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From shame...@apache.org
Subject [47/81] [abbrv] airavata git commit: Resolve compilation issues in gfac module after module refactoring
Date Thu, 04 Jun 2015 20:16:00 GMT
Resolve compilation issues in gfac module after module refactoring


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/19afc7e0
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/19afc7e0
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/19afc7e0

Branch: refs/heads/master
Commit: 19afc7e0d90502f592f1c73aafbf17ae3f4648a1
Parents: 7b80974
Author: Shameera Rathanyaka <shameerainfo@gmail.com>
Authored: Wed Jun 3 17:24:47 2015 -0400
Committer: Shameera Rathanyaka <shameerainfo@gmail.com>
Committed: Wed Jun 3 17:24:47 2015 -0400

----------------------------------------------------------------------
 modules/distribution/gfac-server/pom.xml        |   33 +-
 modules/distribution/server/pom.xml             |   55 +-
 .../gfac-application-specific-handlers/pom.xml  |    4 +-
 modules/gfac/gfac-bes/pom.xml                   |    4 +-
 modules/gfac/gfac-client/pom.xml                |    2 +-
 modules/gfac/gfac-core/pom.xml                  |   30 +-
 .../apache/airavata/gfac/core/GFacUtils.java    |   39 +
 .../airavata/gfac/core/JobDescriptor.java       |  475 ++
 .../gfac/core/JobManagerConfiguration.java      |   52 +
 .../airavata/gfac/core/SSHApiException.java     |   36 +
 .../airavata/gfac/core/cluster/Cluster.java     |  161 +
 .../airavata/gfac/core/cluster/CommandInfo.java |   34 +
 .../gfac/core/cluster/CommandOutput.java        |   49 +
 .../airavata/gfac/core/cluster/JobStatus.java   |  110 +
 .../gfac/core/cluster/OutputParser.java         |   67 +
 .../gfac/core/cluster/RawCommandInfo.java       |   53 +
 .../airavata/gfac/core/cluster/ServerInfo.java  |   65 +
 .../gfac/core/handler/AbstractHandler.java      |    1 -
 .../gfac/core/x2012/x12/AfterAnyList.java       |  166 +
 .../gfac/core/x2012/x12/AfterOKList.java        |  166 +
 .../gfac/core/x2012/x12/ExportProperties.java   |  183 +
 .../airavata/gfac/core/x2012/x12/InputList.java |  166 +
 .../core/x2012/x12/JobDescriptorDocument.java   |  112 +
 .../gfac/core/x2012/x12/ModuleLoadCommands.java |  166 +
 .../airavata/gfac/core/x2012/x12/PbsParams.java | 1421 ++++++
 .../gfac/core/x2012/x12/PostJobCommands.java    |  166 +
 .../gfac/core/x2012/x12/PreJobCommands.java     |  166 +
 .../core/x2012/x12/impl/AfterAnyListImpl.java   |  235 +
 .../core/x2012/x12/impl/AfterOKListImpl.java    |  235 +
 .../x2012/x12/impl/ExportPropertiesImpl.java    |  233 +
 .../gfac/core/x2012/x12/impl/InputListImpl.java |  235 +
 .../x12/impl/JobDescriptorDocumentImpl.java     |   77 +
 .../x2012/x12/impl/ModuleLoadCommandsImpl.java  |  235 +
 .../gfac/core/x2012/x12/impl/PbsParamsImpl.java | 4174 ++++++++++++++++++
 .../x2012/x12/impl/PostJobCommandsImpl.java     |  235 +
 .../core/x2012/x12/impl/PreJobCommandsImpl.java |  235 +
 .../src/main/resources/PBSJobDescriptor.xsd     |  114 +
 .../src/main/resources/gsissh-schemas.xsdconfig |   14 +
 modules/gfac/gfac-impl/pom.xml                  |   32 +-
 .../java/com/jcraft/jsch/ExtendedSession.java   |   42 +
 .../com/jcraft/jsch/GSISSHIdentityFile.java     |  126 +
 .../jcraft/jsch/GSISSHIdentityRepository.java   |   29 +
 .../UserAuthGSSAPIWithMICGSSCredentials.java    |  308 ++
 .../airavata/gfac/gsi/ssh/GSSContextX509.java   |    2 +-
 .../airavata/gfac/gsi/ssh/api/Cluster.java      |  162 -
 .../gfac/gsi/ssh/api/CommandExecutor.java       |   33 +-
 .../airavata/gfac/gsi/ssh/api/CommandInfo.java  |   34 -
 .../gfac/gsi/ssh/api/CommandOutput.java         |   49 -
 .../apache/airavata/gfac/gsi/ssh/api/Core.java  |    4 +-
 .../apache/airavata/gfac/gsi/ssh/api/Node.java  |    2 +-
 .../gfac/gsi/ssh/api/SSHApiException.java       |   36 -
 .../airavata/gfac/gsi/ssh/api/ServerInfo.java   |   65 -
 .../gfac/gsi/ssh/api/job/JobDescriptor.java     |  473 --
 .../ssh/api/job/JobManagerConfiguration.java    |   51 -
 .../airavata/gfac/gsi/ssh/api/job/JobType.java  |   32 -
 .../gsi/ssh/api/job/LSFJobConfiguration.java    |    6 +-
 .../gfac/gsi/ssh/api/job/LSFOutputParser.java   |    8 +-
 .../gfac/gsi/ssh/api/job/OutputParser.java      |   67 -
 .../gsi/ssh/api/job/PBSJobConfiguration.java    |    6 +-
 .../gfac/gsi/ssh/api/job/PBSOutputParser.java   |    8 +-
 .../gsi/ssh/api/job/SlurmJobConfiguration.java  |    8 +-
 .../gfac/gsi/ssh/api/job/SlurmOutputParser.java |    8 +-
 .../gsi/ssh/api/job/UGEJobConfiguration.java    |    6 +-
 .../gfac/gsi/ssh/api/job/UGEOutputParser.java   |   10 +-
 .../gfac/gsi/ssh/config/ConfigReader.java       |    2 +-
 .../ssh/impl/DefaultJobSubmissionListener.java  |    9 +-
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     |   80 +-
 .../airavata/gfac/gsi/ssh/impl/JobStatus.java   |  110 -
 .../airavata/gfac/gsi/ssh/impl/PBSCluster.java  |    9 +-
 .../gfac/gsi/ssh/impl/RawCommandInfo.java       |   55 -
 .../airavata/gfac/gsi/ssh/impl/SSHUserInfo.java |    2 +-
 .../gfac/gsi/ssh/impl/StandardOutReader.java    |    4 +-
 .../gfac/gsi/ssh/impl/SystemCommandOutput.java  |    4 +-
 .../DefaultPasswordAuthenticationInfo.java      |    2 +-
 .../DefaultPublicKeyAuthentication.java         |    2 +-
 .../DefaultPublicKeyFileAuthentication.java     |    2 +-
 .../MyProxyAuthenticationInfo.java              |    2 +-
 .../gfac/gsi/ssh/jsch/ExtendedJSch.java         |    2 +-
 .../gsi/ssh/listener/JobSubmissionListener.java |    8 +-
 .../airavata/gfac/gsi/ssh/util/CommonUtils.java |    8 +-
 .../ssh/util/SSHAPIUIKeyboardInteractive.java   |    2 +-
 .../gsi/ssh/util/SSHKeyPasswordHandler.java     |    2 +-
 .../airavata/gfac/gsi/ssh/util/SSHUtils.java    |   61 +-
 .../handler/GSISSHDirectorySetupHandler.java    |    2 +-
 .../gfac/gsissh/handler/GSISSHInputHandler.java |    2 +-
 .../gsissh/handler/GSISSHOutputHandler.java     |    2 +-
 .../gsissh/handler/NewGSISSHOutputHandler.java  |    2 +-
 .../gsissh/provider/impl/GSISSHProvider.java    |    8 +-
 .../gsissh/security/GSISecurityContext.java     |    9 +-
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |   14 +-
 .../gfac/local/provider/impl/LocalProvider.java |    2 -
 .../airavata/gfac/monitor/HPCMonitorID.java     |    6 +-
 .../handlers/GridPullMonitorHandler.java        |    4 +-
 .../handlers/GridPushMonitorHandler.java        |    4 +-
 .../monitor/impl/pull/qstat/HPCPullMonitor.java |    6 +-
 .../impl/pull/qstat/ResourceConnection.java     |    8 +-
 .../impl/push/amqp/ComputingActivity.java       |   19 +
 .../impl/push/amqp/JSONMessageParser.java       |    1 -
 .../gfac/ssh/context/SSHAuthWrapper.java        |    2 +-
 .../ssh/handler/AdvancedSCPInputHandler.java    |    8 +-
 .../ssh/handler/AdvancedSCPOutputHandler.java   |    8 +-
 .../gfac/ssh/handler/NewSSHOutputHandler.java   |    2 +-
 .../ssh/handler/SSHDirectorySetupHandler.java   |    2 +-
 .../gfac/ssh/handler/SSHInputHandler.java       |    2 +-
 .../gfac/ssh/handler/SSHOutputHandler.java      |    2 +-
 .../gfac/ssh/provider/impl/SSHProvider.java     |   16 +-
 .../gfac/ssh/security/SSHSecurityContext.java   |    2 +-
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |   15 +-
 .../airavata/gfac/ssh/util/HandleOutputs.java   |    2 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |    1 +
 modules/gfac/gfac-service/pom.xml               |   11 +-
 .../airavata/gfac/server/GfacServerHandler.java |    4 +-
 modules/orchestrator/orchestrator-core/pom.xml  |   22 +-
 modules/workflow-model/workflow-engine/pom.xml  |    4 +-
 modules/xbaya-gui/pom.xml                       |    7 +-
 115 files changed, 10720 insertions(+), 1456 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/distribution/gfac-server/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/gfac-server/pom.xml b/modules/distribution/gfac-server/pom.xml
index 2496ae7..6e80212 100644
--- a/modules/distribution/gfac-server/pom.xml
+++ b/modules/distribution/gfac-server/pom.xml
@@ -133,49 +133,24 @@
 			<artifactId>airavata-standalone-server</artifactId>
 			<version>${project.version}</version>
 	   </dependency>
-      <!--<dependency>-->
-            <!--<groupId>org.apache.airavata</groupId>-->
-            <!--<artifactId>airavata-gfac-gram</artifactId>-->
-            <!--<version>${project.version}</version>-->
-        <!--</dependency>-->
-        <!--<dependency>-->
-            <!--<groupId>org.apache.airavata</groupId>-->
-            <!--<artifactId>airavata-gfac-bes</artifactId>-->
-            <!--<version>${project.version}</version>-->
-        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-gsissh</artifactId>
+            <artifactId>gfac-impl</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-hpc-monitor</artifactId>
+            <artifactId>gfac-core</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-local</artifactId>
+            <artifactId>gfac-service</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <!--<dependency>-->
-            <!--<groupId>org.apache.airavata</groupId>-->
-            <!--<artifactId>airavata-gfac-hadoop</artifactId>-->
-            <!--<version>${project.version}</version>-->
-        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-service</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-application-specific-handlers</artifactId>
+            <artifactId>gfac-application-specific-handlers</artifactId>
             <version>${project.version}</version>
         </dependency>
     </dependencies>

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/distribution/server/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/server/pom.xml b/modules/distribution/server/pom.xml
index fc2df04..cf8a73c 100644
--- a/modules/distribution/server/pom.xml
+++ b/modules/distribution/server/pom.xml
@@ -268,7 +268,7 @@
 		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-stubs</artifactId>
+			<artifactId>gfac-client</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>
@@ -298,47 +298,22 @@
 		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-ssh</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-		<!--<dependency> -->
-		<!--<groupId>org.apache.airavata</groupId> -->
-		<!--<artifactId>airavata-gfac-gram</artifactId> -->
-		<!--<version>${project.version}</version> -->
-		<!--</dependency> -->
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-bes</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-gsissh</artifactId>
+			<artifactId>gfac-impl</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-hpc-monitor</artifactId>
+			<artifactId>gfac-bes</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-local</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-		<!--<dependency> -->
-		<!--<groupId>org.apache.airavata</groupId> -->
-		<!--<artifactId>airavata-gfac-hadoop</artifactId> -->
-		<!--<version>${project.version}</version> -->
-		<!--</dependency> -->
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-core</artifactId>
+			<artifactId>gfac-core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-service</artifactId>
+			<artifactId>gfac-service</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<!--<dependency> -->
@@ -351,26 +326,6 @@
 			<artifactId>airavata-workflow-model-core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
-		<!--<dependency> -->
-		<!--<groupId>org.apache.airavata</groupId> -->
-		<!--<artifactId>airavata-messenger-commons</artifactId> -->
-		<!--<version>${project.version}</version> -->
-		<!--</dependency> -->
-		<!--<dependency> -->
-		<!--<groupId>org.apache.airavata</groupId> -->
-		<!--<artifactId>airavata-messenger-client</artifactId> -->
-		<!--<version>${project.version}</version> -->
-		<!--</dependency> -->
-		<!--<dependency> -->
-		<!--<groupId>org.apache.airavata</groupId> -->
-		<!--<artifactId>airavata-workflow-tracking</artifactId> -->
-		<!--<version>${project.version}</version> -->
-		<!--</dependency> -->
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>gsissh</artifactId>
-			<version>${project.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
 			<artifactId>airavata-model-utils</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-application-specific-handlers/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-application-specific-handlers/pom.xml b/modules/gfac/gfac-application-specific-handlers/pom.xml
index 801313d..638c81f 100644
--- a/modules/gfac/gfac-application-specific-handlers/pom.xml
+++ b/modules/gfac/gfac-application-specific-handlers/pom.xml
@@ -7,11 +7,11 @@
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
-    <artifactId>airavata-gfac-application-specific-handlers</artifactId>
+    <artifactId>gfac-application-specific-handlers</artifactId>
     <dependencies>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
+            <artifactId>gfac-core</artifactId>
             <version>${project.version}</version>
         </dependency>
     </dependencies>

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-bes/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/pom.xml b/modules/gfac/gfac-bes/pom.xml
index 7335d53..4e61ae0 100644
--- a/modules/gfac/gfac-bes/pom.xml
+++ b/modules/gfac/gfac-bes/pom.xml
@@ -20,7 +20,7 @@
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>
-	<artifactId>airavata-gfac-bes</artifactId>
+	<artifactId>gfac-bes</artifactId>
 	<name>Airavata GFac BES implementation</name>
 	<description>This is the extension of GFAC to use GRAM </description>
 	<url>http://airavata.apache.org/</url>
@@ -36,7 +36,7 @@
 		<!-- GFAC schemas -->
 		<dependency>
 			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-core</artifactId>
+			<artifactId>gfac-core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<!-- Credential Store -->

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-client/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-client/pom.xml b/modules/gfac/gfac-client/pom.xml
index f94d85b..20423e0 100644
--- a/modules/gfac/gfac-client/pom.xml
+++ b/modules/gfac/gfac-client/pom.xml
@@ -20,7 +20,7 @@
     </parent>
 
     <name>Airavata Gfac Client SDK</name>
-    <artifactId>airavata-gfac-stubs</artifactId>
+    <artifactId>gfac-client</artifactId>
     <packaging>jar</packaging>
     <url>http://airavata.apache.org/</url>
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/pom.xml b/modules/gfac/gfac-core/pom.xml
index 2169734..0203865 100644
--- a/modules/gfac/gfac-core/pom.xml
+++ b/modules/gfac/gfac-core/pom.xml
@@ -17,7 +17,7 @@
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
-    <artifactId>airavata-gfac-core</artifactId>
+    <artifactId>gfac-core</artifactId>
     <name>Airavata GFac Core</name>
     <description>The core GFAC functionality independent from any webservice implementation.</description>
     <url>http://airavata.apache.org/</url>
@@ -50,6 +50,11 @@
             <artifactId>airavata-jpa-registry</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.xmlbeans</groupId>
+            <artifactId>xmlbeans</artifactId>
+            <version>${xmlbeans.version}</version>
+        </dependency>
         <!-- Credential Store -->
         <dependency>
             <groupId>org.apache.airavata</groupId>
@@ -112,6 +117,7 @@
             <groupId>org.apache.xmlbeans</groupId>
             <artifactId>xmlbeans</artifactId>
             <version>${xmlbeans.version}</version>
+            <scope>compile</scope>
         </dependency>
         <!-- this is the dependency for amqp implementation -->
         <!-- zookeeper dependencies -->
@@ -125,6 +131,28 @@
     <build>
         <plugins>
             <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>xmlbeans-maven-plugin</artifactId>
+                <version>2.3.3</version>
+                <executions>
+                    <execution>
+                        <phase>generate-sources</phase>
+                        <goals>
+                            <goal>xmlbeans</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <inherited>true</inherited>
+                <configuration>
+                    <schemaDirectory>src/main/resources</schemaDirectory>
+                    <xmlConfigs>
+                        <xmlConfig implementation="java.io.File">src/main/resources/gsissh-schemas.xsdconfig </xmlConfig>
+                    </xmlConfigs>
+                    <sourceGenerationDirectory>src/main/java</sourceGenerationDirectory>
+                    <outputJar>target/generated/${project.artifactId}-${project.version}.jar</outputJar>
+                </configuration>
+            </plugin>
+            <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
                 <configuration>

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
index 407db94..b716099 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
@@ -139,6 +139,45 @@ public class GFacUtils {
 	}
 
 	/**
+	 * This returns true if the give job is finished
+	 * otherwise false
+	 *
+	 * @param job
+	 * @return
+	 */
+	public static boolean isJobFinished(JobDescriptor job) {
+		if (org.apache.airavata.gfac.core.cluster.JobStatus.C.toString().equals(job.getStatus())) {
+			return true;
+		} else {
+			return false;
+		}
+	}
+
+	/**
+	 * This will read
+	 *
+	 * @param maxWalltime
+	 * @return
+	 */
+	public static String maxWallTimeCalculator(int maxWalltime) {
+		if (maxWalltime < 60) {
+			return "00:" + maxWalltime + ":00";
+		} else {
+			int minutes = maxWalltime % 60;
+			int hours = maxWalltime / 60;
+			return hours + ":" + minutes + ":00";
+		}
+	}
+	public static String maxWallTimeCalculatorForLSF(int maxWalltime) {
+		if (maxWalltime < 60) {
+			return "00:" + maxWalltime;
+		} else {
+			int minutes = maxWalltime % 60;
+			int hours = maxWalltime / 60;
+			return hours + ":" + minutes;
+		}
+	}
+	/**
 	 * this can be used to do framework opertaions specific to different modes
 	 * 
 	 * @param jobExecutionContext

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java
new file mode 100644
index 0000000..678f41f
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobDescriptor.java
@@ -0,0 +1,475 @@
+/*
+ *
+ * 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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java
new file mode 100644
index 0000000..661aba0
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/JobManagerConfiguration.java
@@ -0,0 +1,52 @@
+/*
+ *
+ * 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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/SSHApiException.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/SSHApiException.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/SSHApiException.java
new file mode 100644
index 0000000..a2db122
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/SSHApiException.java
@@ -0,0 +1,36 @@
+/*
+ *
+ * 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;
+
+/**
+ * An exception class to wrap SSH command execution related errors.
+ */
+public class SSHApiException extends Exception {
+
+    public SSHApiException(String message) {
+        super(message);
+    }
+
+    public SSHApiException(String message, Exception e) {
+        super(message, e);
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/Cluster.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/Cluster.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/Cluster.java
new file mode 100644
index 0000000..b116bdc
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/Cluster.java
@@ -0,0 +1,161 @@
+/*
+ *
+ * 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.cluster;
+
+import com.jcraft.jsch.Session;
+import org.apache.airavata.gfac.core.JobDescriptor;
+import org.apache.airavata.gfac.core.SSHApiException;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * This interface represents a Cluster machine
+ * End users of the API can implement this and come up with their own
+ * implementations, but mostly this interface is for internal usage.
+ */
+public interface Cluster {
+
+    /**
+     * This will submit a job to the cluster with a given pbs file and some parameters
+     *
+     * @param pbsFilePath  path of the pbs file
+     * @param workingDirectory working directory where pbs should has to copy
+     * @return jobId after successful job submission
+     * @throws SSHApiException throws exception during error
+     */
+    public String submitBatchJobWithScript(String pbsFilePath, String workingDirectory) throws SSHApiException;
+
+    /**
+     * This will submit the given job and not performing any monitoring
+     *
+     * @param jobDescriptor  job descriptor to submit to cluster, this contains all the parameter
+     * @return jobID after successful job submission.
+     * @throws SSHApiException  throws exception during error
+     */
+    public String submitBatchJob(JobDescriptor jobDescriptor) throws SSHApiException;
+
+    /**
+     * This will copy the localFile to remoteFile location in configured cluster
+     *
+     * @param remoteFile remote file location, this can be a directory too
+     * @param localFile local file path of the file which needs to copy to remote location
+     * @throws SSHApiException throws exception during error
+     */
+    public void scpTo(String remoteFile, String localFile) throws SSHApiException;
+
+    /**
+     * This will copy a remote file in path rFile to local file lFile
+     * @param remoteFile remote file path, this has to be a full qualified path
+     * @param localFile This is the local file to copy, this can be a directory too
+     * @throws SSHApiException
+     */
+    public void scpFrom(String remoteFile, String localFile) throws SSHApiException;
+
+    /**
+     * This will copy a remote file in path rFile to local file lFile
+     * @param remoteFile remote file path, this has to be a full qualified path
+     * @param localFile This is the local file to copy, this can be a directory too
+     * @throws SSHApiException
+     */
+    public void scpThirdParty(String remoteFileSorce, String remoteFileTarget) throws SSHApiException;
+    
+    /**
+     * This will create directories in computing resources
+     * @param directoryPath the full qualified path for the directory user wants to create
+     * @throws SSHApiException throws during error
+     */
+    public void makeDirectory(String directoryPath) throws SSHApiException;
+
+
+    /**
+     * This will get the job description of a job which is there in the cluster
+     * if jbo is not available with the given ID it returns
+     * @param jobID jobId has to pass
+     * @return Returns full job description of the job which submitted successfully
+     * @throws SSHApiException throws exception during error
+     */
+    public JobDescriptor getJobDescriptorById(String jobID) throws SSHApiException;
+
+    /**
+     * This will delete the given job from the queue
+     *
+     * @param jobID  jobId of the job which user wants to delete
+     * @return return the description of the deleted job
+     * @throws SSHApiException throws exception during error
+     */
+    public JobDescriptor cancelJob(String jobID) throws SSHApiException;
+
+    /**
+     * This will get the job status of the the job associated with this jobId
+     *
+     * @param jobID jobId of the job user want to get the status
+     * @return job status of the given jobID
+     * @throws SSHApiException throws exception during error
+     */
+    public JobStatus getJobStatus(String jobID) throws SSHApiException;
+    /**
+     * This will get the job status of the the job associated with this jobId
+     *
+     * @param jobName jobName of the job user want to get the status
+     * @return jobId of the given jobName
+     * @throws SSHApiException throws exception during error
+     */
+    public String getJobIdByJobName(String jobName, String userName) throws SSHApiException;
+
+    /**
+     * This method can be used to poll the jobstatuses based on the given
+     * user but we should pass the jobID list otherwise we will get unwanted
+     * job statuses which submitted by different middleware outside apache
+     * airavata with the same uername which we are not considering
+     * @param userName userName of the jobs which required to get the status
+     * @param jobIDs precises set of jobIDs
+     * @return
+     */
+    public void getJobStatuses(String userName,Map<String,JobStatus> jobIDs)throws SSHApiException;
+    /**
+     * This will list directories in computing resources
+     * @param directoryPath the full qualified path for the directory user wants to create
+     * @throws SSHApiException throws during error
+     */
+    public List<String> listDirectory(String directoryPath) throws SSHApiException;
+
+    /**
+     * This method can be used to get created ssh session
+     * to reuse the created session.
+     * @throws SSHApiException
+     */
+    public Session getSession() throws SSHApiException;
+    
+    /**
+     * This method can be used to close the connections initialized
+     * to handle graceful shutdown of the system
+     * @throws SSHApiException
+     */
+    public void disconnect() throws SSHApiException;
+
+    /**
+     * This gives the server Info
+     * @return
+     */
+    public ServerInfo getServerInfo();
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java
new file mode 100644
index 0000000..18e3e4e
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandInfo.java
@@ -0,0 +1,34 @@
+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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java
new file mode 100644
index 0000000..e50d25a
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/CommandOutput.java
@@ -0,0 +1,49 @@
+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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/JobStatus.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/JobStatus.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/JobStatus.java
new file mode 100644
index 0000000..6e8e144
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/JobStatus.java
@@ -0,0 +1,110 @@
+ /*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+ package org.apache.airavata.gfac.core.cluster;
+
+ /**
+  * This will contains all the PBS specific job statuses.
+  * C -  Job is completed after having run/
+  * E -  Job is exiting after having run.
+  * H -  Job is held.
+  * Q -  job is queued, eligible to run or routed.
+  * R -  job is running.
+  * T -  job is being moved to new location.
+  * W -  job is waiting for its execution time
+  * (-a option) to be reached.
+  * S -  (Unicos only) job is suspend.
+  */
+ public enum JobStatus {
+     C, E, H, Q, R, T, W, S,U,F,CA,CD,CF,CG,NF,PD,PR,TO,qw,t,r,h,Er,Eqw,PEND,RUN,PSUSP,USUSP,SSUSP,DONE,EXIT,UNKWN,ZOMBI;
+
+     public static JobStatus fromString(String status){
+        if(status != null){
+            if("C".equals(status)){
+                return JobStatus.C;
+            }else if("E".equals(status)){
+                return JobStatus.E;
+            }else if("H".equals(status)){
+                return JobStatus.H;
+            }else if("Q".equals(status)){
+                return JobStatus.Q;
+            }else if("R".equals(status)){
+                return JobStatus.R;
+            }else if("T".equals(status)){
+                return JobStatus.T;
+            }else if("W".equals(status)){
+                return JobStatus.W;
+            }else if("S".equals(status)){
+                return JobStatus.S;
+            }else if("F".equals(status)){
+                return JobStatus.F;
+            }else if("S".equals(status)){
+                return JobStatus.S;
+            }else if("CA".equals(status)){
+                return JobStatus.CA;
+            }else if("CF".equals(status)){
+                return JobStatus.CF;
+            }else if("CD".equals(status)){
+                return JobStatus.CD;
+            }else if("CG".equals(status)){
+                return JobStatus.CG;
+            }else if("NF".equals(status)){
+                return JobStatus.NF;
+            }else if("PD".equals(status)){
+                return JobStatus.PD;
+            }else if("PR".equals(status)){
+                return JobStatus.PR;
+            }else if("TO".equals(status)){
+                return JobStatus.TO;
+            }else if("U".equals(status)){
+                return JobStatus.U;
+            }else if("qw".equals(status)){
+                return JobStatus.qw;
+            }else if("t".equals(status)){
+                return JobStatus.t;
+            }else if("r".equals(status)){
+                return JobStatus.r;
+            }else if("h".equals(status)){
+                return JobStatus.h;
+            }else if("Er".equals(status)){
+                return JobStatus.Er;
+            }else if("Eqw".equals(status)){
+                return JobStatus.Er;
+            }else if("RUN".equals(status)){      // LSF starts here
+                return JobStatus.RUN;
+            }else if("PEND".equals(status)){
+                return JobStatus.PEND;
+            }else if("DONE".equals(status)){
+                return JobStatus.DONE;
+            }else if("PSUSP".equals(status)){
+                return JobStatus.PSUSP;
+            }else if("USUSP".equals(status)){
+                return JobStatus.USUSP;
+            }else if("SSUSP".equals(status)){
+                return JobStatus.SSUSP;
+            }else if("EXIT".equals(status)){
+                return JobStatus.EXIT;
+            }else if("ZOMBI".equals(status)){
+                return JobStatus.ZOMBI;
+            }
+        }
+         return JobStatus.U;
+     }
+ }

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/OutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/OutputParser.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/OutputParser.java
new file mode 100644
index 0000000..658a5bc
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/OutputParser.java
@@ -0,0 +1,67 @@
+/*
+ *
+ * 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.cluster;
+
+import org.apache.airavata.gfac.core.JobDescriptor;
+import org.apache.airavata.gfac.core.SSHApiException;
+
+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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/RawCommandInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/RawCommandInfo.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/RawCommandInfo.java
new file mode 100644
index 0000000..80f5d0a
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/RawCommandInfo.java
@@ -0,0 +1,53 @@
+/*
+ *
+ * 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.cluster;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 8/14/13
+ * Time: 5:18 PM
+ */
+
+/**
+ * The raw command information. String returned by getCommand is directly executed in SSH
+ * shell. E.g :- getCommand return string set for rawCommand - "/opt/torque/bin/qsub /home/ogce/test.pbs".
+ */
+public class RawCommandInfo implements CommandInfo {
+
+    private String rawCommand;
+
+    public RawCommandInfo(String cmd) {
+        this.rawCommand = cmd;
+    }
+
+    public String getCommand() {
+        return this.rawCommand;
+    }
+
+    public String getRawCommand() {
+        return rawCommand;
+    }
+
+    public void setRawCommand(String rawCommand) {
+        this.rawCommand = rawCommand;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java
new file mode 100644
index 0000000..183f60b
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/ServerInfo.java
@@ -0,0 +1,65 @@
+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/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/handler/AbstractHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/handler/AbstractHandler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/handler/AbstractHandler.java
index aa98ef6..8d2609a 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/handler/AbstractHandler.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/handler/AbstractHandler.java
@@ -22,7 +22,6 @@ package org.apache.airavata.gfac.core.handler;
 
 import org.apache.airavata.common.utils.MonitorPublisher;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
 import org.apache.airavata.gfac.core.states.GfacHandlerState;
 import org.apache.airavata.gfac.core.GFacUtils;
 import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;

http://git-wip-us.apache.org/repos/asf/airavata/blob/19afc7e0/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/x2012/x12/AfterAnyList.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/x2012/x12/AfterAnyList.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/x2012/x12/AfterAnyList.java
new file mode 100644
index 0000000..e552eb7
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/x2012/x12/AfterAnyList.java
@@ -0,0 +1,166 @@
+/*
+ * XML Type:  afterAnyList
+ * Namespace: http://airavata.apache.org/gfac/core/2012/12
+ * Java type: org.apache.airavata.gfac.core.x2012.x12.AfterAnyList
+ *
+ * Automatically generated - do not modify.
+ */
+package org.apache.airavata.gfac.core.x2012.x12;
+
+
+/**
+ * An XML afterAnyList(@http://airavata.apache.org/gfac/core/2012/12).
+ *
+ * This is a complex type.
+ */
+public interface AfterAnyList extends org.apache.xmlbeans.XmlObject
+{
+    public static final org.apache.xmlbeans.SchemaType type = (org.apache.xmlbeans.SchemaType)
+        org.apache.xmlbeans.XmlBeans.typeSystemForClassLoader(AfterAnyList.class.getClassLoader(), "schemaorg_apache_xmlbeans.system.sCF8C40CE6FDA0A41BEE004F5930560FF").resolveHandle("afteranylisteefatype");
+    
+    /**
+     * Gets array of all "afterAny" elements
+     */
+    java.lang.String[] getAfterAnyArray();
+    
+    /**
+     * Gets ith "afterAny" element
+     */
+    java.lang.String getAfterAnyArray(int i);
+    
+    /**
+     * Gets (as xml) array of all "afterAny" elements
+     */
+    org.apache.xmlbeans.XmlString[] xgetAfterAnyArray();
+    
+    /**
+     * Gets (as xml) ith "afterAny" element
+     */
+    org.apache.xmlbeans.XmlString xgetAfterAnyArray(int i);
+    
+    /**
+     * Returns number of "afterAny" element
+     */
+    int sizeOfAfterAnyArray();
+    
+    /**
+     * Sets array of all "afterAny" element
+     */
+    void setAfterAnyArray(java.lang.String[] afterAnyArray);
+    
+    /**
+     * Sets ith "afterAny" element
+     */
+    void setAfterAnyArray(int i, java.lang.String afterAny);
+    
+    /**
+     * Sets (as xml) array of all "afterAny" element
+     */
+    void xsetAfterAnyArray(org.apache.xmlbeans.XmlString[] afterAnyArray);
+    
+    /**
+     * Sets (as xml) ith "afterAny" element
+     */
+    void xsetAfterAnyArray(int i, org.apache.xmlbeans.XmlString afterAny);
+    
+    /**
+     * Inserts the value as the ith "afterAny" element
+     */
+    void insertAfterAny(int i, java.lang.String afterAny);
+    
+    /**
+     * Appends the value as the last "afterAny" element
+     */
+    void addAfterAny(java.lang.String afterAny);
+    
+    /**
+     * Inserts and returns a new empty value (as xml) as the ith "afterAny" element
+     */
+    org.apache.xmlbeans.XmlString insertNewAfterAny(int i);
+    
+    /**
+     * Appends and returns a new empty value (as xml) as the last "afterAny" element
+     */
+    org.apache.xmlbeans.XmlString addNewAfterAny();
+    
+    /**
+     * Removes the ith "afterAny" element
+     */
+    void removeAfterAny(int i);
+    
+    /**
+     * A factory class with static methods for creating instances
+     * of this type.
+     */
+    
+    public static final class Factory
+    {
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList newInstance() {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().newInstance( type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList newInstance(org.apache.xmlbeans.XmlOptions options) {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().newInstance( type, options ); }
+        
+        /** @param xmlAsString the string value to parse */
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.lang.String xmlAsString) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( xmlAsString, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.lang.String xmlAsString, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( xmlAsString, type, options ); }
+        
+        /** @param file the file from which to load an xml document */
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.File file) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( file, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.File file, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( file, type, options ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.net.URL u) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( u, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.net.URL u, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( u, type, options ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.InputStream is) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( is, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.InputStream is, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( is, type, options ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.Reader r) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( r, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(java.io.Reader r, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, java.io.IOException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( r, type, options ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(javax.xml.stream.XMLStreamReader sr) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( sr, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(javax.xml.stream.XMLStreamReader sr, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( sr, type, options ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(org.w3c.dom.Node node) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( node, type, null ); }
+        
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(org.w3c.dom.Node node, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( node, type, options ); }
+        
+        /** @deprecated {@link org.apache.xmlbeans.xml.stream.XMLInputStream} */
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(org.apache.xmlbeans.xml.stream.XMLInputStream xis) throws org.apache.xmlbeans.XmlException, org.apache.xmlbeans.xml.stream.XMLStreamException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( xis, type, null ); }
+        
+        /** @deprecated {@link org.apache.xmlbeans.xml.stream.XMLInputStream} */
+        public static org.apache.airavata.gfac.core.x2012.x12.AfterAnyList parse(org.apache.xmlbeans.xml.stream.XMLInputStream xis, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, org.apache.xmlbeans.xml.stream.XMLStreamException {
+          return (org.apache.airavata.gfac.core.x2012.x12.AfterAnyList) org.apache.xmlbeans.XmlBeans.getContextTypeLoader().parse( xis, type, options ); }
+        
+        /** @deprecated {@link org.apache.xmlbeans.xml.stream.XMLInputStream} */
+        public static org.apache.xmlbeans.xml.stream.XMLInputStream newValidatingXMLInputStream(org.apache.xmlbeans.xml.stream.XMLInputStream xis) throws org.apache.xmlbeans.XmlException, org.apache.xmlbeans.xml.stream.XMLStreamException {
+          return org.apache.xmlbeans.XmlBeans.getContextTypeLoader().newValidatingXMLInputStream( xis, type, null ); }
+        
+        /** @deprecated {@link org.apache.xmlbeans.xml.stream.XMLInputStream} */
+        public static org.apache.xmlbeans.xml.stream.XMLInputStream newValidatingXMLInputStream(org.apache.xmlbeans.xml.stream.XMLInputStream xis, org.apache.xmlbeans.XmlOptions options) throws org.apache.xmlbeans.XmlException, org.apache.xmlbeans.xml.stream.XMLStreamException {
+          return org.apache.xmlbeans.XmlBeans.getContextTypeLoader().newValidatingXMLInputStream( xis, type, options ); }
+        
+        private Factory() { } // No instance of this class allowed
+    }
+}


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