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From chath...@apache.org
Subject airavata git commit: removing gfac-schema from pom
Date Thu, 13 Nov 2014 22:00:42 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 7a352c462 -> a0afbd8b5


removing gfac-schema from pom


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/a0afbd8b
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/a0afbd8b
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/a0afbd8b

Branch: refs/heads/master
Commit: a0afbd8b51cd756d838b4b93323a7506d970beb4
Parents: 7a352c4
Author: Chathuri Wimalasena <kamalasini@gmail.com>
Authored: Thu Nov 13 17:00:18 2014 -0500
Committer: Chathuri Wimalasena <kamalasini@gmail.com>
Committed: Thu Nov 13 17:00:18 2014 -0500

----------------------------------------------------------------------
 modules/distribution/client/java/pom.xml        |  10 +-
 .../java/src/main/assembly/bin-assembly.xml     |   4 +-
 modules/distribution/gfac-server/pom.xml        |  10 +-
 .../src/main/assembly/bin-assembly.xml          |   4 +-
 modules/distribution/server/pom.xml             |  10 +-
 .../server/src/main/assembly/bin-assembly.xml   |   4 +-
 .../org/apache/airavata/gfac/Scheduler.java     |  11 +-
 .../airavata/gfac/core/utils/GFacUtils.java     |  62 +---------
 .../apache/airavata/job/GFacConfigXmlTest.java  |   2 -
 .../apache/airavata/gfac/ec2/EC2Provider.java   |  58 ++++-----
 .../handler/GSISSHDirectorySetupHandler.java    |  13 +-
 .../gsissh/provider/impl/GSISSHProvider.java    |  10 +-
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |   8 --
 .../monitor/impl/pull/qstat/HPCPullMonitor.java |   2 -
 .../airavata/gfac/monitor/util/CommonUtils.java |  50 +-------
 .../ssh/handler/AdvancedSCPInputHandler.java    |  82 ++++++-------
 .../ssh/handler/AdvancedSCPOutputHandler.java   |  14 +--
 .../ssh/handler/SSHDirectorySetupHandler.java   |  12 +-
 .../gfac/ssh/handler/SSHInputHandler.java       |  24 ++--
 .../gfac/ssh/provider/impl/SSHProvider.java     | 118 +++++++++----------
 modules/messaging/core/pom.xml                  |  11 +-
 modules/registry/airavata-jpa-registry/pom.xml  |  10 +-
 modules/test-suite/pom.xml                      |  10 +-
 modules/workflow-model/workflow-engine/pom.xml  |  10 +-
 modules/xbaya-gui/pom.xml                       |  10 +-
 25 files changed, 195 insertions(+), 364 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/client/java/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/client/java/pom.xml b/modules/distribution/client/java/pom.xml
index d36492c..58a71f6 100644
--- a/modules/distribution/client/java/pom.xml
+++ b/modules/distribution/client/java/pom.xml
@@ -227,11 +227,11 @@
             <artifactId>airavata-orchestrator-core</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-common-utils</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/client/java/src/main/assembly/bin-assembly.xml b/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
index a5d9d01..4df667f 100644
--- a/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/client/java/src/main/assembly/bin-assembly.xml
@@ -108,8 +108,8 @@
 				<include>net.java.dev.jets3t:jets3t</include>
 				<include>org.apache.airavata:airavata-orchestrator-core:jar
 				</include>
-				<include>org.apache.airavata:airavata-gfac-schema-utils:jar
-				</include>
+				<!--<include>org.apache.airavata:airavata-gfac-schema-utils:jar-->
+				<!--</include>-->
 				<include>org.apache.airavata:airavata-common-utils:jar</include>
 				<include>org.apache.airavata:airavata-workflow-execution-context:jar
 				</include>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/gfac-server/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/gfac-server/pom.xml b/modules/distribution/gfac-server/pom.xml
index 7337f1d..a7114e7 100644
--- a/modules/distribution/gfac-server/pom.xml
+++ b/modules/distribution/gfac-server/pom.xml
@@ -229,11 +229,11 @@
             <artifactId>airavata-common-utils</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-workflow-execution-context</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/orchestrator-server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/orchestrator-server/src/main/assembly/bin-assembly.xml b/modules/distribution/orchestrator-server/src/main/assembly/bin-assembly.xml
index 74bf2c3..63af038 100644
--- a/modules/distribution/orchestrator-server/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/orchestrator-server/src/main/assembly/bin-assembly.xml
@@ -188,8 +188,8 @@
 				</include>
 				<include>org.apache.airavata:airavata-orchestrator-core:jar
 				</include>
-				<include>org.apache.airavata:airavata-gfac-schema-utils:jar
-				</include>
+				<!--<include>org.apache.airavata:airavata-gfac-schema-utils:jar-->
+				<!--</include>-->
 				<include>org.apache.airavata:airavata-workflow-execution-context:jar
 				</include>
 				<include>org.apache.airavata:airavata-registry-cpi:jar</include>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/server/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/server/pom.xml b/modules/distribution/server/pom.xml
index 263112b..00e3745 100644
--- a/modules/distribution/server/pom.xml
+++ b/modules/distribution/server/pom.xml
@@ -279,11 +279,11 @@
             <artifactId>airavata-orchestrator-core</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-workflow-execution-context</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/distribution/server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/server/src/main/assembly/bin-assembly.xml b/modules/distribution/server/src/main/assembly/bin-assembly.xml
index 1f07188..26884c8 100644
--- a/modules/distribution/server/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/server/src/main/assembly/bin-assembly.xml
@@ -207,8 +207,8 @@
 				</include>
 				<include>org.apache.airavata:airavata-orchestrator-core:jar
 				</include>
-				<include>org.apache.airavata:airavata-gfac-schema-utils:jar
-				</include>
+				<!--<include>org.apache.airavata:airavata-gfac-schema-utils:jar-->
+				<!--</include>-->
 				<include>org.apache.airavata:airavata-workflow-execution-context:jar
 				</include>
 				<include>org.apache.airavata:airavata-registry-cpi:jar</include>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
index d8c7663..a9940b8 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
@@ -23,8 +23,6 @@ package org.apache.airavata.gfac;
 
 import org.airavata.appcatalog.cpi.AppCatalog;
 import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
-import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.provider.GFacProvider;
 import org.apache.airavata.gfac.core.provider.GFacProviderConfig;
@@ -34,7 +32,6 @@ import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterfa
 import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
 import org.apache.airavata.model.appcatalog.computeresource.LOCALSubmission;
 import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
-import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
@@ -220,8 +217,8 @@ public class Scheduler {
         return ExecutionMode.fromString(executionMode);
     }
 
-    private static HostDescription scheduleHost(List<HostDescription> registeredHosts) {
-        //todo implement an algorithm to pick a host among different hosts, ideally this could be configurable in an xml
-        return registeredHosts.get(0);
-    }
+//    private static HostDescription scheduleHost(List<HostDescription> registeredHosts) {
+//        //todo implement an algorithm to pick a host among different hosts, ideally this could be configurable in an xml
+//        return registeredHosts.get(0);
+//    }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java
index 6e1b8b7..c71ed27 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java
@@ -27,7 +27,6 @@ import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.AiravataZKUtils;
 import org.apache.airavata.common.utils.DBUtil;
 import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.common.utils.StringUtil;
 import org.apache.airavata.credential.store.store.CredentialReader;
 import org.apache.airavata.credential.store.store.impl.CredentialReaderImpl;
 import org.apache.airavata.gfac.Constants;
@@ -40,46 +39,13 @@ import org.apache.airavata.gfac.core.states.GfacExperimentState;
 import org.apache.airavata.gfac.core.states.GfacPluginState;
 import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
 import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.appcatalog.computeresource.CloudJobSubmission;
-import org.apache.airavata.model.appcatalog.computeresource.GlobusJobSubmission;
-import org.apache.airavata.model.appcatalog.computeresource.LOCALSubmission;
-import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
-import org.apache.airavata.model.appcatalog.computeresource.UnicoreJobSubmission;
-import org.apache.airavata.model.workspace.experiment.ActionableGroup;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.ErrorDetails;
-import org.apache.airavata.model.workspace.experiment.JobDetails;
-import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.model.workspace.experiment.JobStatus;
+import org.apache.airavata.model.appcatalog.computeresource.*;
+import org.apache.airavata.model.workspace.experiment.*;
 import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
 import org.apache.airavata.registry.cpi.ChildDataType;
 import org.apache.airavata.registry.cpi.CompositeIdentifier;
 import org.apache.airavata.registry.cpi.Registry;
-import org.apache.airavata.schemas.gfac.BooleanArrayType;
-import org.apache.airavata.schemas.gfac.BooleanParameterType;
-import org.apache.airavata.schemas.gfac.DataType;
-import org.apache.airavata.schemas.gfac.DoubleArrayType;
-import org.apache.airavata.schemas.gfac.DoubleParameterType;
-import org.apache.airavata.schemas.gfac.FileArrayType;
-import org.apache.airavata.schemas.gfac.FileParameterType;
-import org.apache.airavata.schemas.gfac.FloatArrayType;
-import org.apache.airavata.schemas.gfac.FloatParameterType;
-import org.apache.airavata.schemas.gfac.IntegerArrayType;
-import org.apache.airavata.schemas.gfac.IntegerParameterType;
-import org.apache.airavata.schemas.gfac.Parameter;
-import org.apache.airavata.schemas.gfac.StdErrParameterType;
-import org.apache.airavata.schemas.gfac.StdOutParameterType;
-import org.apache.airavata.schemas.gfac.StringArrayType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.apache.axiom.om.OMElement;
-import org.apache.zookeeper.CreateMode;
-import org.apache.zookeeper.KeeperException;
-import org.apache.zookeeper.ZKUtil;
-import org.apache.zookeeper.ZooDefs;
-import org.apache.zookeeper.ZooKeeper;
+import org.apache.zookeeper.*;
 import org.apache.zookeeper.data.Stat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -88,28 +54,12 @@ import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpression;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
+import javax.xml.xpath.*;
+import java.io.*;
 import java.net.InetAddress;
 import java.net.URISyntaxException;
 import java.net.UnknownHostException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 //import org.apache.airavata.commons.gfac.type.ActualParameter;
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/job/GFacConfigXmlTest.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/job/GFacConfigXmlTest.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/job/GFacConfigXmlTest.java
index 7e6bc0d..4744772 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/job/GFacConfigXmlTest.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/job/GFacConfigXmlTest.java
@@ -24,7 +24,6 @@ import junit.framework.Assert;
 import org.airavata.appcatalog.cpi.AppCatalog;
 import org.airavata.appcatalog.cpi.AppCatalogException;
 import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
-import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.ExecutionMode;
 import org.apache.airavata.gfac.GFacConfiguration;
 import org.apache.airavata.gfac.GFacException;
@@ -33,7 +32,6 @@ import org.apache.airavata.gfac.core.context.ApplicationContext;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
 import org.apache.airavata.model.appcatalog.computeresource.*;
-import org.apache.airavata.schemas.gfac.GsisshHostType;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 import org.xml.sax.SAXException;

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ec2/src/main/java/org/apache/airavata/gfac/ec2/EC2Provider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ec2/src/main/java/org/apache/airavata/gfac/ec2/EC2Provider.java b/modules/gfac/gfac-ec2/src/main/java/org/apache/airavata/gfac/ec2/EC2Provider.java
index 53e0f93..29efb73 100644
--- a/modules/gfac/gfac-ec2/src/main/java/org/apache/airavata/gfac/ec2/EC2Provider.java
+++ b/modules/gfac/gfac-ec2/src/main/java/org/apache/airavata/gfac/ec2/EC2Provider.java
@@ -21,16 +21,23 @@
 
 package org.apache.airavata.gfac.ec2;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Calendar;
-import java.util.List;
-import java.util.Map;
-
+import com.amazonaws.AmazonServiceException;
+import com.amazonaws.auth.AWSCredentials;
+import com.amazonaws.auth.BasicAWSCredentials;
+import com.amazonaws.services.ec2.AmazonEC2Client;
+import com.amazonaws.services.ec2.model.*;
+import com.sshtools.j2ssh.SshClient;
+import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
+import com.sshtools.j2ssh.authentication.PublicKeyAuthenticationClient;
+import com.sshtools.j2ssh.configuration.SshConnectionProperties;
+import com.sshtools.j2ssh.session.SessionChannelClient;
+import com.sshtools.j2ssh.transport.HostKeyVerification;
+import com.sshtools.j2ssh.transport.TransportProtocolException;
+import com.sshtools.j2ssh.transport.publickey.InvalidSshKeyException;
+import com.sshtools.j2ssh.transport.publickey.SshPrivateKey;
+import com.sshtools.j2ssh.transport.publickey.SshPrivateKeyFile;
+import com.sshtools.j2ssh.transport.publickey.SshPublicKey;
 import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.provider.AbstractProvider;
@@ -42,39 +49,18 @@ import org.apache.airavata.gfac.ec2.util.EC2ProviderUtil;
 import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
 import org.apache.airavata.model.appcatalog.computeresource.CloudJobSubmission;
 import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
-import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
 import org.apache.airavata.model.appcatalog.computeresource.ProviderName;
 import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.Ec2ApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.OutputParameterType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
 import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
-import com.amazonaws.AmazonServiceException;
-import com.amazonaws.auth.AWSCredentials;
-import com.amazonaws.auth.BasicAWSCredentials;
-import com.amazonaws.services.ec2.AmazonEC2Client;
-import com.amazonaws.services.ec2.model.AuthorizeSecurityGroupIngressRequest;
-import com.amazonaws.services.ec2.model.DescribeInstancesRequest;
-import com.amazonaws.services.ec2.model.DescribeInstancesResult;
-import com.amazonaws.services.ec2.model.GroupIdentifier;
-import com.amazonaws.services.ec2.model.Instance;
-import com.amazonaws.services.ec2.model.IpPermission;
-import com.sshtools.j2ssh.SshClient;
-import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
-import com.sshtools.j2ssh.authentication.PublicKeyAuthenticationClient;
-import com.sshtools.j2ssh.configuration.SshConnectionProperties;
-import com.sshtools.j2ssh.session.SessionChannelClient;
-import com.sshtools.j2ssh.transport.HostKeyVerification;
-import com.sshtools.j2ssh.transport.TransportProtocolException;
-import com.sshtools.j2ssh.transport.publickey.InvalidSshKeyException;
-import com.sshtools.j2ssh.transport.publickey.SshPrivateKey;
-import com.sshtools.j2ssh.transport.publickey.SshPrivateKeyFile;
-import com.sshtools.j2ssh.transport.publickey.SshPublicKey;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Calendar;
+import java.util.List;
+import java.util.Map;
 
 public class EC2Provider extends AbstractProvider {
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
index b2c40a7..c360909 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
@@ -20,28 +20,21 @@
 */
 package org.apache.airavata.gfac.gsissh.handler;
 
-import java.util.Properties;
-
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.handler.AbstractRecoverableHandler;
 import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
 import org.apache.airavata.gfac.core.utils.GFacUtils;
 import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
 import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
 import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
+import org.apache.airavata.model.workspace.experiment.*;
 import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Properties;
+
 public class GSISSHDirectorySetupHandler extends AbstractRecoverableHandler {
       private static final Logger log = LoggerFactory.getLogger(GSISSHDirectorySetupHandler.class);
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
index 9918f42..28b6686 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
@@ -21,8 +21,6 @@
 package org.apache.airavata.gfac.gsissh.provider.impl;
 
 import org.airavata.appcatalog.cpi.AppCatalog;
-import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.gfac.ExecutionMode;
 import org.apache.airavata.gfac.GFacException;
@@ -42,24 +40,20 @@ import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
 import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
 import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
 import org.apache.airavata.model.appcatalog.computeresource.MonitorMode;
-import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager;
 import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
 import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
 import org.apache.airavata.model.workspace.experiment.ErrorCategory;
 import org.apache.airavata.model.workspace.experiment.JobDetails;
 import org.apache.airavata.model.workspace.experiment.JobState;
-//import org.apache.airavata.schemas.gfac.GsisshHostType;
-import org.apache.airavata.schemas.gfac.HostDescriptionType;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
 import org.apache.zookeeper.KeeperException;
-import org.apache.zookeeper.ZooKeeper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.management.monitor.Monitor;
 import java.util.List;
 import java.util.Map;
 
+//import org.apache.airavata.schemas.gfac.GsisshHostType;
+
 public class GSISSHProvider extends AbstractRecoverableProvider {
     private static final Logger log = LoggerFactory.getLogger(GSISSHProvider.class);
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
index 73b2462..d040ca4 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
@@ -21,15 +21,10 @@
 package org.apache.airavata.gfac.gsissh.util;
 
 import org.airavata.appcatalog.cpi.AppCatalog;
-import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
 import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.gfac.Constants;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.RequestData;
 import org.apache.airavata.gfac.core.context.ApplicationContext;
@@ -53,9 +48,6 @@ import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
 import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
 import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
 import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.schemas.gfac.FileArrayType;
-import org.apache.airavata.schemas.gfac.StringArrayType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
index 824ab71..4802122 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
@@ -26,7 +26,6 @@ import org.apache.airavata.common.logger.AiravataLoggerFactory;
 import org.apache.airavata.common.utils.MonitorPublisher;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.gfac.monitor.util.CommonUtils;
-import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.core.cpi.GFac;
 import org.apache.airavata.gfac.core.monitor.MonitorID;
 import org.apache.airavata.gfac.core.utils.GFacThreadPoolExecutor;
@@ -152,7 +151,6 @@ public class HPCPullMonitor extends PullMonitor {
         UserMonitorData take = null;
         JobStatusChangeRequestEvent jobStatus = new JobStatusChangeRequestEvent();
         MonitorID currentMonitorID = null;
-        HostDescription currentHostDescription = null;
         try {
             take = this.queue.take();
             List<HostMonitorData> hostMonitorData = take.getHostMonitorData();

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
index 0949bd9..135349f 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
@@ -25,7 +25,6 @@ import org.apache.airavata.common.logger.AiravataLogger;
 import org.apache.airavata.common.logger.AiravataLoggerFactory;
 import org.apache.airavata.common.utils.AiravataZKUtils;
 import org.apache.airavata.common.utils.Constants;
-import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.handler.GFacHandler;
@@ -35,13 +34,7 @@ import org.apache.airavata.gfac.monitor.HostMonitorData;
 import org.apache.airavata.gfac.monitor.UserMonitorData;
 import org.apache.airavata.gfac.monitor.exception.AiravataMonitorException;
 import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
-import org.apache.airavata.schemas.gfac.GsisshHostType;
-import org.apache.zookeeper.CreateMode;
-import org.apache.zookeeper.KeeperException;
-import org.apache.zookeeper.WatchedEvent;
-import org.apache.zookeeper.Watcher;
-import org.apache.zookeeper.ZooDefs;
-import org.apache.zookeeper.ZooKeeper;
+import org.apache.zookeeper.*;
 
 import java.io.IOException;
 import java.util.HashMap;
@@ -54,31 +47,6 @@ import java.util.concurrent.CountDownLatch;
 public class CommonUtils {
     private final static AiravataLogger logger = AiravataLoggerFactory.getLogger(CommonUtils.class);
 
-    public static boolean isPBSHost(HostDescription host){
-        if("pbs".equals(((GsisshHostType)host.getType()).getJobManager()) ||
-                "".equals(((GsisshHostType)host.getType()).getJobManager())){
-         return true;
-        }else{
-            // default is pbs so we return true
-            return false;
-        }
-    }
-    public static boolean isSlurm(HostDescription host){
-        if("slurm".equals(((GsisshHostType)host.getType()).getJobManager())){
-         return true;
-        }else{
-            // default is pbs so we return true
-            return false;
-        }
-    }
-    public static boolean isSGE(HostDescription host){
-        if("sge".equals(((GsisshHostType)host.getType()).getJobManager())){
-         return true;
-        }else{
-            // default is pbs so we return true
-            return false;
-        }
-    }
     public static String getChannelID(MonitorID monitorID) {
         return monitorID.getUserName() + "-" + monitorID.getComputeResourceDescription().getHostName();
     }
@@ -189,22 +157,6 @@ public class CommonUtils {
         logger.info("This might not be an error because someone else removed this job from the queue");
     }
 
-    public static boolean isEqual(HostDescription host1,HostDescription host2) {
-        if ((host1.getType() instanceof GsisshHostType) && (host2.getType() instanceof GsisshHostType)) {
-            GsisshHostType hostType1 = (GsisshHostType)host1.getType();
-            GsisshHostType hostType2 = (GsisshHostType)host2.getType();
-            if(hostType1.getHostAddress().equals(hostType2.getHostAddress())
-                    && hostType1.getJobManager().equals(hostType2.getJobManager())
-                    && (hostType1.getPort() == hostType2.getPort())
-                    && hostType1.getMonitorMode().equals(hostType2.getMonitorMode())){
-                return true;
-            }
-        } else {
-            logger.error("This method is only impmlemented to handle Gsissh host types");
-        }
-        return false;
-    }
-
     public static void invokeOutFlowHandlers(JobExecutionContext jobExecutionContext) throws GFacException {
         List<GFacHandlerConfig> handlers = jobExecutionContext.getGFacConfiguration().getOutHandlers();
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
index 36a7c8d..f3dd193 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPInputHandler.java
@@ -20,37 +20,23 @@
 */
 package org.apache.airavata.gfac.ssh.handler;
 
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.handler.AbstractHandler;
 import org.apache.airavata.gfac.core.handler.AbstractRecoverableHandler;
 import org.apache.airavata.gfac.core.handler.GFacHandlerException;
 import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.ssh.context.SSHAuthWrapper;
 import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
 import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
 import org.apache.airavata.gsi.ssh.api.Cluster;
 import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.ServerInfo;
 import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
-import org.apache.airavata.gsi.ssh.impl.PBSCluster;
 import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
 import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
-import org.apache.airavata.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
+import org.apache.airavata.model.appcatalog.appinterface.DataType;
+import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+import org.apache.airavata.model.workspace.experiment.*;
 import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -150,10 +136,10 @@ public class AdvancedSCPInputHandler extends AbstractRecoverableHandler {
             MessageContext input = jobExecutionContext.getInMessageContext();
             Set<String> parameters = input.getParameters().keySet();
             for (String paramName : parameters) {
-                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
-                String paramValue = MappingFactory.toString(actualParameter);
+                InputDataObjectType inputParamType = (InputDataObjectType) input.getParameters().get(paramName);
+                String paramValue = inputParamType.getValue();
                 // TODO: Review this with type
-                if ("URI".equals(actualParameter.getType().getType().toString())) {
+                if (inputParamType.getType() == DataType.URI) {
                     try {
                         URL file = new URL(paramValue);
                         String key = file.getUserInfo() + file.getHost() + DEFAULT_SSH_PORT;
@@ -169,11 +155,11 @@ public class AdvancedSCPInputHandler extends AbstractRecoverableHandler {
 
                     if (index < oldIndex) {
                         log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
-                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
+                        inputParamType.setValue(oldFiles.get(index));
                         data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                     } else {
                         String stageInputFile = stageInputFiles(pbsCluster, paramValue, parentPath);
-                        ((URIParameterType) actualParameter.getType()).setValue(stageInputFile);
+                        inputParamType.setValue(stageInputFile);
                         StringBuffer temp = new StringBuffer(data.append(stageInputFile).append(",").toString());
                         status.setTransferState(TransferState.UPLOAD);
                         detail.setTransferStatus(status);
@@ -182,32 +168,34 @@ public class AdvancedSCPInputHandler extends AbstractRecoverableHandler {
 
                         GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                     }
-                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
-                    List<String> newFiles = new ArrayList<String>();
-                    for (String paramValueEach : split) {
-                        try {
-                            URL file = new URL(paramValue);
-                            this.userName = file.getUserInfo();
-                            this.hostName = file.getHost();
-                            paramValueEach = file.getPath();
-                        } catch (MalformedURLException e) {
-                            log.error(e.getLocalizedMessage(), e);
-                        }
-                        if (index < oldIndex) {
-                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
-                            newFiles.add(oldFiles.get(index));
-                            data.append(oldFiles.get(index++)).append(",");
-                        } else {
-                            String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
-                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
-                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
-                            newFiles.add(stageInputFiles);
-                        }
-                    }
-                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                 }
-                inputNew.getParameters().put(paramName, actualParameter);
+                // FIXME: what is the thrift model DataType equivalent for URIArray type?
+//                else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
+//                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
+//                    List<String> newFiles = new ArrayList<String>();
+//                    for (String paramValueEach : split) {
+//                        try {
+//                            URL file = new URL(paramValue);
+//                            this.userName = file.getUserInfo();
+//                            this.hostName = file.getHost();
+//                            paramValueEach = file.getPath();
+//                        } catch (MalformedURLException e) {
+//                            log.error(e.getLocalizedMessage(), e);
+//                        }
+//                        if (index < oldIndex) {
+//                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
+//                            newFiles.add(oldFiles.get(index));
+//                            data.append(oldFiles.get(index++)).append(",");
+//                        } else {
+//                            String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
+//                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
+//                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
+//                            newFiles.add(stageInputFiles);
+//                        }
+//                    }
+//                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
+//                }
+                inputNew.getParameters().put(paramName, inputParamType);
             }
         } catch (Exception e) {
             log.error(e.getMessage());

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
index caefe7a..266dfac 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
@@ -21,8 +21,6 @@
 package org.apache.airavata.gfac.ssh.handler;
 
 import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.handler.AbstractHandler;
@@ -46,11 +44,7 @@ import org.slf4j.LoggerFactory;
 import java.io.File;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
+import java.util.*;
 
 /**
  * This handler will copy outputs from airavata installed local directory
@@ -149,9 +143,9 @@ public class AdvancedSCPOutputHandler extends AbstractHandler {
             Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
             Set<String> keys = output.keySet();
             for (String paramName : keys) {
-                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
-                if ("URI".equals(actualParameter.getType().getType().toString())) {
-                	String downloadFile = MappingFactory.toString(actualParameter);
+                OutputDataObjectType outputDataObjectType = (OutputDataObjectType) output.get(paramName);
+                if (outputDataObjectType.getType() == DataType.URI) {
+                	String downloadFile = outputDataObjectType.getValue();
                 	if(downloadFile == null || !(new File(downloadFile).isFile())){
                         GFacUtils.saveErrorDetails(jobExecutionContext, "Empty Output returned from the application", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
                 		throw new GFacHandlerException("Empty Output returned from the application");

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
index 1baed57..634ee07 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
@@ -20,8 +20,6 @@
 */
 package org.apache.airavata.gfac.ssh.handler;
 
-import java.util.Properties;
-
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.handler.AbstractHandler;
@@ -30,17 +28,13 @@ import org.apache.airavata.gfac.core.utils.GFacUtils;
 import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
 import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
 import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
+import org.apache.airavata.model.workspace.experiment.*;
 import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Properties;
+
 public class SSHDirectorySetupHandler extends AbstractHandler {
     private static final Logger log = LoggerFactory.getLogger(SSHDirectorySetupHandler.class);
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
index 66cafaf..4d47128 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
@@ -20,14 +20,7 @@
 */
 package org.apache.airavata.gfac.ssh.handler;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.*;
-
 import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.StringUtil;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.gfac.GFacException;
 import org.apache.airavata.gfac.core.context.JobExecutionContext;
 import org.apache.airavata.gfac.core.context.MessageContext;
@@ -37,21 +30,20 @@ import org.apache.airavata.gfac.core.utils.GFacUtils;
 import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
 import org.apache.airavata.gfac.ssh.util.GFACSSHUtils;
 import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
 import org.apache.airavata.model.appcatalog.appinterface.DataType;
 import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TransferState;
-import org.apache.airavata.model.workspace.experiment.TransferStatus;
+import org.apache.airavata.model.workspace.experiment.*;
 import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.URIArrayType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
+
 public class SSHInputHandler extends AbstractHandler {
 
     private static final Logger log = LoggerFactory.getLogger(SSHInputHandler.class);

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
index 85b4b5f..b1000c5 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
@@ -21,19 +21,7 @@
 
 package org.apache.airavata.gfac.ssh.provider.impl;
 
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.airavata.appcatalog.cpi.AppCatalog;
-import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.gfac.Constants;
 import org.apache.airavata.gfac.ExecutionMode;
 import org.apache.airavata.gfac.GFacException;
@@ -55,18 +43,24 @@ import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
 import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
 import org.apache.airavata.gsi.ssh.impl.StandardOutReader;
 import org.apache.airavata.model.appcatalog.appdeployment.SetEnvPaths;
-import org.apache.airavata.model.appcatalog.computeresource.*;
+import org.apache.airavata.model.appcatalog.appinterface.DataType;
+import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager;
+import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType;
 import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
 import org.apache.airavata.model.workspace.experiment.ErrorCategory;
 import org.apache.airavata.model.workspace.experiment.JobDetails;
 import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.schemas.gfac.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
 import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
-import javax.naming.OperationNotSupportedException;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.*;
 
 /**
  * Execute application using remote SSH
@@ -246,41 +240,42 @@ public class SSHProvider extends AbstractProvider {
         }
     }
 
-    public void removeFromMonitorHandlers(JobExecutionContext jobExecutionContext, GsisshHostType host, String jobID) throws GFacHandlerException {
-        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        if (daemonHandlers == null) {
-            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
-        }
-        ThreadedHandler pullMonitorHandler = null;
-        ThreadedHandler pushMonitorHandler = null;
-        String monitorMode = host.getMonitorMode();
-        for (ThreadedHandler threadedHandler : daemonHandlers) {
-            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pullMonitorHandler = threadedHandler;
-                if ("".equals(monitorMode) || monitorMode == null || org.apache.airavata.common.utils.Constants.PULL.equals(monitorMode)) {
-                    jobExecutionContext.setProperty("cancel","true");
-                    pullMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
-                            " to handle by the GridPullMonitorHandler");
-                }
-            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
-                pushMonitorHandler = threadedHandler;
-                if ("".equals(monitorMode) || monitorMode == null || org.apache.airavata.common.utils.Constants.PUSH.equals(monitorMode)) {
-                    log.info("Job is launched successfully now parsing it to monitoring in push mode, JobID Returned:  " + jobID);
-                    pushMonitorHandler.invoke(jobExecutionContext);
-                } else {
-                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
-                            " to handle by the GridPushMonitorHandler");
-                }
-            }
-            // have to handle the GridPushMonitorHandler logic
-        }
-        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
-            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
-                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
-        }
-    }
+//    public void removeFromMonitorHandlers(JobExecutionContext jobExecutionContext, GsisshHostType host, String jobID) throws GFacHandlerException {
+//        List<ThreadedHandler> daemonHandlers = BetterGfacImpl.getDaemonHandlers();
+//        if (daemonHandlers == null) {
+//            daemonHandlers = BetterGfacImpl.getDaemonHandlers();
+//        }
+//        ThreadedHandler pullMonitorHandler = null;
+//        ThreadedHandler pushMonitorHandler = null;
+//        String monitorMode = host.getMonitorMode();
+//        for (ThreadedHandler threadedHandler : daemonHandlers) {
+//            if ("org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler".equals(threadedHandler.getClass().getName())) {
+//                pullMonitorHandler = threadedHandler;
+//                if ("".equals(monitorMode) || monitorMode == null || org.apache.airavata.common.utils.Constants.PULL.equals(monitorMode)) {
+//                    jobExecutionContext.setProperty("cancel","true");
+//                    pullMonitorHandler.invoke(jobExecutionContext);
+//                } else {
+//                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PULL" +
+//                            " to handle by the GridPullMonitorHandler");
+//                }
+//            } else if ("org.apache.airavata.gfac.monitor.handlers.GridPushMonitorHandler".equals(threadedHandler.getClass().getName())) {
+//                pushMonitorHandler = threadedHandler;
+//                if ("".equals(monitorMode) || monitorMode == null || org.apache.airavata.common.utils.Constants.PUSH.equals(monitorMode)) {
+//                    log.info("Job is launched successfully now parsing it to monitoring in push mode, JobID Returned:  " + jobID);
+//                    pushMonitorHandler.invoke(jobExecutionContext);
+//                } else {
+//                    log.error("Currently we only support Pull and Push monitoring and monitorMode should be PUSH" +
+//                            " to handle by the GridPushMonitorHandler");
+//                }
+//            }
+//            // have to handle the GridPushMonitorHandler logic
+//        }
+//        if (pullMonitorHandler == null && pushMonitorHandler == null && ExecutionMode.ASYNCHRONOUS.equals(jobExecutionContext.getGFacConfiguration().getExecutionMode())) {
+//            log.error("No Daemon handler is configured in gfac-config.xml, either pull or push, so monitoring will not invoked" +
+//                    ", execution is configured as asynchronous, so Outhandler will not be invoked");
+//        }
+//    }
+
     private File createShellScript(JobExecutionContext context) throws IOException {
         String uniqueDir = jobExecutionContext.getApplicationName() + System.currentTimeMillis()
                 + new Random().nextLong();
@@ -307,19 +302,22 @@ public class SSHProvider extends AbstractProvider {
         cmd.append(SPACE);
 
         MessageContext input = context.getInMessageContext();
-        ;
         Map<String, Object> inputs = input.getParameters();
         Set<String> keys = inputs.keySet();
         for (String paramName : keys) {
-            ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
-            if ("URIArray".equals(actualParameter.getType().getType().toString())) {
-                String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
-                for (String value : values) {
-                    cmd.append(value);
-                    cmd.append(SPACE);
-                }
+            InputDataObjectType inputParamType = (InputDataObjectType) input.getParameters().get(paramName);
+            //if ("URIArray".equals(actualParameter.getType().getType().toString())) {
+            if (inputParamType.getType() == DataType.URI) {
+                String value = inputParamType.getValue();
+                cmd.append(value);
+                cmd.append(SPACE);
+//                String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
+//                for (String value : values) {
+//                    cmd.append(value);
+//                    cmd.append(SPACE);
+//                }
             } else {
-                String paramValue = MappingFactory.toString(actualParameter);
+                String paramValue = inputParamType.getValue();
                 cmd.append(paramValue);
                 cmd.append(SPACE);
             }

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/messaging/core/pom.xml
----------------------------------------------------------------------
diff --git a/modules/messaging/core/pom.xml b/modules/messaging/core/pom.xml
index 428c46d..2b3d198 100644
--- a/modules/messaging/core/pom.xml
+++ b/modules/messaging/core/pom.xml
@@ -29,10 +29,15 @@
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
+        <groupId>org.apache.airavata</groupId>
+        <artifactId>airavata-common-utils</artifactId>
+        <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/registry/airavata-jpa-registry/pom.xml
----------------------------------------------------------------------
diff --git a/modules/registry/airavata-jpa-registry/pom.xml b/modules/registry/airavata-jpa-registry/pom.xml
index 8fc0e48..d7b2d62 100644
--- a/modules/registry/airavata-jpa-registry/pom.xml
+++ b/modules/registry/airavata-jpa-registry/pom.xml
@@ -28,11 +28,11 @@
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <!--dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-common-utils</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/test-suite/pom.xml
----------------------------------------------------------------------
diff --git a/modules/test-suite/pom.xml b/modules/test-suite/pom.xml
index 260051c..e70ec41 100644
--- a/modules/test-suite/pom.xml
+++ b/modules/test-suite/pom.xml
@@ -48,11 +48,11 @@
         </dependency>
 
         <!-- GFAC schemas -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-gfac-core</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/workflow-model/workflow-engine/pom.xml
----------------------------------------------------------------------
diff --git a/modules/workflow-model/workflow-engine/pom.xml b/modules/workflow-model/workflow-engine/pom.xml
index 304f883..098f34e 100644
--- a/modules/workflow-model/workflow-engine/pom.xml
+++ b/modules/workflow-model/workflow-engine/pom.xml
@@ -256,11 +256,11 @@
         </dependency>
         <!-- JCR Support -->
         <!-- TODO need clean up -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-gfac-core</artifactId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a0afbd8b/modules/xbaya-gui/pom.xml
----------------------------------------------------------------------
diff --git a/modules/xbaya-gui/pom.xml b/modules/xbaya-gui/pom.xml
index 3550322..2143939 100644
--- a/modules/xbaya-gui/pom.xml
+++ b/modules/xbaya-gui/pom.xml
@@ -242,11 +242,11 @@
 
         <!-- JCR Support -->
         <!-- TODO need clean up -->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.apache.airavata</groupId>-->
+            <!--<artifactId>airavata-gfac-schema-utils</artifactId>-->
+            <!--<version>${project.version}</version>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-gfac-core</artifactId>


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