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From lah...@apache.org
Subject git commit: fixing gsi ssh job execution error
Date Tue, 29 Apr 2014 13:09:14 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 64c6657e7 -> e218fc08e


fixing gsi ssh job execution error


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/e218fc08
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/e218fc08
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/e218fc08

Branch: refs/heads/master
Commit: e218fc08e28ffd5a27defa041bbf9785c71e730d
Parents: 64c6657
Author: lahiru <lahiru@apache.org>
Authored: Tue Apr 29 09:08:56 2014 -0400
Committer: lahiru <lahiru@apache.org>
Committed: Tue Apr 29 09:08:56 2014 -0400

----------------------------------------------------------------------
 .../server/src/main/resources/gfac-config.xml   |   2 +-
 .../gfac/deployment/DeploymentEngine.java       |  54 ---
 .../gfac/deployment/DeploymentException.java    |  34 --
 .../gfac/deployment/ResourceFinder.java         |  56 ---
 .../classloaders/JarFileClassLoader.java        | 336 -------------
 .../classloaders/MultiParentClassLoader.java    | 485 -------------------
 .../deployment/classloaders/ResourceHandle.java | 101 ----
 .../classloaders/UrlResourceFinder.java         | 316 ------------
 .../airavata/gfac/util/GFACGSISSHUtils.java     |   2 +-
 9 files changed, 2 insertions(+), 1384 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/configuration/server/src/main/resources/gfac-config.xml
----------------------------------------------------------------------
diff --git a/modules/configuration/server/src/main/resources/gfac-config.xml b/modules/configuration/server/src/main/resources/gfac-config.xml
index 1d30eac..1651205 100644
--- a/modules/configuration/server/src/main/resources/gfac-config.xml
+++ b/modules/configuration/server/src/main/resources/gfac-config.xml
@@ -86,7 +86,7 @@
                 <Handler class="org.apache.airavata.gfac.handler.GSISSHInputHandler"/>
             </InHandlers>
             <OutHandlers>
-                <Handler class="org.apache.airavata.gfac.handler.SOutputHandler"/>
+                <Handler class="org.apache.airavata.gfac.handler.GSISSHOutputHandler"/>
                 <!--Handler class="org.apache.airavata.gfac.handler.AdvancedSCPOutputHandler">
                             <property name="privateKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa"/>
                             <property name="publicKeyPath" value="/Users/lahirugunathilake/.ssh/id_dsa.pub"/>

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentEngine.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentEngine.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentEngine.java
deleted file mode 100644
index 7ec6834..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentEngine.java
+++ /dev/null
@@ -1,54 +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.deployment;
-
-import org.apache.airavata.gfac.GFacConfiguration;
-import org.apache.airavata.gfac.GFacException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class DeploymentEngine {
-    private static final Logger logger = LoggerFactory.getLogger(DeploymentEngine.class);
-
-    public static final String PLUGINS_DIR = "plugins";
-    private GFacConfiguration configuration = null;
-    private File repoPath = null;
-    private File extensionDirectory = null;
-    public DeploymentEngine(GFacConfiguration configuration) {
-        this.configuration = configuration;
-    }
-
-    public void loadRepository(String repoDir) throws DeploymentException {
-        repoPath = new File(repoDir);
-        if(!repoPath.exists()){
-            logger.error("repository path is missing");
-        }
-        if(extensionDirectory == null) {
-            extensionDirectory = new File(repoDir, PLUGINS_DIR);
-        }
-        if(!extensionDirectory.exists()){
-            logger.error("plugins directory is missing");
-        }
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentException.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentException.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentException.java
deleted file mode 100644
index 6e5576c..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/DeploymentException.java
+++ /dev/null
@@ -1,34 +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.deployment;
-
-import org.apache.airavata.gfac.GFacException;
-
-public class DeploymentException extends GFacException{
-    private static final long serialVersionUID = 1L;
-
-	public DeploymentException(String s) {
-        super(s);
-    }
-	public DeploymentException(String s, Throwable throwable) {
-        super(s, throwable);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/ResourceFinder.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/ResourceFinder.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/ResourceFinder.java
deleted file mode 100644
index 6f2fd08..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/ResourceFinder.java
+++ /dev/null
@@ -1,56 +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.deployment;
-import org.apache.airavata.gfac.deployment.classloaders.ResourceHandle;
-
-import java.net.URL;
-import java.util.Enumeration;
-
-/**
- * Abstraction of resource searching policy. Given resource name, the resource
- * finder performs implementation-specific lookup, and, if it is able to locate
- * the resource, returns the {@link AbstractResourceHandle handle(s)} or URL(s) of it.
- *
- * @version $Rev: 704201 $ $Date: 2008-10-13 14:52:25 -0400 (Mon, 13 Oct 2008) $
- */
-public interface ResourceFinder {
-    /**
-     * Find the resource by name and return URL of it if found.
-     *
-     * @param name the resource name
-     * @return resource URL or null if resource was not found
-     */
-    public URL findResource(String name);
-
-    /**
-     * Find all resources with given name and return enumeration of their URLs.
-     *
-     * @param name the resource name
-     * @return enumeration of resource URLs (possibly empty).
-     */
-    public Enumeration findResources(String name);
-
-    /**
-     * Get the resource by name and, if found, open connection to it and return
-     * the {@link AbstractResourceHandle handle} of it.
-     *
-     * @param name the resource name
-     * @return resource handle or null if resource was not found
-     */
-    public ResourceHandle getResource(String name);
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/JarFileClassLoader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/JarFileClassLoader.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/JarFileClassLoader.java
deleted file mode 100644
index e82ad5e..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/JarFileClassLoader.java
+++ /dev/null
@@ -1,336 +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.deployment.classloaders;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.security.*;
-import java.security.cert.Certificate;
-import java.util.Collection;
-import java.util.Enumeration;
-import java.util.jar.Attributes;
-import java.util.jar.Manifest;
-
-public class JarFileClassLoader extends MultiParentClassLoader{
-     private static final URL[] EMPTY_URLS = new URL[0];
-
-    private final UrlResourceFinder resourceFinder = new UrlResourceFinder();
-    private final AccessControlContext acc;
-
-    /**
-     * Creates a JarFileClassLoader that is a child of the system class loader.
-     * @param urls a list of URLs from which classes and resources should be loaded
-     */
-    public JarFileClassLoader(URL[] urls) {
-        super(EMPTY_URLS);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    /**
-     * Creates a JarFileClassLoader that is a child of the specified class loader.
-     * @param urls a list of URLs from which classes and resources should be loaded
-     * @param parent the parent of this class loader
-     */
-    public JarFileClassLoader(URL[] urls, ClassLoader parent) {
-        super(EMPTY_URLS, parent);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    public JarFileClassLoader(URL[] urls, ClassLoader parent, boolean inverseClassLoading, String[] hiddenClasses, String[] nonOverridableClasses) {
-        super(EMPTY_URLS, parent, inverseClassLoading, hiddenClasses, nonOverridableClasses);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    /**
-     * Creates a named class loader as a child of the specified parents.
-     * @param urls the urls from which this class loader will classes and resources
-     * @param parents the parents of this class loader
-     */
-    public JarFileClassLoader(URL[] urls, ClassLoader[] parents) {
-        super(EMPTY_URLS, parents);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    public JarFileClassLoader(URL[] urls, ClassLoader[] parents, boolean inverseClassLoading, Collection hiddenClasses, Collection nonOverridableClasses) {
-        super(EMPTY_URLS, parents, inverseClassLoading, hiddenClasses, nonOverridableClasses);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    public JarFileClassLoader(URL[] urls, ClassLoader[] parents, boolean inverseClassLoading, String[] hiddenClasses, String[] nonOverridableClasses) {
-        super(EMPTY_URLS, parents, inverseClassLoading, hiddenClasses, nonOverridableClasses);
-        this.acc = AccessController.getContext();
-        addURLs(urls);
-    }
-
-    public JarFileClassLoader(JarFileClassLoader source) {
-        super(source);
-        this.acc = AccessController.getContext();
-        addURLs(source.getURLs());
-    }
-
-    public static ClassLoader copy(ClassLoader source) {
-        if (source instanceof JarFileClassLoader) {
-            return new JarFileClassLoader((JarFileClassLoader) source);
-        } else if (source instanceof org.apache.axis2.classloader.MultiParentClassLoader) {
-            return new org.apache.axis2.classloader.MultiParentClassLoader((org.apache.axis2.classloader.MultiParentClassLoader) source);
-        } else if (source instanceof URLClassLoader) {
-            return new URLClassLoader(((URLClassLoader)source).getURLs(), source.getParent());
-        } else {
-            return new URLClassLoader(new URL[0], source);
-        }
-    }
-
-    ClassLoader copy() {
-        return JarFileClassLoader.copy(this);
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    public URL[] getURLs() {
-        return resourceFinder.getUrls();
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    public void addURL(final URL url) {
-        AccessController.doPrivileged(new PrivilegedAction() {
-            public Object run() {
-                resourceFinder.addUrl(url);
-                return null;
-            }
-        }, acc);
-    }
-
-    /**
-     * Adds an array of urls to the end of this class loader.
-     * @param urls the URLs to add
-     */
-    protected void addURLs(final URL[] urls) {
-        AccessController.doPrivileged(new PrivilegedAction() {
-            public Object run() {
-                resourceFinder.addUrls(urls);
-                return null;
-            }
-        }, acc);
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    public void destroy() {
-        resourceFinder.destroy();
-        super.destroy();
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    public URL findResource(final String resourceName) {
-        return (URL) AccessController.doPrivileged(new PrivilegedAction() {
-            public Object run() {
-                return resourceFinder.findResource(resourceName);
-            }
-        }, acc);
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    protected Enumeration<URL> internalfindResources(final String name) throws IOException {
-        return  AccessController.doPrivileged(new PrivilegedAction<Enumeration<URL>>() {
-            public Enumeration<URL> run() {
-                return resourceFinder.findResources(name);
-            }
-        }, acc);
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    protected String findLibrary(String libraryName) {
-        // if the libraryName is actually a directory it is invalid
-        int pathEnd = libraryName.lastIndexOf('/');
-        if (pathEnd == libraryName.length() - 1) {
-            throw new IllegalArgumentException("libraryName ends with a '/' character: " + libraryName);
-        }
-
-        // get the name if the library file
-        final String resourceName;
-        if (pathEnd < 0) {
-            resourceName = System.mapLibraryName(libraryName);
-        } else {
-            String path = libraryName.substring(0, pathEnd + 1);
-            String file = libraryName.substring(pathEnd + 1);
-            resourceName = path + System.mapLibraryName(file);
-        }
-
-        // get a resource handle to the library
-        ResourceHandle resourceHandle = (ResourceHandle) AccessController.doPrivileged(new PrivilegedAction() {
-            public Object run() {
-                return resourceFinder.getResource(resourceName);
-            }
-        }, acc);
-
-        if (resourceHandle == null) {
-            return null;
-        }
-
-        // the library must be accessable on the file system
-        URL url = resourceHandle.getUrl();
-        if (!"file".equals(url.getProtocol())) {
-            return null;
-        }
-
-        return new File(URI.create(url.toString())).getPath();
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    protected Class findClass(final String className) throws ClassNotFoundException {
-        try {
-            return (Class) AccessController.doPrivileged(new PrivilegedExceptionAction() {
-                public Object run() throws ClassNotFoundException {
-                    // first think check if we are allowed to define the package
-                    SecurityManager securityManager = System.getSecurityManager();
-                    if (securityManager != null) {
-                        String packageName;
-                        int packageEnd = className.lastIndexOf('.');
-                        if (packageEnd >= 0) {
-                            packageName = className.substring(0, packageEnd);
-                            securityManager.checkPackageDefinition(packageName);
-                        }
-                    }
-
-
-                    // convert the class name to a file name
-                    String resourceName = className.replace('.', '/') + ".class";
-
-                    // find the class file resource
-                    ResourceHandle resourceHandle = resourceFinder.getResource(resourceName);
-                    if (resourceHandle == null) {
-                        throw new ClassNotFoundException(className);
-                    }
-
-                    byte[] bytes;
-                    Manifest manifest;
-                    try {
-                        // get the bytes from the class file
-                        bytes = resourceHandle.getBytes();
-
-                        // get the manifest for defining the packages
-                        manifest = resourceHandle.getManifest();
-                    } catch (IOException e) {
-                        throw new ClassNotFoundException(className, e);
-                    }
-
-                    // get the certificates for the code source
-                    Certificate[] certificates = resourceHandle.getCertificates();
-
-                    // the code source url is used to define the package and as the security context for the class
-                    URL codeSourceUrl = resourceHandle.getCodeSourceUrl();
-
-                    // define the package (required for security)
-                    definePackage(className, codeSourceUrl, manifest);
-
-                    // this is the security context of the class
-                    CodeSource codeSource = new CodeSource(codeSourceUrl, certificates);
-
-                    // load the class into the vm
-                    return defineClass(className, bytes, 0, bytes.length, codeSource);
-                }
-            }, acc);
-        } catch (PrivilegedActionException e) {
-            throw (ClassNotFoundException) e.getException();
-        }
-    }
-
-    private void definePackage(String className, URL jarUrl, Manifest manifest) {
-        int packageEnd = className.lastIndexOf('.');
-        if (packageEnd < 0) {
-            return;
-        }
-
-        String packageName = className.substring(0, packageEnd);
-        String packagePath = packageName.replace('.', '/') + "/";
-
-        Attributes packageAttributes = null;
-        Attributes mainAttributes = null;
-        if (manifest != null) {
-            packageAttributes = manifest.getAttributes(packagePath);
-            mainAttributes = manifest.getMainAttributes();
-        }
-        Package pkg = getPackage(packageName);
-        if (pkg != null) {
-            if (pkg.isSealed()) {
-                if (!pkg.isSealed(jarUrl)) {
-                    throw new SecurityException("Package was already sealed with another URL: package=" + packageName + ", url=" + jarUrl);
-                }
-            } else {
-                if (isSealed(packageAttributes, mainAttributes)) {
-                    throw new SecurityException("Package was already been loaded and not sealed: package=" + packageName + ", url=" + jarUrl);
-                }
-            }
-        } else {
-            String specTitle = getAttribute(Attributes.Name.SPECIFICATION_TITLE, packageAttributes, mainAttributes);
-            String specVendor = getAttribute(Attributes.Name.SPECIFICATION_VENDOR, packageAttributes, mainAttributes);
-            String specVersion = getAttribute(Attributes.Name.SPECIFICATION_VERSION, packageAttributes, mainAttributes);
-            String implTitle = getAttribute(Attributes.Name.IMPLEMENTATION_TITLE, packageAttributes, mainAttributes);
-            String implVendor = getAttribute(Attributes.Name.IMPLEMENTATION_VENDOR, packageAttributes, mainAttributes);
-            String implVersion = getAttribute(Attributes.Name.IMPLEMENTATION_VERSION, packageAttributes, mainAttributes);
-
-            URL sealBase = null;
-            if (isSealed(packageAttributes, mainAttributes)) {
-                sealBase = jarUrl;
-            }
-
-            definePackage(packageName, specTitle, specVersion, specVendor, implTitle, implVersion, implVendor, sealBase);
-        }
-    }
-
-    private String getAttribute(Attributes.Name name, Attributes packageAttributes, Attributes mainAttributes) {
-        if (packageAttributes != null) {
-            String value = packageAttributes.getValue(name);
-            if (value != null) {
-                return value;
-            }
-        }
-        if (mainAttributes != null) {
-            return mainAttributes.getValue(name);
-        }
-        return null;
-    }
-
-    private boolean isSealed(Attributes packageAttributes, Attributes mainAttributes) {
-        String sealed = getAttribute(Attributes.Name.SEALED, packageAttributes, mainAttributes);
-        return sealed != null && "true".equalsIgnoreCase(sealed);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/MultiParentClassLoader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/MultiParentClassLoader.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/MultiParentClassLoader.java
deleted file mode 100644
index b9b53d6..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/MultiParentClassLoader.java
+++ /dev/null
@@ -1,485 +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.deployment.classloaders;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-import org.apache.commons.logging.LogFactory;
-
-import java.beans.Introspector;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.net.URLStreamHandlerFactory;
-import java.util.*;
-
-
-import org.apache.commons.logging.LogFactory;
-
-import java.beans.Introspector;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.net.URLStreamHandlerFactory;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.List;
-
-/**
- * A MultiParentClassLoader is a simple extension of the URLClassLoader that simply changes the single parent class
- * loader model to support a list of parent class loaders.  Each operation that accesses a parent, has been replaced
- * with a operation that checks each parent in order.  This getParent method of this class will always return null,
- * which may be interpreted by the calling code to mean that this class loader is a direct child of the system class
- * loader.
- *
- * @version $Rev$ $Date$
- */
-public class MultiParentClassLoader extends URLClassLoader {
-    private final ClassLoader[] parents;
-    private final boolean inverseClassLoading;
-    private final String[] hiddenClasses;
-    private final String[] nonOverridableClasses;
-    private final String[] hiddenResources;
-    private final String[] nonOverridableResources;
-    private boolean destroyed = false;
-
-    /**
-     * Creates a named class loader with no parents.
-     *
-     * @param urls the urls from which this class loader will classes and resources
-     */
-    public MultiParentClassLoader(URL[] urls) {
-        super(urls);
-        parents = new ClassLoader[]{ClassLoader.getSystemClassLoader()};
-        inverseClassLoading = false;
-        hiddenClasses = new String[0];
-        nonOverridableClasses = new String[0];
-        hiddenResources = new String[0];
-        nonOverridableResources = new String[0];
-    }
-
-
-    /**
-     * Creates a named class loader as a child of the specified parent.
-     *
-     * @param urls   the urls from which this class loader will classes and resources
-     * @param parent the parent of this class loader
-     */
-    public MultiParentClassLoader(URL[] urls, ClassLoader parent) {
-        this(urls, new ClassLoader[]{parent});
-    }
-
-    public MultiParentClassLoader(URL[] urls, ClassLoader parent, boolean inverseClassLoading,
-                                  String[] hiddenClasses, String[] nonOverridableClasses) {
-        this(urls, new ClassLoader[]{parent}, inverseClassLoading, hiddenClasses,
-             nonOverridableClasses);
-    }
-
-    /**
-     * Creates a named class loader as a child of the specified parent and using the specified URLStreamHandlerFactory
-     * for accessing the urls..
-     *
-     * @param urls    the urls from which this class loader will classes and resources
-     * @param parent  the parent of this class loader
-     * @param factory the URLStreamHandlerFactory used to access the urls
-     */
-    public MultiParentClassLoader(URL[] urls, ClassLoader parent, URLStreamHandlerFactory factory) {
-        this(urls, new ClassLoader[]{parent}, factory);
-    }
-
-    /**
-     * Creates a named class loader as a child of the specified parents.
-     *
-     * @param urls    the urls from which this class loader will classes and resources
-     * @param parents the parents of this class loader
-     */
-    public MultiParentClassLoader(URL[] urls, ClassLoader[] parents) {
-        super(urls);
-        this.parents = copyParents(parents);
-        inverseClassLoading = false;
-        hiddenClasses = new String[0];
-        nonOverridableClasses = new String[0];
-        hiddenResources = new String[0];
-        nonOverridableResources = new String[0];
-    }
-
-    public MultiParentClassLoader(URL[] urls, ClassLoader[] parents, boolean inverseClassLoading,
-                                  Collection hiddenClasses, Collection nonOverridableClasses) {
-        this(urls, parents, inverseClassLoading,
-             (String[]) hiddenClasses.toArray(new String[hiddenClasses.size()]),
-             (String[]) nonOverridableClasses.toArray(new String[nonOverridableClasses.size()]));
-    }
-
-    public MultiParentClassLoader(URL[] urls, ClassLoader[] parents, boolean inverseClassLoading,
-                                  String[] hiddenClasses, String[] nonOverridableClasses) {
-        super(urls);
-        this.parents = copyParents(parents);
-        this.inverseClassLoading = inverseClassLoading;
-        this.hiddenClasses = hiddenClasses;
-        this.nonOverridableClasses = nonOverridableClasses;
-        hiddenResources = toResources(hiddenClasses);
-        nonOverridableResources = toResources(nonOverridableClasses);
-    }
-
-    public MultiParentClassLoader(MultiParentClassLoader source) {
-        this(source.getURLs(), deepCopyParents(source.parents), source.inverseClassLoading, source.hiddenClasses, source.nonOverridableClasses);
-    }
-
-    static ClassLoader copy(ClassLoader source) {
-        if (source instanceof MultiParentClassLoader) {
-            return new MultiParentClassLoader((MultiParentClassLoader) source);
-        } else if (source instanceof URLClassLoader) {
-            return new URLClassLoader(((URLClassLoader) source).getURLs(), source.getParent());
-        } else {
-            return new URLClassLoader(new URL[0], source);
-        }
-    }
-
-    ClassLoader copy() {
-        return MultiParentClassLoader.copy(this);
-    }
-
-    private String[] toResources(String[] classes) {
-        String[] resources = new String[classes.length];
-        for (int i = 0; i < classes.length; i++) {
-            String className = classes[i];
-            resources[i] = className.replace('.', '/');
-        }
-        return resources;
-    }
-
-    /**
-     * Creates a named class loader as a child of the specified parents and using the specified URLStreamHandlerFactory
-     * for accessing the urls..
-     *
-     * @param urls    the urls from which this class loader will classes and resources
-     * @param parents the parents of this class loader
-     * @param factory the URLStreamHandlerFactory used to access the urls
-     */
-    public MultiParentClassLoader(URL[] urls, ClassLoader[] parents,
-                                  URLStreamHandlerFactory factory) {
-        super(urls, null, factory);
-        this.parents = copyParents(parents);
-        inverseClassLoading = false;
-        hiddenClasses = new String[0];
-        nonOverridableClasses = new String[0];
-        hiddenResources = new String[0];
-        nonOverridableResources = new String[0];
-    }
-
-    private static ClassLoader[] copyParents(ClassLoader[] parents) {
-        ClassLoader[] newParentsArray = new ClassLoader[parents.length];
-        for (int i = 0; i < parents.length; i++) {
-            ClassLoader parent = parents[i];
-            if (parent == null) {
-                throw new RuntimeException("parent[" + i + "] is null");
-            }
-            newParentsArray[i] = parent;
-        }
-        return newParentsArray;
-    }
-
-    private static ClassLoader[] deepCopyParents(ClassLoader[] parents) {
-        ClassLoader[] newParentsArray = new ClassLoader[parents.length];
-        for (int i = 0; i < parents.length; i++) {
-            ClassLoader parent = parents[i];
-            if (parent == null) {
-                throw new RuntimeException("parent[" + i + "] is null");
-            }
-            if (parent instanceof MultiParentClassLoader) {
-                parent = ((MultiParentClassLoader) parent).copy();
-            }
-            newParentsArray[i] = parent;
-        }
-        return newParentsArray;
-    }
-
-    /**
-     * Gets the parents of this class loader.
-     *
-     * @return the parents of this class loader
-     */
-    public ClassLoader[] getParents() {
-        return parents;
-    }
-
-    public void addURL(URL url) {
-        // todo this needs a security check
-        super.addURL(url);
-    }
-
-    protected synchronized Class loadClass(String name, boolean resolve)
-            throws ClassNotFoundException {
-        //
-        // Check if class is in the loaded classes cache
-        //
-        Class cachedClass = findLoadedClass(name);
-        if (cachedClass != null) {
-            return resolveClass(cachedClass, resolve);
-        }
-
-        //
-        // if we are using inverse class loading, check local urls first
-        //
-        if (inverseClassLoading && !isDestroyed() && !isNonOverridableClass(name)) {
-            try {
-                Class clazz = findClass(name);
-                return resolveClass(clazz, resolve);
-            } catch (ClassNotFoundException ignored) {
-            }
-        }
-
-        //
-        // Check parent class loaders
-        //
-        if (!isHiddenClass(name)) {
-            for (int i = 0; i < parents.length; i++) {
-                ClassLoader parent = parents[i];
-                try {
-                    Class clazz = parent.loadClass(name);
-                    return resolveClass(clazz, resolve);
-                } catch (ClassNotFoundException ignored) {
-                    // this parent didn't have the class; try the next one
-                    //  TODO REVIEW FOR JAVA 6
-                    // In Java 5, if you passed an array string such as "[Lcom.mypackage.MyClass;" to
-                    // loadClass, the class would indeed be loaded.
-                    // In JDK6, a ClassNotFoundException is thrown.
-                    // The work-around is to use code Class.forName instead.
-                    // Example:
-                    // try {
-                    //       classLoader.loadClass(name);
-                    //  } catch (ClassNotFoundException e) {
-                    //       Class.forName(name, false, loader);
-                    //  }
-                }
-            }
-        }
-
-        //
-        // if we are not using inverse class loading, check local urls now
-        //
-        // don't worry about excluding non-overridable classes here... we
-        // have alredy checked he parent and the parent didn't have the
-        // class, so we can override now
-        if (!isDestroyed()) {
-            try {
-                Class clazz = findClass(name);
-                return resolveClass(clazz, resolve);
-            } catch (ClassNotFoundException ignored) {
-            }
-        }
-
-        throw new ClassNotFoundException(name);
-    }
-
-    private boolean isNonOverridableClass(String name) {
-        for (int i = 0; i < nonOverridableClasses.length; i++) {
-            if (name.startsWith(nonOverridableClasses[i])) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    private boolean isHiddenClass(String name) {
-        for (int i = 0; i < hiddenClasses.length; i++) {
-            if (name.startsWith(hiddenClasses[i])) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    private Class resolveClass(Class clazz, boolean resolve) {
-        if (resolve) {
-            resolveClass(clazz);
-        }
-        return clazz;
-    }
-
-    public URL getResource(String name) {
-        if (isDestroyed()) {
-            return null;
-        }
-
-        //
-        // if we are using inverse class loading, check local urls first
-        //
-        if (inverseClassLoading && !isDestroyed() && !isNonOverridableResource(name)) {
-            URL url = findResource(name);
-            if (url != null) {
-                return url;
-            }
-        }
-
-        //
-        // Check parent class loaders
-        //
-        if (!isHiddenResource(name)) {
-            for (int i = 0; i < parents.length; i++) {
-                ClassLoader parent = parents[i];
-                URL url = parent.getResource(name);
-                if (url != null) {
-                    return url;
-                }
-            }
-        }
-
-        //
-        // if we are not using inverse class loading, check local urls now
-        //
-        // don't worry about excluding non-overridable resources here... we
-        // have alredy checked he parent and the parent didn't have the
-        // resource, so we can override now
-        if (!isDestroyed()) {
-            // parents didn't have the resource; attempt to load it from my urls
-            return findResource(name);
-        }
-
-        return null;
-    }
-
-    public Enumeration findResources(String name) throws IOException {
-        if (isDestroyed()) {
-            return Collections.enumeration(Collections.EMPTY_SET);
-        }
-
-        List resources = new ArrayList();
-
-        //
-        // if we are using inverse class loading, add the resources from local urls first
-        //
-        if (inverseClassLoading && !isDestroyed()) {
-            List myResources = Collections.list(super.findResources(name));
-            resources.addAll(myResources);
-        }
-
-        //
-        // Add parent resources
-        //
-        for (int i = 0; i < parents.length; i++) {
-            ClassLoader parent = parents[i];
-            List parentResources = Collections.list(parent.getResources(name));
-            resources.addAll(parentResources);
-        }
-
-        //
-        // if we are not using inverse class loading, add the resources from local urls now
-        //
-        if (!inverseClassLoading && !isDestroyed()) {
-            List myResources = Collections.list(super.findResources(name));
-            resources.addAll(myResources);
-        }
-
-        return Collections.enumeration(resources);
-    }
-
-    private boolean isNonOverridableResource(String name) {
-        for (int i = 0; i < nonOverridableResources.length; i++) {
-            if (name.startsWith(nonOverridableResources[i])) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    private boolean isHiddenResource(String name) {
-        for (int i = 0; i < hiddenResources.length; i++) {
-            if (name.startsWith(hiddenResources[i])) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    public String toString() {
-        return "[" + getClass().getName() + "]";
-    }
-
-    public synchronized boolean isDestroyed() {
-        return destroyed;
-    }
-
-    public void destroy() {
-        synchronized (this) {
-            if (destroyed) {
-                return;
-            }
-            destroyed = true;
-        }
-
-        LogFactory.release(this);
-//        clearSoftCache(ObjectInputStream.class, "subclassAudits");
-//        clearSoftCache(ObjectOutputStream.class, "subclassAudits");
-//        clearSoftCache(ObjectStreamClass.class, "localDescs");
-//        clearSoftCache(ObjectStreamClass.class, "reflectors");
-
-        // The beanInfoCache in java.beans.Introspector will hold on to Classes which
-        // it has introspected. If we don't flush the cache, we may run out of
-        // Permanent Generation space.
-        Introspector.flushCaches();
-    }
-
-//    private static final Object lock = new Object();
-//    private static boolean clearSoftCacheFailed = false;
-//
-//    private static void clearSoftCache(Class clazz, String fieldName) {
-//        Map cache = null;
-//        try {
-//            Field f = clazz.getDeclaredField(fieldName);
-//            f.setAccessible(true);
-//            cache = (Map) f.get(null);
-//        } catch (Throwable e) {
-//            synchronized (lock) {
-//                if (!clearSoftCacheFailed) {
-//                    clearSoftCacheFailed = true;
-//                    LogFactory.getLog(ConfigurationClassLoader.class).error("Unable to clear SoftCache field " + fieldName + " in class " + clazz);
-//                }
-//            }
-//        }
-//
-//        if (cache != null) {
-//            synchronized (cache) {
-//                cache.clear();
-//            }
-//        }
-//    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/ResourceHandle.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/ResourceHandle.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/ResourceHandle.java
deleted file mode 100644
index 3e5c93f..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/ResourceHandle.java
+++ /dev/null
@@ -1,101 +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.deployment.classloaders;
-
-import java.net.URL;
-import java.io.InputStream;
-import java.io.IOException;
-import java.util.jar.Manifest;
-import java.util.jar.Attributes;
-import java.security.cert.Certificate;
-
-/**
- * This is a handle (a connection) to some resource, which may
- * be a class, native library, text file, image, etc. Handles are returned
- * by a ResourceFinder. A resource handle allows easy access to the resource data
- * (using methods {@link #getInputStream} or {@link #getBytes}) as well as
- * access resource metadata, such as attributes, certificates, etc.
- * <p/>
- * As soon as the handle is no longer in use, it should be explicitly
- * {@link #close}d, similarly to I/O streams.
- *
- * @version $Rev: 704201 $ $Date: 2008-10-13 14:52:25 -0400 (Mon, 13 Oct 2008) $
- */
-public interface ResourceHandle {
-    /**
-     * Return the name of the resource. The name is a "/"-separated path
-     * name that identifies the resource.
-     */
-    String getName();
-
-    /**
-     * Returns the URL of the resource.
-     */
-    URL getUrl();
-
-    /**
-     * Does this resource refer to a directory.  Directory resources are commly used
-     * as the basis for a URL in client application.  A directory resource has 0 bytes for it's content.
-     */
-    boolean isDirectory();
-
-    /**
-     * Returns the CodeSource URL for the class or resource.
-     */
-    URL getCodeSourceUrl();
-
-    /**
-     * Returns and InputStream for reading this resource data.
-     */
-    InputStream getInputStream() throws IOException;
-
-    /**
-     * Returns the length of this resource data, or -1 if unknown.
-     */
-    int getContentLength();
-
-    /**
-     * Returns this resource data as an array of bytes.
-     */
-    byte[] getBytes() throws IOException;
-
-    /**
-     * Returns the Manifest of the JAR file from which this resource
-     * was loaded, or null if none.
-     */
-    Manifest getManifest() throws IOException;
-
-    /**
-     * Return the Certificates of the resource, or null if none.
-     */
-    Certificate[] getCertificates();
-
-    /**
-     * Return the Attributes of the resource, or null if none.
-     */
-    Attributes getAttributes() throws IOException;
-
-    /**
-     * Closes a connection to the resource indentified by this handle. Releases
-     * any I/O objects associated with the handle.
-     */
-    void close();
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/UrlResourceFinder.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/UrlResourceFinder.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/UrlResourceFinder.java
deleted file mode 100644
index f7727cd..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/deployment/classloaders/UrlResourceFinder.java
+++ /dev/null
@@ -1,316 +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.deployment.classloaders;
-
-
-import org.apache.airavata.gfac.deployment.ResourceFinder;
-import org.apache.axis2.classloader.DirectoryResourceLocation;
-import org.apache.axis2.classloader.JarResourceLocation;
-import org.apache.axis2.classloader.ResourceEnumeration;
-import org.apache.axis2.classloader.ResourceLocation;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.*;
-import java.util.jar.Attributes;
-import java.util.jar.Manifest;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.jar.Attributes;
-import java.util.jar.Manifest;
-
-/**
- * @version $Rev: 704201 $ $Date: 2008-10-13 14:52:25 -0400 (Mon, 13 Oct 2008) $
- */
-public class UrlResourceFinder implements ResourceFinder {
-    private final Object lock = new Object();
-    private final LinkedHashSet<URL> urls = new LinkedHashSet<URL>();
-    private final LinkedHashMap<URL, ResourceLocation> classPath = new LinkedHashMap<URL, ResourceLocation>();
-    private final LinkedHashSet<File> watchedFiles = new LinkedHashSet<File>();
-
-    private boolean destroyed = false;
-
-    public UrlResourceFinder() {
-    }
-
-    public UrlResourceFinder(URL[] urls) {
-        addUrls(urls);
-    }
-
-    public void destroy() {
-        synchronized (lock) {
-            if (destroyed) {
-                return;
-            }
-            destroyed = true;
-            urls.clear();
-            for (ResourceLocation resourceLocation : classPath.values()) {
-                resourceLocation.close();
-            }
-            classPath.clear();
-        }
-    }
-
-    public ResourceHandle getResource(String resourceName) {
-        synchronized (lock) {
-            if (destroyed) {
-                return null;
-            }
-            for (Map.Entry<URL, ResourceLocation> entry : getClassPath().entrySet()) {
-                ResourceLocation resourceLocation = entry.getValue();
-                ResourceHandle resourceHandle = (ResourceHandle) resourceLocation.getResourceHandle(resourceName);
-                if (resourceHandle != null && !resourceHandle.isDirectory()) {
-                    return resourceHandle;
-                }
-            }
-        }
-        return null;
-    }
-
-    public URL findResource(String resourceName) {
-        synchronized (lock) {
-            if (destroyed) {
-                return null;
-            }
-            for (Map.Entry<URL, ResourceLocation> entry : getClassPath().entrySet()) {
-                ResourceLocation resourceLocation = entry.getValue();
-                ResourceHandle resourceHandle = (ResourceHandle) resourceLocation.getResourceHandle(resourceName);
-                if (resourceHandle != null) {
-                    return resourceHandle.getUrl();
-                }
-            }
-        }
-        return null;
-    }
-
-    public Enumeration findResources(String resourceName) {
-        synchronized (lock) {
-            return new ResourceEnumeration(new ArrayList<ResourceLocation>(getClassPath().values()), resourceName);
-        }
-    }
-
-    public void addUrl(URL url) {
-        addUrls(Collections.singletonList(url));
-    }
-
-    public URL[] getUrls() {
-        synchronized (lock) {
-            return urls.toArray(new URL[urls.size()]);
-        }
-    }
-
-    /**
-     * Adds an array of urls to the end of this class loader.
-     *
-     * @param urls the URLs to add
-     */
-    protected void addUrls(URL[] urls) {
-        addUrls(Arrays.asList(urls));
-    }
-
-    /**
-     * Adds a list of urls to the end of this class loader.
-     *
-     * @param urls the URLs to add
-     */
-    protected void addUrls(List<URL> urls) {
-        synchronized (lock) {
-            if (destroyed) {
-                throw new IllegalStateException("UrlResourceFinder has been destroyed");
-            }
-
-            boolean shouldRebuild = this.urls.addAll(urls);
-            if (shouldRebuild) {
-                rebuildClassPath();
-            }
-        }
-    }
-
-    private LinkedHashMap<URL, ResourceLocation> getClassPath() {
-        assert Thread.holdsLock(lock) : "This method can only be called while holding the lock";
-
-        for (File file : watchedFiles) {
-            if (file.canRead()) {
-                rebuildClassPath();
-                break;
-            }
-        }
-
-        return classPath;
-    }
-
-    /**
-     * Rebuilds the entire class path.  This class is called when new URLs are added or one of the watched files
-     * becomes readable.  This method will not open jar files again, but will add any new entries not alredy open
-     * to the class path.  If any file based url is does not exist, we will watch for that file to appear.
-     */
-    private void rebuildClassPath() {
-        assert Thread.holdsLock(lock) : "This method can only be called while holding the lock";
-
-        // copy all of the existing locations into a temp map and clear the class path
-        Map<URL, ResourceLocation> existingJarFiles = new LinkedHashMap<URL, ResourceLocation>(classPath);
-        classPath.clear();
-
-        LinkedList<URL> locationStack = new LinkedList<URL>(urls);
-        try {
-            while (!locationStack.isEmpty()) {
-                URL url = locationStack.removeFirst();
-
-                // Skip any duplicate urls in the classpath
-                if (classPath.containsKey(url)) {
-                    continue;
-                }
-
-                // Check is this URL has already been opened
-                ResourceLocation resourceLocation = existingJarFiles.remove(url);
-
-                // If not opened, cache the url and wrap it with a resource location
-                if (resourceLocation == null) {
-                    try {
-                        File file = cacheUrl(url);
-                        resourceLocation = createResourceLocation(url, file);
-                    } catch (FileNotFoundException e) {
-                        // if this is a file URL, the file doesn't exist yet... watch to see if it appears later
-                        if ("file".equals(url.getProtocol())) {
-                            File file = new File(url.getPath());
-                            watchedFiles.add(file);
-                            continue;
-
-                        }
-                    } catch (IOException ignored) {
-                        // can't seem to open the file... this is most likely a bad jar file
-                        // so don't keep a watch out for it because that would require lots of checking
-                        // Dain: We may want to review this decision later
-                        continue;
-                    } catch (UnsupportedOperationException ex) {
-                        // the protocol for the JAR file's URL is not supported.  This can occur when
-                        // the jar file is embedded in an EAR or CAR file.  Proceed but log the message.
-                        System.out.println("The protocol for the JAR file's URL is not supported" + ex);
-                        continue;
-                    }
-                }
-
-                // add the jar to our class path
-                classPath.put(resourceLocation.getCodeSource(), resourceLocation);
-
-                // push the manifest classpath on the stack (make sure to maintain the order)
-                List<URL> manifestClassPath = getManifestClassPath(resourceLocation);
-                locationStack.addAll(0, manifestClassPath);
-            }
-        } catch (Error e) {
-            destroy();
-            throw e;
-        }
-
-        for (ResourceLocation resourceLocation : existingJarFiles.values()) {
-            resourceLocation.close();
-        }
-    }
-
-    protected File cacheUrl(URL url) throws IOException {
-        if (!"file".equals(url.getProtocol())) {
-            // download the jar
-            throw new UnsupportedOperationException("Only local file jars are supported " + url);
-        }
-
-        File file = new File(url.getPath());
-        if (!file.exists()) {
-            throw new FileNotFoundException(file.getAbsolutePath());
-        }
-        if (!file.canRead()) {
-            throw new IOException("File is not readable: " + file.getAbsolutePath());
-        }
-        return file;
-    }
-
-    protected ResourceLocation createResourceLocation(URL codeSource, File cacheFile) throws IOException {
-        if (!cacheFile.exists()) {
-            throw new FileNotFoundException(cacheFile.getAbsolutePath());
-        }
-        if (!cacheFile.canRead()) {
-            throw new IOException("File is not readable: " + cacheFile.getAbsolutePath());
-        }
-
-        ResourceLocation resourceLocation;
-        if (cacheFile.isDirectory()) {
-            // DirectoryResourceLocation will only return "file" URLs within this directory
-            // do not user the DirectoryResourceLocation for non file based urls
-            resourceLocation = new DirectoryResourceLocation(cacheFile);
-        } else {
-            resourceLocation = new JarResourceLocation(codeSource, cacheFile);
-        }
-        return resourceLocation;
-    }
-
-    private List<URL> getManifestClassPath(ResourceLocation resourceLocation) {
-        try {
-            // get the manifest, if possible
-            Manifest manifest = resourceLocation.getManifest();
-            if (manifest == null) {
-                // some locations don't have a manifest
-                return Collections.EMPTY_LIST;
-            }
-
-            // get the class-path attribute, if possible
-            String manifestClassPath = manifest.getMainAttributes().getValue(Attributes.Name.CLASS_PATH);
-            if (manifestClassPath == null) {
-                return Collections.EMPTY_LIST;
-            }
-
-            // build the urls...
-            // the class-path attribute is space delimited
-            URL codeSource = resourceLocation.getCodeSource();
-            LinkedList<URL> classPathUrls = new LinkedList<URL>();
-            for (StringTokenizer tokenizer = new StringTokenizer(manifestClassPath, " "); tokenizer.hasMoreTokens(); ) {
-                String entry = tokenizer.nextToken();
-                try {
-                    // the class path entry is relative to the resource location code source
-                    URL entryUrl = new URL(codeSource, entry);
-                    classPathUrls.addLast(entryUrl);
-                } catch (MalformedURLException ignored) {
-                    // most likely a poorly named entry
-                }
-            }
-            return classPathUrls;
-        } catch (IOException ignored) {
-            // error opening the manifest
-            return Collections.EMPTY_LIST;
-        }
-    }
-}
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/e218fc08/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
index 29952de..d0f92c1 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
@@ -93,6 +93,6 @@ public class GFACGSISSHUtils {
 
             context.setPbsCluster(pbsCluster);
         }
-
+        jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT,context);
     }
 }


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