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From scnakand...@apache.org
Subject [03/51] [partial] airavata-php-gateway git commit: removing files from wrong merge
Date Tue, 13 Dec 2016 22:14:27 GMT
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/NOTICE
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/NOTICE b/modules/distribution/src/main/resources/NOTICE
deleted file mode 100644
index fa7cba5..0000000
--- a/modules/distribution/src/main/resources/NOTICE
+++ /dev/null
@@ -1,163 +0,0 @@
-Apache Airavata
-Copyright 2014 The Apache Software Foundation
-
-This product includes software developed at
-The Apache Software Foundation (http://www.apache.org/).
-
-===============================================================================
-Apache Xerces Java Notice:
-
-   Portions of this software were originally based on the following:
-     - software copyright (c) 1999, IBM Corporation., http://www.ibm.com.
-     - software copyright (c) 1999, Sun Microsystems., http://www.sun.com.
-     - voluntary contributions made by Paul Eng on behalf of the
-       Apache Software Foundation that were originally developed at iClick, Inc.,
-       software copyright (c) 1999.
-
-================================================================================
-Apache XmlBeans Notice: 
-
-   Portions of this software were originally based on the following:
-     - software copyright (c) 2000-2003, BEA Systems, <http://www.bea.com/>.
-
-   Aside from contributions to the Apache XMLBeans project, this
-   software also includes:
-
-    - one or more source files from the Apache Xerces-J and Apache Axis
-      products, Copyright (c) 1999-2003 Apache Software Foundation
-
-    - W3C XML Schema documents Copyright 2001-2003 (c) World Wide Web
-      Consortium (Massachusetts Institute of Technology, European Research
-      Consortium for Informatics and Mathematics, Keio University)
-
-    - resolver.jar from Apache Xml Commons project,
-      Copyright (c) 2001-2003 Apache Software Foundation
-
-    - Piccolo XML Parser for Java from http://piccolo.sourceforge.net/,
-      Copyright 2002 Yuval Oren under the terms of the Apache Software License 2.0
-
-    - JSR-173 Streaming API for XML from http://sourceforge.net/projects/xmlpullparser/,
-      Copyright 2005 BEA under the terms of the Apache Software License 2.0
-      
-=========================================================================================
-Apache Axis2 Notice: (axis2-*, mex-1.5.1-impl)
-
-Portions Copyright 2006 International Business Machines Corp.
-Portions Copyright 2005-2007 WSO2, Inc.
-
-This product also includes schemas and specification developed by:
-- the W3C consortium (http://www.w3c.org)
-
-This product also includes WS-* schemas developed by International
-Business Machines Corporation, Microsoft Corporation, BEA Systems, 
-TIBCO Software, SAP AG, Sonic Software, and VeriSign
-
-This product also includes a WSDL developed by salesforce.com
-- Copyright 1999-2006 salesforce.com, inc.
-Portions of the included xmlbeans library were originally based on the following:
-- software copyright (c) 2000-2003, BEA Systems, <http://www.bea.com/>.
-
-====================================================================================
-Apache Derby Notice:
-
-Portions of Derby were originally developed by
-International Business Machines Corporation and are
-licensed to the Apache Software Foundation under the
-"Software Grant and Corporate Contribution License Agreement",
-informally known as the "Derby CLA".
-The following copyright notice(s) were affixed to portions of the code
-with which this file is now or was at one time distributed
-and are placed here unaltered.
-
-(C) Copyright 1997,2004 International Business Machines Corporation.  All rights reserved.
-
-(C) Copyright IBM Corp. 2003. 
-
-=======================
-
-The portion of the functionTests under 'nist' was originally 
-developed by the National Institute of Standards and Technology (NIST), 
-an agency of the United States Department of Commerce, and adapted by
-International Business Machines Corporation in accordance with the NIST
-Software Acknowledgment and Redistribution document at
-http://www.itl.nist.gov/div897/ctg/sql_form.htm
-
-========================
-
-The JDBC apis for small devices and JDBC3 (under java/stubs/jsr169 and
-java/stubs/jdbc3) were produced by trimming sources supplied by the
-Apache Harmony project. In addition, the Harmony SerialBlob and
-SerialClob implementations are used. The following notice covers the Harmony sources:
-
-Portions of Harmony were originally developed by
-Intel Corporation and are licensed to the Apache Software
-Foundation under the "Software Grant and Corporate Contribution
-License Agreement", informally known as the "Intel Harmony CLA".
-
-=============================================================================
-Apache Woden Notice:
-
-   This product also includes software developed by :
-   
-     - IBM Corporation (http://www.ibm.com),
-         WSDL4J was the initial code contribution for the Apache Woden
-         project and some of the WSDL4J design and code has been reused.
-     - The W3C Consortium (http://www.w3c.org),
-         Common W3C XML Schema and DTD files are packaged with Apache Woden.
-
-   Please read the different LICENSE files present in the root directory of
-   this distribution.
-
-=========================================================================
-Woodstox Notice: 
-
-This product includes software developed by the Woodstox Project 
-(http://woodstox.codehaus.org/)
-
-This product currently only contains code developed by authors
-of specific components, as identified by the source code files.
-
-Since product implements StAX API, it has dependencies to StAX API
-classes.
-
-For additional credits (generally to people who reported problems)
-see CREDITS file.
-
-===========================================================================
-Apache xml-commons xml-apis Notice:
-
-   Portions of this software were originally based on the following:
-     - software copyright (c) 1999, IBM Corporation., http://www.ibm.com.
-     - software copyright (c) 1999, Sun Microsystems., http://www.sun.com.
-     - software copyright (c) 2000 World Wide Web Consortium, http://www.w3.org
-
-================================================================================================
-Apache  Xalan Notice: 
-
-Portions of this software was originally based on the following:
-     - software copyright (c) 1999-2002, Lotus Development Corporation., http://www.lotus.com.
-     - software copyright (c) 2001-2002, Sun Microsystems., http://www.sun.com.
-     - software copyright (c) 2003, IBM Corporation., http://www.ibm.com.
-     - voluntary contributions made by Ovidiu Predescu (ovidiu@cup.hp.com) on behalf of the 
-       Apache Software Foundation and was originally developed at Hewlett Packard Company. 
-================================================================================================
-Apache  OpenJPA Notice: 
-
-OpenJPA includes software developed by the SERP project
-Copyright (c) 2002-2006, A. Abram White. All rights reserved.
-
-OpenJPA includes the persistence and orm schemas from the JPA specifications.
-Copyright 2005-2009 Sun Microsystems, Inc. All rights reserved.
-OpenJPA elects to include this software in this distribution under the
-CDDL license.  You can obtain a copy of the License at:
-    https://glassfish.dev.java.net/public/CDDL+GPL.html
-The source code is available at:
-    https://glassfish.dev.java.net/source/browse/glassfish/
-
-OpenJPA includes software written by Miroslav Nachev
-OpenJPA uses test code written by Charles Tillman.
-================================================================================================
-Apache XmlSchema Notice:
-
-Portions Copyright 2006 International Business Machines Corp.
-================================================================================================

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/README
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/README b/modules/distribution/src/main/resources/README
deleted file mode 100644
index c2223ff..0000000
--- a/modules/distribution/src/main/resources/README
+++ /dev/null
@@ -1,145 +0,0 @@
-Apache Airavata Source - README.txt
-Licensed under Apache License 2.0 - http://www.apache.org/licenses/LICENSE-2.0
---------------------------------------------------------------------------------
-
-About
-=====
-Apache Airavata, a software framework to executing and managing computational jobs on 
-distributed computing resources including local clusters, supercomputers, national grids, 
-academic and commercial clouds. Airavata builds on general concepts of service oriented computing, 
-distributed messaging, and workflow composition and orchestration. Airavata bundles a server package 
-with an API, client software development Kits and a general purpose GUI XBaya as a application registration, workflow
-construction execution and monitoring. XBaya GUI also provides capabilities to access the workflow 
-produced data.  
-
-Contact
-========
-For additional information about Apache Airavata, please contact the user or dev mailing lists:
-http://airavata.apache.org/community/mailing-lists.html
-
-Description of Airavata Directory Structure
-==================================
-    - airavata-api
-      This directory contains Airavata API related data models, api methods, generated server skeletons, client stubs, server implementations and client samples. 
-
-    - modules
-      This contains the source code of all the airavata maven projects organized as libraries, services and distributions
-
-    - samples
-      This contains all the system wide samples provided in Airavata distribution. All the sample are having its README file
-      So users have to refer each readme file before running each sample.
-
-    - tools
-      This contains source code libraries that can enhance Airavata features.
-
-    - README
-      This document.
-    
-    - RELEASE_NOTES
-      The describe the key features and know issues with the current release. 
-
-    - INSTALL
-      This document will contain information on installing Apache-Airavata.
-
-Airavata Source Distribution Directory Structure
-================================================
-
-    AIRAVATA_MASTER
-		├── airavata-api
-		├── modules
-		│   ├── airavata-client
-		│   ├── app-catalog
-		│   ├── commons
-		│   │   ├── gfac-schema
-		│   │   ├── utils
-		│   │   ├── workflow-execution-context
-		│   │   └── workflow-tracking
-		│   ├── credential-store-service
-		│   ├── distribution
-		│   │   ├── api-server
-		│   │   ├── client
-		│   │   ├── gfac-server
-		│   │   ├── orchestrator-server
-		│   │   ├── server
-		│   │   └── release
-		│   │   └── xbaya-gui
-		│   ├── gfac
-		│   │   ├── airavata-gfac-service
-		│   │   ├── gfac-bes
-		│   │   ├── gfac-core
-		│   │   ├── gfac-ec2
-		│   │   ├── gfac-gram
-		│   │   ├── gfac-gsissh
-		│   │   ├── gfac-hadoop
-		│   │   ├── gfac-local
-		│   │   ├── gfac-monitor
-		│   │   ├── gfac-ssh
-		│   │   ├── gfac-thrift-descriptions
-		│   ├── integration-tests
-		│   ├── messaging
-		│   ├── orchestrator
-		│   ├── registry
-		│   │   ├── airavata-jpa-registry
-		│   │   ├── registry-cpi
-		│   ├── security
-		│   ├── credential-store
-		│   ├── server
-		│   ├── test-suite
-		│   ├── workflow-model
-		│   │   ├── workflow-engine
-		│   │   ├── workflow-model-component-node
-		│   │   └── workflow-model-core
-		│   ├── ws-messenger
-		│   │   ├── commons
-		│   │   ├── distribution
-		│   │   ├── messagebox
-		│   │   ├── messagebroker
-		│   │   ├── message-monitor
-		│   │   └── samples
-		│   └── xbaya-gui
-		├── samples
-		├── tools
-		│   ├── gsissh
-		│   ├── gsissh-cli-tools
-		│   ├── phoebus-integration
-		│   └── registry-migrate
-		├── INSTALL
-		├── LICENSE
-		├── NOTICE
-		├── README
-		└── RELEASE_NOTES
-
-Available Binary Distributions
-==============================
-
-Server Distributions
---------------------
-* Airavata Server
-  The Airavata Server binary distribution allows you to run a standalone Airavata Server which includes all the airavata services 
-  shipped with a default derby database as the backend registry. For stable purposes, a mysql configuration is recommended. 
-
-* Airavata API Server
-  This is the server that contains Airavata API Server.
-
-* Airavata Orchestrator Server
-  This is the stand-alone orchestrator server
-
-* Airavata GFac Server
-  This is the standalone GFac Server
-
-Client Distributions
---------------------
-* Airavata XBaya
-  The Airavata XBaya distribution is a client GUI application with features to register applications as web services, construct workflows,
-  execute and monitor workflows and browse the generated results from the airavata registry.
-
-* Airavata Client
-  The Airavata Client distribution is a set of libraries and configurations files that allow a 3rd party application to programatically 
-  access Airavata functionality through Airavata API. 
-  
- How to test and run samples
-===========================
-* If you built Airavata from source, and if you see "BUILD SUCCESS", then the test cases should have passes.
-* The test cases are beyond unit level, they startup embedded services and run through basic workflow use cases.
-* To walk through Airavata features, follow "XBAYA Quick-Start Tutorial" tutorial at https://cwiki.apache.org/confluence/display/AIRAVATA/XBAYA+Quick-Start+Tutorial.
-* For advanced use cases, please contact mailing lists - http://airavata.apache.org/community/mailing-lists.html

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server-start.sh
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diff --git a/modules/distribution/src/main/resources/bin/airavata-server-start.sh b/modules/distribution/src/main/resources/bin/airavata-server-start.sh
deleted file mode 100644
index f44661b..0000000
--- a/modules/distribution/src/main/resources/bin/airavata-server-start.sh
+++ /dev/null
@@ -1,123 +0,0 @@
-#!/usr/bin/env bash
-
-# 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.
-
-. `dirname $0`/setenv.sh
-cd ${AIRAVATA_HOME}/bin
-LOGO_FILE="logo.txt"
-
-JAVA_OPTS=""
-AIRAVATA_COMMAND=""
-EXTRA_ARGS=""
-SERVERS=""
-IS_DAEMON_MODE=false
-LOGO=true
-IS_SUBSET=false
-SUBSET=""
-
-# parse command arguments
-for var in "$@"
-do
-    case ${var} in
-        -xdebug)
-        	AIRAVATA_COMMAND="${AIRAVATA_COMMAND}"
-            JAVA_OPTS="$JAVA_OPTS -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,address=8000"
-            shift
-        ;;
-        -security)
-            JAVA_OPTS="${JAVA_OPTS} -Djava.security.manager -Djava.security.policy=${AIRAVATA_HOME}/conf/axis2.policy -Daxis2.home=${AIRAVATA_HOME}"
-            shift
-        ;;
-	    apiserver | gfac | orchestrator | credentialstore | regserver)
-	        if [ -z ${SERVERS} ] ; then
-	            SERVERS="${var}"
-	        else
-	            SERVERS="${SERVERS},${var}"
-	        fi
-            shift
-        ;;
-        all | api-orch | execution )
-            IS_SUBSET=true
-            SUBSET="${var}"
-            shift
-            ;;
-        -d)
-	        IS_DAEMON_MODE=true
-	        shift
-	        ;;
-	    -nologo)
-	        LOGO=false
-            shift
-        ;;
-        -h)
-            echo "Usage: airavata-server-start.sh [server-name/s] [command-options]"
-            echo "Server names:"
-            echo "  apiserver           Start apiserver"
-            echo "  gfac                Start gfac server"
-            echo "  orchestrator        Start orchestrator server"
-            echo "  credentialstore     Start credentialstore server"
-            echo "  regserver           Start registry server"
-            echo "  all                 Start all servers in one JVM"
-
-            echo "command options:"
-	        echo "  -d                  Start server in daemon mode"
-            echo "  -xdebug             Start Airavata Server under JPDA debugger"
-            echo "  -nologo             Do not show airavata logo"
-            echo "  -security           Enable Java 2 security"
-	        echo "  --<key>[=<value>]   Server setting(s) to override or introduce (overrides values in airavata-server.properties)"
-            echo "  -h                  Display this help and exit"
-            shift
-            exit 0
-        ;;
-	    *)
-	        EXTRA_ARGS="${EXTRA_ARGS} ${var}"
-            shift
-        ;;
-    esac
-done
-
-#Construct Airavata command arguments in proper order.
-if ${IS_SUBSET} ; then
-    AIRAVATA_COMMAND="--servers=${SUBSET} ${AIRAVATA_COMMAND} ${EXTRA_ARGS}"
-else
-    if [ -z ${SERVERS} ] ; then
-        echo "You should provide at least one server component to start the airavata server. Please use -h option to get more details."
-        exit -1
-    else
-        AIRAVATA_COMMAND="--servers=${SERVERS} ${AIRAVATA_COMMAND} ${EXTRA_ARGS}"
-    fi
-fi
-
-#print logo file
-if ${LOGO} ; then
-	if [ -e ${LOGO_FILE} ]
-	then
-		cat ${LOGO_FILE}
-	fi
-fi
-
-
-if ${IS_DAEMON_MODE} ; then
-	echo "Starting airavata server/s in daemon mode..."
-	nohup java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \
-    org.apache.airavata.server.ServerMain ${AIRAVATA_COMMAND} $* > /dev/null 2>&1 &
-else
-	java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \
-    org.apache.airavata.server.ServerMain ${AIRAVATA_COMMAND} $*
-fi
-

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server-stop.sh
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diff --git a/modules/distribution/src/main/resources/bin/airavata-server-stop.sh b/modules/distribution/src/main/resources/bin/airavata-server-stop.sh
deleted file mode 100644
index 7f83f48..0000000
--- a/modules/distribution/src/main/resources/bin/airavata-server-stop.sh
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/env bash
-
-# 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.
-
-. `dirname $0`/setenv.sh
-cd ${AIRAVATA_HOME}/bin
-
-JAVA_OPTS=""
-AIRAVATA_COMMAND=""
-FORCE=false
-
-for var in "$@"
-do
-    case ${var} in
-    	-f | --force)
-	        FORCE=true
-            shift
-        ;;
-        -h)
-            echo "Usage: airavata-server-stop.sh [command-options]"
-            echo "command options:"
-	        echo "  -f , --force       Force stop all airavata servers."
-	        echo "  --<key>[=<value>]  Server setting(s) to override or introduce (overrides values in airavata-server.properties)"
-            echo "  -h                 Display this help and exit"
-            shift
-            exit 0
-        ;;
-	*)
-            shift
-    esac
-done
-
-if ${FORCE} ; then
-	for f in `find . -name "server_start_*"`; do
-	    # split file name using "_" underscore
-		f_split=(${f//_/ });
-		echo "Found process file : $f"
-		echo -n "    Sending kill signals to process ${f_split[2]}..."
-		out=`kill -9 ${f_split[2]} 2>&1`
-		if [ -z "$out" ]; then
-		    echo "done"
-		else
-		    echo "failed (REASON: $out)"
-		fi
-		echo -n "    Removing process file..."
-		out=`rm ${f} 2>&1`
-		if [ -z "$out" ]; then
-		    echo "done"
-		else
-		    echo "failed (REASON: $out)"
-		fi
-	done
-else
-    java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \
-    org.apache.airavata.server.ServerMain stop ${AIRAVATA_COMMAND} $*
-fi

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server.bat
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/airavata-server.bat b/modules/distribution/src/main/resources/bin/airavata-server.bat
deleted file mode 100644
index be2c584..0000000
--- a/modules/distribution/src/main/resources/bin/airavata-server.bat
+++ /dev/null
@@ -1,55 +0,0 @@
-@echo off
-rem Licensed to the Apache Software Foundation (ASF) under one
-rem or more contributor license agreements. See the NOTICE file
-rem distributed with this work for additional information
-rem regarding copyright ownership. The ASF licenses this file
-rem to you under the Apache License, Version 2.0 (the
-rem "License"); you may not use this file except in compliance
-rem with the License. You may obtain a copy of the License at
-rem
-rem http://www.apache.org/licenses/LICENSE-2.0
-rem
-rem Unless required by applicable law or agreed to in writing,
-rem software distributed under the License is distributed on an
-rem "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-rem KIND, either express or implied. See the License for the
-rem specific language governing permissions and limitations
-rem under the License.
-
-setlocal EnableDelayedExpansion
-
-call "%~dp0"setenv.bat
-
-:loop
-if ""%1""==""-xdebug"" goto xdebug
-if ""%1""==""-security"" goto security
-if ""%1""=="""" goto run
-goto help
-
-:xdebug
-set JAVA_OPTS= %JAVA_OPTS% -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,address=8000
-shift
-goto loop
-
-:security
-set JAVA_OPTS=%JAVA_OPTS% -Djava.security.manager -Djava.security.policy=%AIRAVATA_HOME%\conf\axis2.policy -Daxis2.home=%AIRAVATA_HOME%
-shift
-goto loop
-
-:help
-echo  Usage: %0 [-options]
-echo.
-echo  where options include:
-echo   -xdebug    Start Airavata Server under JPDA debugger
-echo   -security  Enable Java 2 security
-echo   -h         Help
-goto end
-
-:run
-cd "%AIRAVATA_HOME%\bin"
-set LOGO_FILE="logo.txt"
-if exist "%LOGO_FILE%" type "%LOGO_FILE%"
-
-java %JAVA_OPTS% -classpath "%AIRAVATA_CLASSPATH%" org.apache.airavata.server.ServerMain %*
-
-:end

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/derby.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/derby.sh b/modules/distribution/src/main/resources/bin/derby.sh
deleted file mode 100644
index 134f7b9..0000000
--- a/modules/distribution/src/main/resources/bin/derby.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-. `dirname $0`/setenv.sh
-export DERBY_HOME=$AIRAVATA_HOME/standalone-server
-cd $AIRAVATA_HOME/bin
-./startNetworkServer $*
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/logo.txt
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/logo.txt b/modules/distribution/src/main/resources/bin/logo.txt
deleted file mode 100644
index e886438..0000000
--- a/modules/distribution/src/main/resources/bin/logo.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-...._....................._..............._...._......................_.........
-.../ \..._.__...__._..___| |__...___...../ \..(_)_.__.__.___...____._|.|_.__._..
-../ _ \.| '_ \./ _` |/ __| '_ \./ _ \.../ _ \.| | '__/ _` \ \./ / _` | __/ _` |.
-./ ___ \| |_) | (_| | (__| |.| |  __/../ ___ \| | |.| (_| |\ V / (_| | || (_| |.
-/_/...\_\ .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|\__\__,_|.
-........|_|.....................................................................
-................................................................................
-................,+????++~..~~++..+????????+??++.++~...~+=???+++.................
-..............:???????....:::...~??????????????.~..::...=????????...............
-............????????..~~..?????..??????????????.?????..~~~.~???????.............
-...........?????????I,~I~~??????.+????????????.~??????~=~..?????????~...........
-.........?????++??????..????????:.??????????I..????????..????????+????..........
-........??.....???????....???????...???????+..+??????+.I.????????.....?,........
-........????==????????..??..?????..=???????=..?????,.=+?.?????????===??=........
-......=??????????+????..+??=.???=.~??????????,.???=,???,.????=+??????????.......
-....??????????+...+I++..???,=...:??????????????.....+??..++I?+..,??????????.....
-....???????=??..........??..+??.:=:.???????......??..??=..........?=???????=....
-....??????..?...........+?..???.....???????......???.??...........~=.??????=....
-....~???~.~..............?..???.~=..,??????...7..???.?.:..............~????:....
-...7....7 ...............?..????. ...??????... .????.?.?.............I ..:.:....
-.....+7=,.+?................????:,I...?????..=.?????.?.............??~.=7+......
-..........????..............??????~...~??..~~??????..?...........+???,..........
-...........???............=.+???????,.?+:.?????????..+...........???+...........
-............??............?,.??????.,??..??????????.,............???............
-...........??,.............=.,????.?+....????????I.I..............=?............
-..........I?..................+??.:?~.....=??????..................??...........
-..........??...?...............??.:?=......??????..............?...??...........
-............++?..............?.????...?....??????.+..............++I............
-.............................?.??????~....???????.?.............................
-............................~~.??????......??????...............................
-.............................=???????......???????+.............................
-..........................=I??++?+++?......?+++++++?+...........................
-..........................,..77..77.........  ..  ...7..........................
-................................................................................

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/setenv.bat
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/setenv.bat b/modules/distribution/src/main/resources/bin/setenv.bat
deleted file mode 100644
index 5f1fda1..0000000
--- a/modules/distribution/src/main/resources/bin/setenv.bat
+++ /dev/null
@@ -1,33 +0,0 @@
-rem Licensed to the Apache Software Foundation (ASF) under one
-rem or more contributor license agreements. See the NOTICE file
-rem distributed with this work for additional information
-rem regarding copyright ownership. The ASF licenses this file
-rem to you under the Apache License, Version 2.0 (the
-rem "License"); you may not use this file except in compliance
-rem with the License. You may obtain a copy of the License at
-rem
-rem http://www.apache.org/licenses/LICENSE-2.0
-rem
-rem Unless required by applicable law or agreed to in writing,
-rem software distributed under the License is distributed on an
-rem "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-rem KIND, either express or implied. See the License for the
-rem specific language governing permissions and limitations
-rem under the License.
-
-@echo off
-
-:initialize
-if "%AIRAVATA_HOME%"=="" set AIRAVATA_HOME=%~sdp0..
-SET curDrive=%cd:~0,1%
-SET airavataDrive=%AIRAVATA_HOME:~0,1%
-if not "%curDrive%" == "%airavataDrive%" %airavataDrive%:
-goto updateClasspath
-
-rem ----- update classpath -----------------------------------------------------
-:updateClasspath
-cd %AIRAVATA_HOME%
-set AIRAVATA_CLASSPATH=
-FOR %%C in ("%AIRAVATA_HOME%\lib\*.jar") DO set AIRAVATA_CLASSPATH=!AIRAVATA_CLASSPATH!;..\lib\%%~nC%%~xC
-
-:end
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/setenv.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/setenv.sh b/modules/distribution/src/main/resources/bin/setenv.sh
deleted file mode 100755
index 9e894e1..0000000
--- a/modules/distribution/src/main/resources/bin/setenv.sh
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-# resolve links - $0 may be a softlink
-PRG="$0"
-
-while [ -h "$PRG" ]; do
-  ls=`ls -ld "$PRG"`
-  link=`expr "$ls" : '.*-> \(.*\)$'`
-  if expr "$link" : '.*/.*' > /dev/null; then
-    PRG="$link"
-  else
-    PRG=`dirname "$PRG"`/"$link"
-  fi
-done
-
-PRGDIR=`dirname "$PRG"`
-
-# Only set AIRAVATA_HOME if not already set
-[ -z "$AIRAVATA_HOME" ] && AIRAVATA_HOME=`cd "$PRGDIR/.." ; pwd`
-
-AIRAVATA_CLASSPATH=""
-
-for f in "$AIRAVATA_HOME"/lib/*.jar
-do
-  AIRAVATA_CLASSPATH="$AIRAVATA_CLASSPATH":$f
-done
-
-export AIRAVATA_HOME
-export AIRAVATA_CLASSPATH

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/startNetworkServer
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/bin/startNetworkServer b/modules/distribution/src/main/resources/bin/startNetworkServer
deleted file mode 100644
index 808566c..0000000
--- a/modules/distribution/src/main/resources/bin/startNetworkServer
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-if [ -n "$derby_common_debug" ] ; then
-  set -x
-fi
-
-# OS specific support.  $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
-  CYGWIN*) cygwin=true ;;
-  Darwin*) darwin=true
-           if [ -z "$JAVA_HOME" ] ; then
-             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
-           fi
-           ;;
-esac
-
-if [ -z "$DERBY_HOME" -o ! -d "$DERBY_HOME" ] ; then
-  ## resolve links - $0 may be a link to derby's home
-  PRG="$0"
-  progname=`basename "$0"`
-
-  # need this for relative symlinks
-  while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-    PRG="$link"
-    else
-    PRG=`dirname "$PRG"`"/$link"
-    fi
-  done
-
-  DERBY_HOME=`dirname "$PRG"`/..
-
-  # make it fully qualified
-  DERBY_HOME=`cd "$DERBY_HOME" && pwd`
-fi
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin ; then
-  [ -n "$DERBY_HOME" ] &&
-    DERBY_HOME=`cygpath --unix "$DERBY_HOME"`
-  [ -n "$JAVA_HOME" ] &&
-    JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-fi
-
-# set DERBY_LIB location
-DERBY_LIB="${DERBY_HOME}/lib"
-
-if [ -z "$JAVACMD" ] ; then
-  if [ -n "$JAVA_HOME"  ] ; then
-    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
-      # IBM's JDK on AIX uses strange locations for the executables
-      JAVACMD="$JAVA_HOME/jre/sh/java"
-    else
-      JAVACMD="$JAVA_HOME/bin/java"
-    fi
-  else
-    JAVACMD=`which java 2> /dev/null `
-    if [ -z "$JAVACMD" ] ; then
-        JAVACMD=java
-    fi
-  fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
-  echo "Error: JAVA_HOME is not defined correctly."
-  echo "  We cannot execute $JAVACMD"
-  exit 1
-fi
-
-# set local classpath, don't overwrite the user's
-LOCALCLASSPATH=$DERBY_LIB/derby.jar:$DERBY_LIB/derbynet.jar:$DERBY_LIB/derbytools.jar:$DERBY_LIB/derbyclient.jar
-
-# if CLASSPATH_OVERRIDE env var is set, LOCALCLASSPATH will be
-# user CLASSPATH first and derby-found jars after.
-# In that case, the user CLASSPATH will override derby-found jars
-#
-# if CLASSPATH_OVERRIDE is not set, we'll have the normal behaviour
-# with derby-found jars first and user CLASSPATH after
-if [ -n "$CLASSPATH" ] ; then
-  # merge local and specified classpath 
-  if [ -z "$LOCALCLASSPATH" ] ; then 
-    LOCALCLASSPATH="$CLASSPATH"
-  elif [ -n "$CLASSPATH_OVERRIDE" ] ; then
-    LOCALCLASSPATH="$CLASSPATH:$LOCALCLASSPATH"
-  else
-    LOCALCLASSPATH="$LOCALCLASSPATH:$CLASSPATH"
-  fi
-
-  # remove class path from launcher -cp option
-  CLASSPATH=""
-fi
-
-# For Cygwin, switch paths to appropriate format before running java
-# For PATHs convert to unix format first, then to windows format to ensure
-# both formats are supported. Probably this will fail on directories with ;
-# in the name in the path. Let's assume that paths containing ; are more
-# rare than windows style paths on cygwin.
-if $cygwin; then
-  if [ "$OS" = "Windows_NT" ] && cygpath -m .>/dev/null 2>/dev/null ; then
-    format=mixed
-  else
-    format=windows
-  fi
-  DERBY_HOME=`cygpath --$format "$DERBY_HOME"`
-  DERBY_LIB=`cygpath --$format "$DERBY_LIB"`
-  if [ -n "$JAVA_HOME" ]; then
-    JAVA_HOME=`cygpath --$format "$JAVA_HOME"`
-  fi
-  LCP_TEMP=`cygpath --path --unix "$LOCALCLASSPATH"`
-  LOCALCLASSPATH=`cygpath --path --$format "$LCP_TEMP"`
-  if [ -n "$CLASSPATH" ] ; then
-    CP_TEMP=`cygpath --path --unix "$CLASSPATH"`
-    CLASSPATH=`cygpath --path --$format "$CP_TEMP"`
-  fi
-  CYGHOME=`cygpath --$format "$HOME"`
-fi
-
-# add a second backslash to variables terminated by a backslash under cygwin
-if $cygwin; then
-  case "$DERBY_HOME" in
-    *\\ )
-    DERBY_HOME="$DERBY_HOME\\"
-    ;;
-  esac
-  case "$CYGHOME" in
-    *\\ )
-    CYGHOME="$CYGHOME\\"
-    ;;
-  esac
-  case "$LOCALCLASSPATH" in
-    *\\ )
-    LOCALCLASSPATH="$LOCALCLASSPATH\\"
-    ;;
-  esac
-  case "$CLASSPATH" in
-    *\\ )
-    CLASSPATH="$CLASSPATH\\"
-    ;;
-  esac
-fi
-
-# Readjust classpath for MKS
-# expr match 
-if [ \( "`expr $SHELL : '.*sh.exe$'`" -gt 0 \) -a \( "$cygwin" = "false" \) ]; then
-  LOCALCLASSPATH=`echo $LOCALCLASSPATH | sed -E 's/([\d\w]*):([\d\w]*)/\1;\2/g
-'`
-fi
-#!/bin/sh
-
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-
-#   http://www.apache.org/licenses/LICENSE-2.0
-
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-
-derby_exec_command="exec \"$JAVACMD\" $DERBY_OPTS -classpath \"$LOCALCLASSPATH\" org.apache.derby.drda.NetworkServerControl start $@"
-eval $derby_exec_command

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/registerSample.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/samples/registerSample.sh b/modules/distribution/src/main/resources/samples/registerSample.sh
deleted file mode 100644
index 384ec0e..0000000
--- a/modules/distribution/src/main/resources/samples/registerSample.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-. `dirname $0`/../bin/setenv.sh
-JAVA_OPTS=""
-
-java -classpath "$AIRAVATA_CLASSPATH" \
-		     org.apache.airavata.client.samples.RegisterSampleData $*

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/add.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/samples/scripts/add.sh b/modules/distribution/src/main/resources/samples/scripts/add.sh
deleted file mode 100755
index daa140b..0000000
--- a/modules/distribution/src/main/resources/samples/scripts/add.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/sh
-# 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.
-
-# add two numbers
-sleep 10
-/bin/echo  "Result=`expr $1 + $2`"

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/echo.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/samples/scripts/echo.sh b/modules/distribution/src/main/resources/samples/scripts/echo.sh
deleted file mode 100755
index 9dbaab9..0000000
--- a/modules/distribution/src/main/resources/samples/scripts/echo.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-#echo wrapper
-sleep 10
-/bin/echo "Echoed_Output=$1"

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/multiply.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/samples/scripts/multiply.sh b/modules/distribution/src/main/resources/samples/scripts/multiply.sh
deleted file mode 100755
index a5b5f7f..0000000
--- a/modules/distribution/src/main/resources/samples/scripts/multiply.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-# mutiply two numbers
-sleep 10
-/bin/echo "Result=`expr $1 \* $2`"

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/subtract.sh
----------------------------------------------------------------------
diff --git a/modules/distribution/src/main/resources/samples/scripts/subtract.sh b/modules/distribution/src/main/resources/samples/scripts/subtract.sh
deleted file mode 100755
index a21bec7..0000000
--- a/modules/distribution/src/main/resources/samples/scripts/subtract.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/sh
-
-# 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.
-
-# substract two numbers
-sleep 10
-/bin/echo "Result=`expr $1 - $2`"

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/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
deleted file mode 100644
index 662a871..0000000
--- a/modules/gfac/gfac-application-specific-handlers/pom.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--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 (theÏ "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. -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <parent>
-        <artifactId>airavata-gfac</artifactId>
-        <groupId>org.apache.airavata</groupId>
-        <version>0.17-SNAPSHOT</version>
-    </parent>
-    <modelVersion>4.0.0</modelVersion>
-
-    <artifactId>airavata-gfac-application-specific-handlers</artifactId>
-    <dependencies>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-    </dependencies>
-
-
-</project>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java b/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java
deleted file mode 100644
index 2481ec9..0000000
--- a/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java
+++ /dev/null
@@ -1,163 +0,0 @@
-///*
-// *
-// * Licensed to the Apache Software Foundation (ASF) under one
-// * or more contributor license agreements.  See the NOTICE file
-// * distributed with this work for additional information
-// * regarding copyright ownership.  The ASF licenses this file
-// * to you under the Apache License, Version 2.0 (the
-// * "License"); you may not use this file except in compliance
-// * with the License.  You may obtain a copy of the License at
-// *
-// *   http://www.apache.org/licenses/LICENSE-2.0
-// *
-// * Unless required by applicable law or agreed to in writing,
-// * software distributed under the License is distributed on an
-// * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// * KIND, either express or implied.  See the License for the
-// * specific language governing permissions and limitations
-// * under the License.
-// *
-// */
-//
-//package org.apache.airavata.application.gaussian.handler;
-//
-//import org.apache.airavata.gfac.core.context.JobExecutionContext;
-//import org.apache.airavata.gfac.core.handler.AbstractHandler;
-//import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-//import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-//import org.apache.airavata.model.experiment.ComputationalResourceScheduling;
-//import org.apache.airavata.registry.cpi.ExperimentCatalogModelType;
-//import org.apache.airavata.registry.cpi.RegistryException;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//import java.io.BufferedReader;
-//import java.io.File;
-//import java.io.FileReader;
-//import java.io.IOException;
-//import java.util.HashMap;
-//import java.util.Map;
-//import java.util.Properties;
-//
-//public class GaussianHandler extends AbstractHandler {
-//
-//    private static final Logger logger = LoggerFactory.getLogger(GaussianHandler.class);
-//    public static final String LINK_SECTION = "%";
-//    public static final String ROUTE_SECTION = "#";
-//    public static final String PROC_SHARED = "procshared";
-//    public static final String MEM = "mem";
-//    public static final String CHK = "chk";
-//    public static final String PROC = "proc";
-//
-//    public static final String EQUAL = "=";
-//    public static final String OPEN_PARENTHESES = "(";
-//    public static final String CLOSE_PARENTHESES = ")";
-//
-//    private String mainInputFilePath;
-//    @Override
-//    public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-//        super.invoke(jobExecutionContext);
-//        Map<String, String> configurations;
-//        Map<String, Object> parameters = jobExecutionContext.getInMessageContext().getParameters();
-//        // only get first input file, which is the main input file
-//        for (Object paraValue : parameters.values()) {
-//            if (paraValue instanceof InputDataObjectType) {
-//                InputDataObjectType inputDataObjectType = (InputDataObjectType) paraValue;
-//                mainInputFilePath = inputDataObjectType.getValue();
-//                break;
-//            }
-//        }
-//        if (mainInputFilePath != null) {
-//            File mainInputFile = new File(mainInputFilePath);
-//            if (mainInputFile.exists()) {
-//                try {
-//                    configurations = parseGaussianInputFile(mainInputFile);
-//                    ComputationalResourceScheduling taskScheduling = jobExecutionContext.getTaskData().getTaskScheduling();
-//                    for (Map.Entry<String, String> inputConfig : configurations.entrySet()) {
-//                        if (inputConfig.getKey().equals(PROC_SHARED)) {
-//                            taskScheduling.setTotalCPUCount(Integer.parseInt(inputConfig.getValue()));
-//                        } else if (inputConfig.getKey().equals(MEM)) {
-//                            int userRequestedMem = Integer.parseInt(inputConfig.getValue());
-//                            int additionalMem = (int) (userRequestedMem * 0.2);
-//                            // TODO check (userRequestedMem + additionalMem)  > maxNode or Queue allowed Mem
-//                            taskScheduling.setTotalPhysicalMemory(userRequestedMem + additionalMem);
-//                        } else if (inputConfig.getKey().equals(PROC)) {
-//                            taskScheduling.setTotalCPUCount(Integer.parseInt(inputConfig.getValue()));
-//                        } else {
-//                            // TODO - handle other input configurations
-//                        }
-//                        logger.info("$$$$$$$$ " + inputConfig.getKey() + " --> " + inputConfig.getValue() + " $$$$$$$$$$$");
-//                    }
-//                    experimentCatalog.update(ExperimentCatalogModelType.TASK_DETAIL, jobExecutionContext.getTaskData(), jobExecutionContext.getTaskData().getTaskID());
-//                } catch (IOException e) {
-//                    throw new GFacHandlerException("Error while reading main input file ", e);
-//                } catch (RegistryException e) {
-//                    throw new GFacHandlerException("Error while updating task details", e);
-//                }
-//            } else {
-//                throw new GFacHandlerException("Main input file doesn't exists " + mainInputFilePath);
-//            }
-//
-//        } else {
-//            throw new GFacHandlerException("Main input file path shouldn't be null");
-//        }
-//
-//    }
-//
-//    /*   %procshared=6  , put this line to the map key:procshared , value:6
-//       keyword = option
-//       keyword(option)
-//       keyword=(option1, option2, …)
-//       keyword(option1, option2, …)*/
-//    // TODO - make this method private
-//    public Map<String, String> parseGaussianInputFile(File mainInputFile) throws IOException {
-//        Map<String, String> configs = new HashMap<String, String>();
-//        BufferedReader br = new BufferedReader(new FileReader(mainInputFile));
-//        String line = br.readLine();
-//        while (line != null) {
-//            line = line.trim();
-//            String keyword = null;
-//            String withoutKeyword = null;
-//            String option = null;
-//            if (line.startsWith(LINK_SECTION)) {
-//                int equalIndex = line.indexOf(EQUAL);
-//                int openParenthesesIndex = line.indexOf(OPEN_PARENTHESES);
-//                // read the keyword
-//                if (equalIndex > 0) {
-//                    keyword = line.substring(1, equalIndex).trim();
-//                    withoutKeyword = line.substring(equalIndex + 1, line.length()); // remove up to = sign
-//                } else if (openParenthesesIndex > 0) {
-//                    keyword = line.substring(1, openParenthesesIndex).trim();
-//                    withoutKeyword = line.substring(openParenthesesIndex, line.length()); // remove left side of ( sign
-//                } else {
-//                    // TODO - malformed input configuration
-//                }
-//                // read the option
-//                if (openParenthesesIndex > 0) {
-//                    if (withoutKeyword.endsWith(CLOSE_PARENTHESES)) {
-//                        option = withoutKeyword.substring(1, withoutKeyword.length() - 1);
-//                    } else {
-//                        //TODO -  malformed input configuration
-//                    }
-//                } else {
-//                    option = withoutKeyword.trim();
-//                }
-//                configs.put(keyword, option);
-//            } else if (line.startsWith(ROUTE_SECTION)) {
-//                // parse the line
-//            }
-//            line = br.readLine();
-//        }
-//        return configs;
-//    }
-//
-//    @Override
-//    public void initProperties(Properties properties) throws GFacHandlerException {
-//
-//    }
-//
-//    @Override
-//    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-//        // Implement this method if we need safe recover steps before rerun the task.
-//    }
-//}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/pom.xml b/modules/gfac/gfac-bes/pom.xml
deleted file mode 100644
index 5f313c0..0000000
--- a/modules/gfac/gfac-bes/pom.xml
+++ /dev/null
@@ -1,130 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--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 (theÏ "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. -->
-
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<parent>
-		<groupId>org.apache.airavata</groupId>
-		<artifactId>airavata-gfac</artifactId>
-		<version>0.17-SNAPSHOT</version>
-		<relativePath>../pom.xml</relativePath>
-	</parent>
-
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>airavata-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>
-
-	<dependencies>
-		
-		<!-- Logging -->
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-api</artifactId>
-		</dependency>
-
-		<!-- GFAC schemas -->
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-gfac-core</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-		<!-- Credential Store -->
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-credential-store</artifactId>
-			<version>${project.version}</version>
-			<exclusions>
-				<exclusion>
-					<groupId>org.bouncycastle</groupId>
-					<artifactId>bcprov-jdk16</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-server-configuration</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.airavata</groupId>
-			<artifactId>airavata-client-configuration</artifactId>
-			<scope>test</scope>
-		</dependency>
-
-
-		<!-- Test -->
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.testng</groupId>
-			<artifactId>testng</artifactId>
-			<version>6.1.1</version>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>jcl-over-slf4j</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-log4j12</artifactId>
-			<scope>test</scope>
-		</dependency>
-
-		<!-- gsi-ssh api dependencies -->
-		<dependency>
-			<groupId>org.apache.xmlbeans</groupId>
-			<artifactId>xmlbeans</artifactId>
-			<version>${xmlbeans.version}</version>
-		</dependency>
-		<!-- Unicore dependencies -->
-		<dependency>
-			<groupId>commons-httpclient</groupId>
-			<artifactId>commons-httpclient</artifactId>
-			<version>3.1</version>
-		</dependency>
-		<dependency>
-			<groupId>eu.unicore</groupId>
-			<artifactId>unicore-client-wrapper</artifactId>
-			<version>1.7.2_1</version>
-			<exclusions>
-				<!-- <exclusion>
-					<groupId>org.apache.santuario</groupId>
-					<artifactId>xmlsec</artifactId>
-				</exclusion> -->
-				<exclusion>
-					<groupId>net.sf.saxon</groupId>
-					<artifactId>saxon</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>net.sf.saxon</groupId>
-					<artifactId>saxon-dom</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>net.sf.saxon</groupId>
-					<artifactId>saxon-xpath</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>net.sf.saxon</groupId>
-			<artifactId>Saxon-HE</artifactId>
-			<version>9.6.0-1</version>
-		</dependency>
-	</dependencies>
-</project>

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java
deleted file mode 100644
index faab749..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
-*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements.  See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership.  The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License.  You may obtain a copy of the License at
-*
-*   http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied.  See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*
-*/
-
-package org.apache.airavata.gfac.bes.handlers;
-
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.Properties;
-
-import org.apache.airavata.registry.cpi.AppCatalogException;
-import org.apache.airavata.gfac.core.GFacException;
-import org.apache.airavata.gfac.bes.security.UNICORESecurityContext;
-import org.apache.airavata.gfac.bes.security.X509SecurityContext;
-import org.apache.airavata.gfac.bes.utils.BESConstants;
-import org.apache.airavata.gfac.bes.utils.DataTransferrer;
-import org.apache.airavata.gfac.bes.utils.SecurityUtils;
-import org.apache.airavata.gfac.bes.utils.StorageCreator;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.GFacUtils;
-import org.apache.airavata.model.appcatalog.computeresource.*;
-import org.apache.airavata.model.experiment.CorrectiveAction;
-import org.apache.airavata.model.experiment.ErrorCategory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.w3.x2005.x08.addressing.EndpointReferenceType;
-
-import de.fzj.unicore.uas.client.StorageClient;
-import eu.unicore.util.httpclient.DefaultClientConfiguration;
-
-public abstract class AbstractSMSHandler implements BESConstants, GFacHandler{
-    
-	private final Logger log = LoggerFactory.getLogger(this.getClass());
-	
-    protected DefaultClientConfiguration secProperties;
-	
-	protected StorageClient storageClient; 
-	
-	protected DataTransferrer dataTransferrer;
-	
-	@Override
-	public void initProperties(Properties properties)
-			throws GFacHandlerException {
-		
-	}
-
-	@Override
-	public void invoke(JobExecutionContext jobExecutionContext)
-			throws GFacHandlerException {
-		try {
-            initSecurityProperties(jobExecutionContext);
-            JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
-            JobSubmissionProtocol protocol = preferredJobSubmissionInterface.getJobSubmissionProtocol();
-            String interfaceId = preferredJobSubmissionInterface.getJobSubmissionInterfaceId();
-            String factoryUrl = null;
-            if (protocol.equals(JobSubmissionProtocol.UNICORE)) {
-                    UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(interfaceId);
-                    factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL();
-            }
-            storageClient = null;
-
-            if (!isSMSInstanceExisting(jobExecutionContext)) {
-                EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance();
-                eprt.addNewAddress().setStringValue(factoryUrl);
-                StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null);
-                try {
-                    storageClient = storageCreator.createStorage();
-                } catch (Exception e2) {
-                    log.error("Cannot create storage..");
-                    throw new GFacHandlerException("Cannot create storage..", e2);
-                }
-                jobExecutionContext.setProperty(PROP_SMS_EPR, storageClient.getEPR());
-            } else {
-                EndpointReferenceType eprt = (EndpointReferenceType) jobExecutionContext.getProperty(PROP_SMS_EPR);
-                try {
-                    storageClient = new StorageClient(eprt, secProperties);
-                } catch (Exception e) {
-                    throw new GFacHandlerException("Cannot create storage..", e);
-                }
-            }
-            dataTransferrer = new DataTransferrer(jobExecutionContext, storageClient);
-        } catch (AppCatalogException e) {
-            throw new GFacHandlerException("Error occurred while retrieving unicore job submission interface..", e);
-        }
-    }
-	
-	protected void initSecurityProperties(JobExecutionContext jobExecutionContext) throws GFacHandlerException{
-		log.debug("Initializing SMSInHandler security properties ..");
-        if (secProperties != null) {
-            secProperties = secProperties.clone();
-            return;
-        }
-        UNICORESecurityContext unicoreContext;
-        try {
-	        if (jobExecutionContext.getSecurityContext(X509SecurityContext.X509_SECURITY_CONTEXT) == null ) {
-				SecurityUtils.addSecurityContext(jobExecutionContext);
-				log.info("Successfully added the UNICORE Security Context");
-	        }
-	    }catch (Exception e) {
-        	log.error(e.getMessage());
-            try {
-                StringWriter errors = new StringWriter();
-                e.printStackTrace(new PrintWriter(errors));
-				GFacUtils.saveErrorDetails(jobExecutionContext, errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
-            } catch (GFacException e1) {
-				 log.error(e1.getLocalizedMessage());
-            }  
-            throw new GFacHandlerException("Error while creating UNICORESecurityContext", e, e.getLocalizedMessage());
-        }
-        	
-		try {
-			unicoreContext = (UNICORESecurityContext) jobExecutionContext.getSecurityContext(X509SecurityContext.X509_SECURITY_CONTEXT);
-			log.info("Successfully retrieved the UNICORE Security Context");
-		} catch (GFacException e) {
-			throw new GFacHandlerException(e);
-		}
-        if(log.isDebugEnabled()) {
-        	log.debug("Generating client's default security configuration..");
-        }
-        //TODO: check what kind of credential (server signed or myproxy) should be used
-        try {
-			secProperties = unicoreContext.getDefaultConfiguration(false);
-		} catch (Exception e) {
-			throw new GFacHandlerException(e);
-		} 
-        if(log.isDebugEnabled()) {
-        	log.debug("Security properties are initialized.");
-        }
-        jobExecutionContext.setProperty(PROP_CLIENT_CONF, secProperties);
-	}
-	
-	protected boolean isSMSInstanceExisting(JobExecutionContext jec){
-		boolean hasSMS = true;
-        if((null == jec.getProperty(PROP_SMS_EPR))) {
-        	hasSMS = false;
-        }
-        return hasSMS;
-	}
-
-	/**
-	 * It checks whether the SMSByteIO protocol is used during the creation 
-	 * of the job execution context.
-	 * */
-	protected boolean isSMSEnabled(JobExecutionContext jobExecutionContext){
-//		if(((UnicoreHostType)jobExecutionContext.getApplicationContext().getHostDescription().getType()).getJobDirectoryMode() == JobDirectoryMode.SMS_BYTE_IO) {
-//			return true;
-//		}
-		return false;
-	}
-	
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java
deleted file mode 100644
index add8cb1..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
-*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements.  See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership.  The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License.  You may obtain a copy of the License at
-*
-*   http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied.  See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*
-*/
-
-package org.apache.airavata.gfac.bes.handlers;
-
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-
-/**
- * Download upload job's input files to the temporary SMS directory.
- * 
- * */
-public class SMSByteIOInHandler extends AbstractSMSHandler implements GFacHandler {
-
-
-	@Override
-	public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException	{
-		super.invoke(jobExecutionContext);
-		if(jobExecutionContext.getInMessageContext().getParameters().size() < 1) return;
-		try{    
-        	dataTransferrer.uploadLocalFiles();
-		} catch (GFacProviderException e) {
-			throw new GFacHandlerException("Cannot upload local data",e);
-		}
-
- 	}
-
-    @Override
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        // TODO: Auto generated method body.
-    }
-
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java
deleted file mode 100644
index 1baa2d9..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
-*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements.  See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership.  The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License.  You may obtain a copy of the License at
-*
-*   http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied.  See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*
-*/
-
-package org.apache.airavata.gfac.bes.handlers;
-
-
-
-import org.apache.airavata.gfac.bes.utils.ActivityInfo;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.ggf.schemas.bes.x2006.x08.besFactory.ActivityStateEnumeration;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SMSByteIOOutHandler extends AbstractSMSHandler implements GFacHandler{
-
-	// TODO: later use AbstractHandler, which cannot be used due to error in RegistryFactory
-		private final Logger log = LoggerFactory.getLogger(this.getClass());
-		
-		@Override
-		public void invoke(JobExecutionContext jobExecutionContext)
-				throws GFacHandlerException {
-			super.invoke(jobExecutionContext);
-			
-			ActivityInfo activityInfo = (ActivityInfo)jobExecutionContext.getProperty(PROP_ACTIVITY_INFO);
-			try {
-			if(activityInfo == null) {
-				log.error("No ActivityInfo instance found. The activity execution is ended due to an exception, see provider logs");
-				return;
-			}
-			
-			if ((activityInfo.getActivityStatus().getState() == ActivityStateEnumeration.FAILED)) {
-	            try {Thread.sleep(5000);}catch (InterruptedException e){}
-	            
-	            try {
-					dataTransferrer.downloadStdOuts();
-				} catch (GFacProviderException e) {
-					throw new GFacHandlerException("Cannot download stdout data",e);
-				}
-			}
-	        else if (activityInfo.getActivityStatus().getState() == ActivityStateEnumeration.FINISHED) {
-	        	try {Thread.sleep(5000);}catch (InterruptedException e){}
-	        	
-	        	try {
-						if (activityInfo.getActivityStatus().getExitCode() == 0) {
-							dataTransferrer.downloadRemoteFiles();
-						} else {
-							dataTransferrer.downloadStdOuts();
-						}
-					} catch (GFacProviderException e) {
-						throw new GFacHandlerException(
-								"Cannot download stdout data", e);
-					}
-				}
-			} finally {
-				try {
-					if (storageClient != null) {
-						storageClient.destroy();
-					}
-				} catch (Exception e) {
-					log.warn("Cannot destroy temporary SMS instance", e);
-				}
-
-			}		
-
-	 	}
-
-    @Override
-    public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-        // TODO: Auto generated method body.
-    }
-}
-

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java
deleted file mode 100644
index 13393c9..0000000
--- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
-*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements.  See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership.  The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License.  You may obtain a copy of the License at
-*
-*   http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied.  See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*
-*/
-
-package org.apache.airavata.gfac.bes.handlers;
-
-public class SMSDirectoryHandler {
-
-}


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