallBackPort(String ip){
-        this.jobDescriptionDocument.getJobDescriptor().setCallBackPort(ip);
-    }
-
-
-    public String getCallBackIp(){
-        return this.jobDescriptionDocument.getJobDescriptor().getCallBackIp();
-    }
-    public String getCallBackPort(){
-        return this.jobDescriptionDocument.getJobDescriptor().getCallBackPort();
-    }
-
-    public void setMailType(String emailType) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMailType(emailType);
-    }
-
-    public String getMailType() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getMailType();
-    }
-    public void setMailAddress(String emailAddress) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMailAddress(emailAddress);
-    }
-
-    public String getMailAddress() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getMailAddress();
-    }
-
-    public String getChassisName() {
-        return this.getJobDescriptorDocument().getJobDescriptor().getChassisName();
-    }
-
-    public void setChassisName(String chassisName){
-        this.getJobDescriptorDocument().getJobDescriptor().setChassisName(chassisName);
-    }
-    
-
-}
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
deleted file mode 100644
index d9b6b1c..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobManagerConfiguration.java
+++ /dev/null
@@ -1,51 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-
-public interface JobManagerConfiguration {
-
-	public RawCommandInfo getCancelCommand(String jobID);
-
-	public String getJobDescriptionTemplateName();
-
-	public RawCommandInfo getMonitorCommand(String jobID);
-
-	public RawCommandInfo getUserBasedMonitorCommand(String userName);
-
-    public RawCommandInfo getJobIdMonitorCommand(String jobName , String userName);
-
-	public String getScriptExtension();
-
-	public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath);
-
-	public OutputParser getParser();
-
-	public String getInstalledPath();
-
-	public String getBaseCancelCommand();
-
-	public String getBaseMonitorCommand();
-
-	public String getBaseSubmitCommand();
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobType.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobType.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobType.java
deleted file mode 100644
index 7e1b49b..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobType.java
+++ /dev/null
@@ -1,32 +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.gsi.ssh.api.job;
-
-/**
- * Created by IntelliJ IDEA.
- * User: lahirugunathilake
- * Date: 8/22/13
- * Time: 7:19 AM
- * To change this template use File | Settings | File Templates.
- */
-public enum JobType {
-            SERIAL, SINGLE, MPI, MULTIPLE, CONDOR
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
deleted file mode 100644
index 740c9ac..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFJobConfiguration.java
+++ /dev/null
@@ -1,121 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class LSFJobConfiguration implements JobManagerConfiguration {
-    private final static Logger logger = LoggerFactory.getLogger(LSFJobConfiguration.class);
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public LSFJobConfiguration(){
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-    public LSFJobConfiguration(String jobDescriptionTemplateName,
-                                 String scriptExtension,String installedPath,OutputParser parser) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-        this.scriptExtension = scriptExtension;
-        this.parser = parser;
-        if (installedPath.endsWith("/") || installedPath.isEmpty()) {
-            this.installedPath = installedPath;
-        } else {
-            this.installedPath = installedPath + "/";
-        }
-    }
-
-    @Override
-    public RawCommandInfo getCancelCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "bkill " + jobID);
-    }
-
-    @Override
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    @Override
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "bjobs " + jobID);
-    }
-
-    @Override
-    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
-        return new RawCommandInfo(this.installedPath + "bjobs -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        return new RawCommandInfo(this.installedPath + "bjobs -J " + jobName);
-    }
-
-    @Override
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    @Override
-    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
-        return new RawCommandInfo(this.installedPath + "bsub < " +
-                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
-    }
-
-    @Override
-    public OutputParser getParser() {
-        return parser;
-    }
-
-    public void setParser(OutputParser parser) {
-        this.parser = parser;
-    }
-
-    @Override
-    public String getInstalledPath() {
-        return installedPath;
-    }
-
-
-    @Override
-    public String getBaseCancelCommand() {
-        return "bkill";
-    }
-
-    @Override
-    public String getBaseMonitorCommand() {
-        return "bjobs";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "bsub";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
deleted file mode 100644
index a621ae0..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/LSFOutputParser.java
+++ /dev/null
@@ -1,130 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.impl.JobStatus;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class LSFOutputParser implements OutputParser {
-    private final static Logger logger = LoggerFactory.getLogger(LSFOutputParser.class);
-
-    @Override
-    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-        //todo we need to implement this but we are not using it airavata runtime
-        // if someone is using the gsissh as a tool this will be useful to get a descriptive information about a single job
-    }
-
-    @Override
-    public String parseJobSubmission(String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-        return rawOutput.substring(rawOutput.indexOf("<")+1,rawOutput.indexOf(">"));
-    }
-
-    @Override
-    public JobStatus parseJobStatus(String jobID, String rawOutput) throws SSHApiException {
-        boolean jobFount = false;
-        logger.debug(rawOutput);
-        //todo this is not used anymore
-        return JobStatus.C;
-    }
-
-    @Override
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-
-        String[]    info = rawOutput.split("\n");
-//        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            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
-                    logger.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;
-                    try {
-                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(2)));
-                    }catch(IndexOutOfBoundsException e){
-                        statusMap.put(jobID, JobStatus.valueOf("U"));
-                    }
-                    found = true;
-                    break;
-                }
-            }
-            if(!found)
-                logger.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobID.split(",")[0]);
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        String regJobId = "jobId";
-        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 {
-                logger.error("No match is found for JobName");
-                return null;
-            }
-        } else {
-            logger.error("Error: RawOutput shouldn't be null");
-            return null;
-        }
-    }
-
-    public static void main(String[] args) {
-        String test = "Job <2477982> is submitted to queue <short>.";
-        System.out.println(test.substring(test.indexOf("<")+1, test.indexOf(">")));
-        String test1 = "JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME\n" +
-                "2636607 lg11w   RUN   long       ghpcc06     c11b02      *069656647 Mar  7 00:58\n" +
-                "2636582 lg11w   RUN   long       ghpcc06     c02b01      2134490944 Mar  7 00:48";
-        Map<String, JobStatus> statusMap = new HashMap<String, JobStatus>();
-        statusMap.put("2477983,2134490944", JobStatus.U);
-        LSFOutputParser lsfOutputParser = new LSFOutputParser();
-        try {
-            lsfOutputParser.parseJobStatuses("cjh", statusMap, test1);
-        } catch (SSHApiException e) {
-            logger.error(e.getMessage(), e);
-        }
-        System.out.println(statusMap.get("2477983,2134490944"));
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/OutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/OutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/OutputParser.java
deleted file mode 100644
index fd37b6a..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/OutputParser.java
+++ /dev/null
@@ -1,68 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.impl.JobStatus;
-
-import java.util.List;
-import java.util.Map;
-
-public interface OutputParser {
-
-    /**
-     * Tihs can be used to fill a jobdescriptor based on the output
-     * @param descriptor
-     * @return
-     */
-    public void parseSingleJob(JobDescriptor descriptor, String rawOutput)throws SSHApiException;
-
-    /**
-     * This can be used to parseSingleJob the result of a job submission to get the JobID
-     * @param rawOutput
-     * @return
-     */
-    public String parseJobSubmission(String rawOutput)throws SSHApiException;
-
-
-    /**
-     * This can be used to get the job status from the output
-     * @param jobID
-     * @param rawOutput
-     */
-    public JobStatus parseJobStatus(String jobID, String rawOutput)throws SSHApiException;
-
-    /**
-     * This can be used to parseSingleJob a big output and get multipleJob statuses
-     * @param statusMap list of status map will return and key will be the job ID
-     * @param rawOutput
-     */
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput)throws SSHApiException;
-
-    /**
-     * filter the jobId value of given JobName from rawOutput
-     * @param jobName
-     * @param rawOutput
-     * @return
-     * @throws SSHApiException
-     */
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException;
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
deleted file mode 100644
index b658b16..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
+++ /dev/null
@@ -1,119 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-
-import java.io.File;
-
-public class PBSJobConfiguration implements JobManagerConfiguration {
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public PBSJobConfiguration() {
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-
-    public PBSJobConfiguration(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 -f " + 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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
deleted file mode 100644
index 1458f4c..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
+++ /dev/null
@@ -1,214 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.impl.JobStatus;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.print.attribute.standard.JobState;
-import javax.validation.constraints.Null;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class PBSOutputParser implements OutputParser {
-    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
-
-    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);
-        return rawOutput;  //In PBS stdout is going to be directly the jobID
-    }
-
-    public JobStatus parseJobStatus(String jobID, String rawOutput) {
-        boolean jobFount = false;
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String[] line = null;
-        int index = 0;
-        for (String anInfo : info) {
-            index++;
-            if (anInfo.contains("Job Id:")) {
-                if (anInfo.contains(jobID)) {
-                    jobFount = true;
-                    break;
-                }
-            }
-        }
-        if (jobFount) {
-            for (int i=index;i<info.length;i++) {
-                String anInfo = info[i];
-                if (anInfo.contains("=")) {
-                    line = anInfo.split("=", 2);
-                    if (line.length != 0) {
-                        if (line[0].contains("job_state")) {
-                            return JobStatus.valueOf(line[1].replaceAll(" ", ""));
-                        }
-                    }
-                }
-            }
-        }
-        return null;
-    }
-
-    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()) {
-            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);
-                        }
-                    }
-//                    lastStop = i + 1;
-                    try {
-                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(9)));
-                    }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.split(",")[0]);
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        String regJobId = "jobId";
-        Pattern pattern = Pattern.compile("\\s*(?<" + regJobId + ">[^\\s]*).* " + jobName + " "); // regex , JOB_ID will come as first column
-        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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
deleted file mode 100644
index 5feed86..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmJobConfiguration.java
+++ /dev/null
@@ -1,117 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-
-import java.io.File;
-
-public class SlurmJobConfiguration implements JobManagerConfiguration{
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public SlurmJobConfiguration(){
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-    public SlurmJobConfiguration(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 + "scancel " + jobID);
-    }
-
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-    }
-
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "squeue -j " + jobID);
-    }
-
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    public RawCommandInfo getSubmitCommand(String workingDirectory,String pbsFilePath) {
-          return new RawCommandInfo(this.installedPath + "sbatch " +
-                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 + "squeue -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        return new RawCommandInfo(this.installedPath + "squeue -n " + jobName + " -u " + userName);
-    }
-
-    @Override
-    public String getBaseCancelCommand() {
-        return "scancel";
-    }
-
-    @Override
-    public String getBaseMonitorCommand() {
-        return "squeue";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "sbatch";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java
deleted file mode 100644
index d37d444..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java
+++ /dev/null
@@ -1,190 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
deleted file mode 100644
index 8817c06..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
+++ /dev/null
@@ -1,119 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
deleted file mode 100644
index 1465c4f..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
+++ /dev/null
@@ -1,188 +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.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/config/ConfigReader.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/config/ConfigReader.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/config/ConfigReader.java
deleted file mode 100644
index 088ab38..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/config/ConfigReader.java
+++ /dev/null
@@ -1,81 +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.gsi.ssh.config;
-
-import com.sun.security.auth.login.ConfigFile;
-import sun.security.jgss.LoginConfigImpl;
-
-import javax.security.auth.login.Configuration;
-import javax.security.auth.login.LoginContext;
-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/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
deleted file mode 100644
index 749fc0d..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
+++ /dev/null
@@ -1,42 +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.gsi.ssh.impl;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.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);
-    }
-}


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