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From shame...@apache.org
Subject airavata git commit: Remove axis2 script form distribution and move AbstractSecurityContext to context sub package
Date Fri, 05 Jun 2015 19:20:41 GMT
Repository: airavata
Updated Branches:
  refs/heads/master b393df565 -> de8487878


Remove axis2 script form distribution and move AbstractSecurityContext to context sub package


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/de848787
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/de848787
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/de848787

Branch: refs/heads/master
Commit: de8487878e90d5d16a89428c144a25f2b5c34a17
Parents: b393df5
Author: Shameera Rathanyaka <shameerainfo@gmail.com>
Authored: Fri Jun 5 15:20:38 2015 -0400
Committer: Shameera Rathanyaka <shameerainfo@gmail.com>
Committed: Fri Jun 5 15:20:38 2015 -0400

----------------------------------------------------------------------
 distribution/src/main/assembly/bin-assembly.xml |  20 -
 .../gfac/bes/security/X509SecurityContext.java  |   2 +-
 .../gfac/core/AbstractSecurityContext.java      |  57 ---
 ...ava~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa | 475 -------------------
 .../airavata/gfac/core/JobDescriptor.java~HEAD  | 475 -------------------
 ...ava~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa |  52 --
 .../gfac/core/JobManagerConfiguration.java~HEAD |  52 --
 ...ava~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa |  34 --
 .../gfac/core/cluster/CommandInfo.java~HEAD     |  34 --
 ...ava~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa |  49 --
 .../gfac/core/cluster/CommandOutput.java~HEAD   |  49 --
 ...ava~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa |  65 ---
 .../gfac/core/cluster/ServerInfo.java~HEAD      |  65 ---
 .../core/context/AbstractSecurityContext.java   |  59 +++
 .../gsissh/security/GSISecurityContext.java     |   2 +-
 15 files changed, 61 insertions(+), 1429 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/distribution/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/distribution/src/main/assembly/bin-assembly.xml b/distribution/src/main/assembly/bin-assembly.xml
index 498f6c3..86a7315 100644
--- a/distribution/src/main/assembly/bin-assembly.xml
+++ b/distribution/src/main/assembly/bin-assembly.xml
@@ -106,26 +106,6 @@
 			</includes>
 		</fileSet>
 
-		<!-- ********************** Copy Axis2 startup scripts to stand alone server 
-			********************** -->
-		<fileSet>
-			<directory>src/main/resources/axis2-standalone-bin</directory>
-			<outputDirectory>bin</outputDirectory>
-			<fileMode>777</fileMode>
-			<includes>
-				<include>*.sh</include>
-				<include>*.bat</include>
-			</includes>
-		</fileSet>
-
-		<fileSet>
-			<directory>src/main/resources/conf</directory>
-			<outputDirectory>bin</outputDirectory>
-			<includes>
-				<include>**/*</include>
-			</includes>
-		</fileSet>
-
 		<!-- ********************** Copy samples ********************** -->
 		<fileSet>
 			<directory>${project.build.directory}/samples/applications

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/X509SecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/X509SecurityContext.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/X509SecurityContext.java
index 7d9c754..ff60e99 100644
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/X509SecurityContext.java
+++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/X509SecurityContext.java
@@ -26,7 +26,7 @@ import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.credential.store.credential.Credential;
 import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
 import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.core.AbstractSecurityContext;
+import org.apache.airavata.gfac.core.context.AbstractSecurityContext;
 import org.apache.airavata.gfac.core.Constants;
 import org.apache.airavata.gfac.core.GFacException;
 import org.apache.airavata.gfac.core.RequestData;

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/AbstractSecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/AbstractSecurityContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/AbstractSecurityContext.java
deleted file mode 100644
index bc9c21a..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/AbstractSecurityContext.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.gfac.core;
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 6/26/13
- * Time: 4:33 PM
- */
-
-import java.io.Serializable;
-
-import org.apache.airavata.credential.store.store.CredentialReader;
-
-/**
- * Abstract implementation of the security context.
- */
-public abstract class AbstractSecurityContext implements SecurityContext, Serializable {
-
-    private CredentialReader credentialReader;
-    private RequestData requestData;
-
-    public AbstractSecurityContext(CredentialReader credentialReader, RequestData requestData) {
-        this.credentialReader = credentialReader;
-        this.requestData = requestData;
-    }
-    public AbstractSecurityContext() {
-
-    }
-
-    public CredentialReader getCredentialReader() {
-        return credentialReader;
-    }
-
-    public RequestData getRequestData() {
-        return requestData;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
deleted file mode 100644
index 678f41f..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
+++ /dev/null
@@ -1,475 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.gfac.core;
-
-import org.apache.airavata.gfac.core.cluster.CommandOutput;
-import org.apache.airavata.gfac.core.x2012.x12.AfterAnyList;
-import org.apache.airavata.gfac.core.x2012.x12.AfterOKList;
-import org.apache.airavata.gfac.core.x2012.x12.InputList;
-import org.apache.airavata.gfac.core.x2012.x12.JobDescriptorDocument;
-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(
-                GFacUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
-
-    }
-
-
-    public void setMaxWallTimeForLSF(String minutes) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
-                GFacUtils.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/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~HEAD
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~HEAD b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~HEAD
deleted file mode 100644
index 678f41f..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java~HEAD
+++ /dev/null
@@ -1,475 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.gfac.core;
-
-import org.apache.airavata.gfac.core.cluster.CommandOutput;
-import org.apache.airavata.gfac.core.x2012.x12.AfterAnyList;
-import org.apache.airavata.gfac.core.x2012.x12.AfterOKList;
-import org.apache.airavata.gfac.core.x2012.x12.InputList;
-import org.apache.airavata.gfac.core.x2012.x12.JobDescriptorDocument;
-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(
-                GFacUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
-
-    }
-
-
-    public void setMaxWallTimeForLSF(String minutes) {
-        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
-                GFacUtils.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/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
deleted file mode 100644
index 661aba0..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-package org.apache.airavata.gfac.core;
-
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.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/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~HEAD
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~HEAD b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~HEAD
deleted file mode 100644
index 661aba0..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java~HEAD
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-package org.apache.airavata.gfac.core;
-
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.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/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
deleted file mode 100644
index 18e3e4e..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulates information about
- */
-public interface CommandInfo {
-
-    /**
-     * Gets the executable command as a string.
-     * @return String encoded command. Should be able to execute
-     * directly on remote shell. Should includes appropriate parameters.
-     */
-    String getCommand();
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~HEAD
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~HEAD b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~HEAD
deleted file mode 100644
index 18e3e4e..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java~HEAD
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulates information about
- */
-public interface CommandInfo {
-
-    /**
-     * Gets the executable command as a string.
-     * @return String encoded command. Should be able to execute
-     * directly on remote shell. Should includes appropriate parameters.
-     */
-    String getCommand();
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
deleted file mode 100644
index e50d25a..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-
-import com.jcraft.jsch.Channel;
-
-import java.io.OutputStream;
-
-/**
- * Output of a certain command. TODO rethink
- */
-public interface CommandOutput {
-
-    /**
-     * Gets the output of the command as a stream.
-     * @param  channel Command output as a stream.
-     */
-    void onOutput(Channel channel);
-
-    /**
-     * Gets standard error as a output stream.
-     * @return Command error as a stream.
-     */
-    OutputStream getStandardError();
-
-    /**
-     * The command exit code.
-     * @param code The program exit code
-     */
-    void exitCode(int code);
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~HEAD
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~HEAD b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~HEAD
deleted file mode 100644
index e50d25a..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java~HEAD
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-
-import com.jcraft.jsch.Channel;
-
-import java.io.OutputStream;
-
-/**
- * Output of a certain command. TODO rethink
- */
-public interface CommandOutput {
-
-    /**
-     * Gets the output of the command as a stream.
-     * @param  channel Command output as a stream.
-     */
-    void onOutput(Channel channel);
-
-    /**
-     * Gets standard error as a output stream.
-     * @return Command error as a stream.
-     */
-    OutputStream getStandardError();
-
-    /**
-     * The command exit code.
-     * @param code The program exit code
-     */
-    void exitCode(int code);
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
deleted file mode 100644
index 183f60b..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~30f9d70adbd9ee7dd6f7d3eccbfca4baf19b09fa
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulate server information.
- */
-public class ServerInfo {
-
-    private String host;
-    private String userName;
-    private int port = 22;
-
-    public ServerInfo(String userName, String host) {
-        this.userName = userName;
-        this.host = host;
-    }
-
-    public ServerInfo(String userName,String host,  int port) {
-        this.host = host;
-        this.userName = userName;
-        this.port = port;
-    }
-
-    public String getHost() {
-        return host;
-    }
-
-    public void setHost(String host) {
-        this.host = host;
-    }
-
-    public String getUserName() {
-        return userName;
-    }
-
-    public void setUserName(String userName) {
-        this.userName = userName;
-    }
-
-    public int getPort() {
-        return port;
-    }
-
-    public void setPort(int port) {
-        this.port = port;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~HEAD
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~HEAD b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~HEAD
deleted file mode 100644
index 183f60b..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java~HEAD
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.apache.airavata.gfac.core.cluster;/*
- *
- * 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.
- *
- */
-
-/**
- * Encapsulate server information.
- */
-public class ServerInfo {
-
-    private String host;
-    private String userName;
-    private int port = 22;
-
-    public ServerInfo(String userName, String host) {
-        this.userName = userName;
-        this.host = host;
-    }
-
-    public ServerInfo(String userName,String host,  int port) {
-        this.host = host;
-        this.userName = userName;
-        this.port = port;
-    }
-
-    public String getHost() {
-        return host;
-    }
-
-    public void setHost(String host) {
-        this.host = host;
-    }
-
-    public String getUserName() {
-        return userName;
-    }
-
-    public void setUserName(String userName) {
-        this.userName = userName;
-    }
-
-    public int getPort() {
-        return port;
-    }
-
-    public void setPort(int port) {
-        this.port = port;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/AbstractSecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/AbstractSecurityContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/AbstractSecurityContext.java
new file mode 100644
index 0000000..38d11ee
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/AbstractSecurityContext.java
@@ -0,0 +1,59 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.gfac.core.context;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 6/26/13
+ * Time: 4:33 PM
+ */
+
+import java.io.Serializable;
+
+import org.apache.airavata.credential.store.store.CredentialReader;
+import org.apache.airavata.gfac.core.RequestData;
+import org.apache.airavata.gfac.core.SecurityContext;
+
+/**
+ * Abstract implementation of the security context.
+ */
+public abstract class AbstractSecurityContext implements SecurityContext, Serializable {
+
+    private CredentialReader credentialReader;
+    private RequestData requestData;
+
+    public AbstractSecurityContext(CredentialReader credentialReader, RequestData requestData) {
+        this.credentialReader = credentialReader;
+        this.requestData = requestData;
+    }
+    public AbstractSecurityContext() {
+
+    }
+
+    public CredentialReader getCredentialReader() {
+        return credentialReader;
+    }
+
+    public RequestData getRequestData() {
+        return requestData;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/de848787/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
index dcdb3b0..85216b4 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsissh/security/GSISecurityContext.java
@@ -21,7 +21,7 @@
 package org.apache.airavata.gfac.gsissh.security;
 
 import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.core.AbstractSecurityContext;
+import org.apache.airavata.gfac.core.context.AbstractSecurityContext;
 import org.apache.airavata.gfac.core.RequestData;
 import org.apache.airavata.gfac.core.cluster.RemoteCluster;
 import org.slf4j.Logger;


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