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Posted to commits@airavata.apache.org by sc...@apache.org on 2016/01/12 16:47:46 UTC

[03/24] airavata git commit: renaming the module

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/FileTransferRequestDao.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/FileTransferRequestDao.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/FileTransferRequestDao.java
deleted file mode 100644
index 6bfb40e..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/FileTransferRequestDao.java
+++ /dev/null
@@ -1,92 +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.file.manager.core.db.dao;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.mongodb.*;
-import com.mongodb.util.JSON;
-import org.apache.airavata.file.manager.core.db.conversion.ModelConversionHelper;
-import org.apache.airavata.file.manager.core.db.utils.MongoUtils;
-import org.apache.airavata.model.file.transfer.FileTransferRequestModel;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.util.UUID;
-
-public class FileTransferRequestDao {
-    private final static Logger logger = LoggerFactory.getLogger(FileTransferRequestDao.class);
-
-    private static final String FILE_TRANSFER_REQUESTS_COLLECTION_NAME = "file-transfer-requests";
-    private DBCollection collection;
-    private ModelConversionHelper modelConversionHelper;
-
-    private static final String TRANSFER_ID = "transfer_id";
-
-    public FileTransferRequestDao() throws IOException {
-        collection = MongoUtils.getFileManagerRegistry().getCollection(FILE_TRANSFER_REQUESTS_COLLECTION_NAME);
-        modelConversionHelper = new ModelConversionHelper();
-        collection.dropIndexes();
-        initIndexes();
-    }
-
-    /**
-     * If indexes are already defined this will simply ignore them
-     */
-    private void initIndexes() {
-        collection.createIndex(new BasicDBObject(TRANSFER_ID, 1), new BasicDBObject("unique", true));
-    }
-
-    public String createFileTransferRequest(FileTransferRequestModel fileTransferRequestModel) throws JsonProcessingException {
-        fileTransferRequestModel.setTransferId(UUID.randomUUID().toString());
-        WriteResult result = collection.insert((DBObject) JSON.parse(
-                modelConversionHelper.serializeObject(fileTransferRequestModel)));
-        logger.debug("No of inserted results " + result.getN());
-        return fileTransferRequestModel.getTransferId();
-    }
-
-    public void updateFileTransferRequest(FileTransferRequestModel fileTransferRequestModel) throws JsonProcessingException {
-        DBObject query = BasicDBObjectBuilder.start().add(
-                TRANSFER_ID, fileTransferRequestModel.getTransferId()).get();
-        WriteResult result = collection.update(query, (DBObject) JSON.parse(
-                modelConversionHelper.serializeObject(fileTransferRequestModel)));
-        logger.debug("No of updated results " + result.getN());
-    }
-
-    public void deleteFileTransferRequest(String trasnferId){
-        DBObject query = BasicDBObjectBuilder.start().add(
-                TRANSFER_ID, trasnferId).get();
-        WriteResult result = collection.remove(query);
-        logger.debug("No of removed file transfer requests " + result.getN());
-    }
-
-    public FileTransferRequestModel getFileTransferRequest(String transferId) throws IOException {
-
-        DBObject criteria = new BasicDBObject(TRANSFER_ID, transferId);
-        DBObject doc = collection.findOne(criteria);
-        if (doc != null) {
-            String json = doc.toString();
-            return (FileTransferRequestModel) modelConversionHelper.deserializeObject(
-                    FileTransferRequestModel.class, json);
-        }
-        return null;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/MetadataDao.java
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diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/MetadataDao.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/MetadataDao.java
deleted file mode 100644
index 9f9d494..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/dao/MetadataDao.java
+++ /dev/null
@@ -1,94 +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.file.manager.core.db.dao;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.mongodb.*;
-import com.mongodb.util.JSON;
-import org.apache.airavata.file.manager.core.db.conversion.ModelConversionHelper;
-import org.apache.airavata.file.manager.core.db.utils.MongoUtils;
-import org.apache.airavata.file.manager.cpi.FileManagerConstants;
-import org.apache.airavata.model.file.metadata.MetadataModel;
-import org.apache.airavata.model.file.replica.FileModel;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.util.UUID;
-
-public class MetadataDao {
-    private final static Logger logger = LoggerFactory.getLogger(MetadataDao.class);
-
-    private static final String METADATA_COLLECTION_NAME = "metadata-models";
-    private DBCollection collection;
-    private ModelConversionHelper modelConversionHelper;
-
-    private static final String METADATA_ID = "metadata_id";
-
-    public MetadataDao() throws IOException {
-        collection = MongoUtils.getFileManagerRegistry().getCollection(METADATA_COLLECTION_NAME);
-        modelConversionHelper = new ModelConversionHelper();
-        collection.dropIndexes();
-        initIndexes();
-    }
-
-    /**
-     * If indexes are already defined this will simply ignore them
-     */
-    private void initIndexes() {
-        collection.createIndex(new BasicDBObject(METADATA_ID, 1), new BasicDBObject("unique", true));
-    }
-
-    public String createMetadata(MetadataModel metadataModel) throws JsonProcessingException {
-        metadataModel.setMetadataId(FileManagerConstants.AIRAVATA_METADATA_ID_PREFIX + UUID.randomUUID().toString());
-        WriteResult result = collection.insert((DBObject) JSON.parse(
-                modelConversionHelper.serializeObject(metadataModel)));
-        logger.debug("No of inserted results " + result.getN());
-        return metadataModel.getMetadataId();
-    }
-
-    public void updateMetadata(MetadataModel metadataModel) throws JsonProcessingException {
-        DBObject query = BasicDBObjectBuilder.start().add(
-                METADATA_ID, metadataModel.getMetadataId()).get();
-        WriteResult result = collection.update(query, (DBObject) JSON.parse(
-                modelConversionHelper.serializeObject(metadataModel)));
-        logger.debug("No of updated results " + result.getN());
-    }
-
-    public void deleteMetadata(String metadataId){
-        DBObject query = BasicDBObjectBuilder.start().add(
-                METADATA_ID,metadataId).get();
-        WriteResult result = collection.remove(query);
-        logger.debug("No of removed metadata model requests " + result.getN());
-    }
-
-    public MetadataModel getMetadata(String metadataId) throws IOException {
-
-        DBObject criteria = new BasicDBObject(METADATA_ID, metadataId);
-        DBObject doc = collection.findOne(criteria);
-        if (doc != null) {
-            String json = doc.toString();
-            return (MetadataModel) modelConversionHelper.deserializeObject(
-                    MetadataModel.class, json);
-        }
-        return null;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/utils/MongoUtils.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/utils/MongoUtils.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/utils/MongoUtils.java
deleted file mode 100644
index 5148dd3..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/db/utils/MongoUtils.java
+++ /dev/null
@@ -1,69 +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.file.manager.core.db.utils;
-
-import org.apache.airavata.file.manager.core.utils.FileManagerConstants;
-import org.apache.airavata.file.manager.core.utils.FileManagerProperties;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.mongodb.DB;
-import com.mongodb.MongoClient;
-
-import java.io.IOException;
-
-public class MongoUtils {
-    private final static Logger logger = LoggerFactory.getLogger(MongoUtils.class);
-
-    private static int port;
-    private static String host;
-    private static MongoClient mongoClient = null;
-    private static DB fileManagerRegistry;
-    private static String FILE_MANAGER_REGISTRY_NAME;
-
-    public static MongoClient getMongoClient() throws IOException {
-        if (mongoClient == null) {
-            FileManagerProperties fileManagerProperties = FileManagerProperties.getInstance();
-            host = fileManagerProperties.getProperty(FileManagerConstants.MONGODB_HOST, "localhost");
-            port = Integer.parseInt(fileManagerProperties.getProperty(FileManagerConstants.MONGODB_PORT, "27017"));
-            FILE_MANAGER_REGISTRY_NAME = fileManagerProperties.getProperty(FileManagerConstants.MONGODB_DB_NAME,
-                    "file-manager-db");
-            mongoClient = new MongoClient(host, port);
-            logger.debug("New Mongo Client created with [" + host + "] and ["
-                    + port + "]");
-
-        }
-        return mongoClient;
-    }
-
-    public static DB getFileManagerRegistry() throws IOException {
-        if (fileManagerRegistry == null) {
-            fileManagerRegistry = getMongoClient().getDB(FILE_MANAGER_REGISTRY_NAME);
-        }
-        return fileManagerRegistry;
-    }
-
-    public static void dropFileManagerRegistry() throws IOException {
-        getMongoClient().dropDatabase(FILE_MANAGER_REGISTRY_NAME);
-        logger.debug("Dropped File Manager Registry");
-
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/RemoteStorageClient.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/RemoteStorageClient.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/RemoteStorageClient.java
deleted file mode 100644
index a9e743c..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/RemoteStorageClient.java
+++ /dev/null
@@ -1,107 +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.file.manager.core.remote.client;
-
-import org.apache.airavata.model.file.transfer.LSEntryModel;
-
-import java.io.File;
-import java.util.List;
-
-public interface RemoteStorageClient {
-
-    /**
-     * Reads a remote file, write it to local temporary directory and returns a file pointer to it
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    File readFile(String filePath) throws Exception;
-
-    /**
-     * Writes the source file in the local storage to specified path in the remote storage
-     * @param sourceFile
-     * @return
-     * @throws Exception
-     */
-    void writeFile(File sourceFile, String filePath) throws Exception;
-
-    /**
-     * Returns a directory listing of the specified directory
-     * @param directoryPath
-     * @return
-     * @throws Exception
-     */
-    List<LSEntryModel> getDirectoryListing(String directoryPath) throws Exception;
-
-    /**
-     * Move the specified file from source to destination within the same storage resource
-     * @param currentPath
-     * @param newPath
-     * @throws Exception
-     */
-    void moveFile(String currentPath, String newPath) throws Exception;
-
-    /**
-     *
-     * @param sourcePath
-     * @param destinationPath
-     * @throws Exception
-     */
-    void copyFile(String sourcePath, String destinationPath) throws Exception;
-
-    /**
-     * Rename file with the given name
-     * @param filePath
-     * @param newFileName
-     * @throws Exception
-     */
-    void renameFile(String filePath, String newFileName) throws Exception;
-
-    /**
-     * Delete the specified file
-     * @param filePath
-     * @throws Exception
-     */
-    void deleteFile(String filePath) throws Exception;
-
-    /**
-     * Create new directory in the specified file
-     * @param newDirPath
-     * @throws Exception
-     */
-    void mkdir(String newDirPath) throws Exception;
-
-    /**
-     * Checks whether specified file exists in the remote storage system
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    boolean checkFileExists(String filePath) throws Exception;
-
-    /**
-     * Checks whether the given path is a directory
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    boolean checkIsDirectory(String filePath) throws Exception;
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/ExecutionContext.java
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diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/ExecutionContext.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/ExecutionContext.java
deleted file mode 100644
index 37da5f9..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/ExecutionContext.java
+++ /dev/null
@@ -1,184 +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.file.manager.core.remote.client.gridftp;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.Properties;
-
-@SuppressWarnings("UnusedDeclaration")
-public class ExecutionContext {
-
-    private String testingHost;
-
-    private String loneStarGridFTP;
-    private String rangerGridFTP;
-    private String trestlesGridFTP;
-
-    private String gridFTPServerSource;
-    private String sourceDataLocation;
-    private String gridFTPServerDestination;
-    private String destinationDataLocation;
-    private String uploadingFilePath;
-
-    public static final String PROPERTY_FILE = "airavata-myproxy-client.properties";
-
-    public ExecutionContext() throws IOException {
-        loadConfigurations();
-    }
-
-    private void loadConfigurations() throws IOException {
-        ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
-        InputStream propertyStream = classLoader.getResourceAsStream(PROPERTY_FILE);
-
-        Properties properties = new Properties();
-        if (propertyStream != null) {
-            properties.load(propertyStream);
-
-            String testingHost = properties.getProperty(GridFTPConstants.TESTINGHOST);
-
-            String loneStarGridFtp = properties.getProperty(GridFTPConstants.LONESTARGRIDFTPEPR);
-            String rangerGridFtp = properties.getProperty(GridFTPConstants.RANGERGRIDFTPEPR);
-            String trestlesGridFtp = properties.getProperty(GridFTPConstants.TRESTLESGRIDFTPEPR);
-
-            String gridFTPServerSource = properties.getProperty(GridFTPConstants.GRIDFTPSERVERSOURCE);
-            String gridFTPSourcePath = properties.getProperty(GridFTPConstants.GRIDFTPSOURCEPATH);
-            String gridFTPServerDestination = properties.getProperty(GridFTPConstants.GRIDFTPSERVERDEST);
-            String gridFTPDestinationPath = properties.getProperty(GridFTPConstants.GRIDFTPDESTPATH);
-            String gridFTPUploadingPath = properties.getProperty(GridFTPConstants.UPLOADING_FILE_PATH);
-
-            if (testingHost != null) {
-                this.testingHost = testingHost;
-            }
-
-            if (loneStarGridFtp != null) {
-                this.loneStarGridFTP = loneStarGridFtp;
-            }
-            if (rangerGridFtp != null) {
-                this.rangerGridFTP= rangerGridFtp;
-            }
-            if (trestlesGridFtp != null) {
-                this.trestlesGridFTP = trestlesGridFtp;
-            }
-
-            if (gridFTPServerSource != null && !gridFTPServerSource.isEmpty()) {
-                this.gridFTPServerSource = gridFTPServerSource;
-            }
-            if (gridFTPSourcePath != null && !gridFTPSourcePath.isEmpty()) {
-                this.sourceDataLocation = gridFTPSourcePath;
-            }
-            if (gridFTPServerDestination != null && !gridFTPServerDestination.isEmpty()) {
-                this.gridFTPServerDestination = gridFTPServerDestination;
-            }
-            if (gridFTPDestinationPath != null && !gridFTPDestinationPath.isEmpty()) {
-                this.destinationDataLocation = gridFTPDestinationPath;
-            }
-            if (gridFTPUploadingPath != null && !gridFTPUploadingPath.isEmpty()) {
-                this.uploadingFilePath = gridFTPUploadingPath;
-            }
-
-        }
-    }
-
-    public String getTestingHost() {
-        return testingHost;
-    }
-
-    public void setTestingHost(String testingHost) {
-        this.testingHost = testingHost;
-    }
-
-    public String getLoneStarGridFTP() {
-        return loneStarGridFTP;
-    }
-
-    public void setLoneStarGridFTP(String loneStarGridFTP) {
-        this.loneStarGridFTP = loneStarGridFTP;
-    }
-
-    public String getRangerGridFTP() {
-        return rangerGridFTP;
-    }
-
-    public void setRangerGridFTP(String rangerGridFTP) {
-        this.rangerGridFTP = rangerGridFTP;
-    }
-
-    public String getTrestlesGridFTP() {
-        return trestlesGridFTP;
-    }
-
-    public void setTrestlesGridFTP(String trestlesGridFTP) {
-        this.trestlesGridFTP = trestlesGridFTP;
-    }
-
-    public String getGridFTPServerSource() {
-        return gridFTPServerSource;
-    }
-
-    public void setGridFTPServerSource(String gridFTPServerSource) {
-        this.gridFTPServerSource = gridFTPServerSource;
-    }
-
-    public URI getSourceDataFileUri() throws URISyntaxException {
-        String file = gridFTPServerSource + getSourceDataLocation();
-        return new URI(file);
-    }
-
-    public URI getUploadingFilePathUri() throws URISyntaxException {
-        String file = gridFTPServerSource + getUploadingFilePath();
-        return new URI(file);
-    }
-
-    public String getUploadingFilePath() {
-        return uploadingFilePath;
-    }
-
-    public void setUploadingFilePath(String uploadingFilePath) {
-        this.uploadingFilePath = uploadingFilePath;
-    }
-
-    public String getSourceDataLocation() {
-        return sourceDataLocation;
-    }
-
-    public void setSourceDataLocation(String sourceDataLocation) {
-        this.sourceDataLocation = sourceDataLocation;
-    }
-
-    public String getGridFTPServerDestination() {
-        return gridFTPServerDestination;
-    }
-
-    public void setGridFTPServerDestination(String gridFTPServerDestination) {
-        this.gridFTPServerDestination = gridFTPServerDestination;
-    }
-
-    public String getDestinationDataLocation() {
-        return destinationDataLocation;
-    }
-
-    public void setDestinationDataLocation(String destinationDataLocation) {
-        this.destinationDataLocation = destinationDataLocation;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTP.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTP.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTP.java
deleted file mode 100644
index 89bfba3..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTP.java
+++ /dev/null
@@ -1,430 +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.file.manager.core.remote.client.gridftp;
-
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.net.URISyntaxException;
-
-import org.apache.log4j.Logger;
-import org.globus.ftp.DataChannelAuthentication;
-import org.globus.ftp.DataSourceStream;
-import org.globus.ftp.GridFTPClient;
-import org.globus.ftp.HostPort;
-import org.globus.ftp.Marker;
-import org.globus.ftp.MarkerListener;
-import org.globus.ftp.Session;
-import org.globus.ftp.exception.ClientException;
-import org.globus.ftp.exception.ServerException;
-import org.globus.gsi.gssapi.auth.HostAuthorization;
-import org.ietf.jgss.GSSCredential;
-
-/**
- * GridFTP tools
- */
-public class GridFTP {
-
-    public static final String GSIFTP_SCHEME = "gsiftp";
-    private static final Logger log = Logger.getLogger(GridFTP.class);
-
-    /**
-     * Make directory at remote location
-     *
-     * @param destURI Directory name and server location to create the directory.
-     * @param gssCred Credentials to authenticate with remote server.
-     * @throws ServerException If an error occurred while authenticating.
-     * @throws IOException If an error occurred while creating the directory.
-     */
-    public void makeDir(URI destURI, GSSCredential gssCred) throws Exception {
-        GridFTPClient destClient = null;
-        GridFTPContactInfo destHost = new GridFTPContactInfo(destURI.getHost(), destURI.getPort());
-        try {
-
-            String destPath = destURI.getPath();
-            log.info(("Creating Directory = " + destHost + "=" + destPath));
-
-            destClient = new GridFTPClient(destHost.hostName, destHost.port);
-
-            int tryCount = 0;
-            while (true) {
-                try {
-                    destClient.setAuthorization(new HostAuthorization("host"));
-                    destClient.authenticate(gssCred);
-                    destClient.setDataChannelAuthentication(DataChannelAuthentication.SELF);
-
-                    if (!destClient.exists(destPath)) {
-                        destClient.makeDir(destPath);
-                    }
-                    break;
-                } catch (ServerException e) {
-                    tryCount++;
-                    if (tryCount >= 3) {
-                        throw new Exception(e.getMessage(), e);
-                    }
-                    Thread.sleep(10000);
-                } catch (IOException e) {
-                    tryCount++;
-                    if (tryCount >= 3) {
-                        throw new Exception(e.getMessage(), e);
-                    }
-                    Thread.sleep(10000);
-                }
-            }
-        } catch (ServerException e) {
-            throw new Exception("Cannot Create GridFTP Client to:" + destHost.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot Create GridFTP Client to:" + destHost.toString(), e);
-        } catch (InterruptedException e) {
-            throw new Exception("Internal Error cannot sleep", e);
-        } finally {
-            if (destClient != null) {
-                try {
-                    destClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Upload file from stream
-     *
-     * @param destURI Name of the file to be uploaded.
-     * @param gsCredential Credentials to authenticate.
-     */
-    public void updateFile(URI destURI, GSSCredential gsCredential, InputStream io) throws Exception {
-        GridFTPClient ftpClient = null;
-        GridFTPContactInfo contactInfo = new GridFTPContactInfo(destURI.getHost(), destURI.getPort());
-
-        try {
-
-            String remoteFile = destURI.getPath();
-            log.info("The remote file is " + remoteFile);
-
-            log.info("Setup GridFTP Client");
-
-            ftpClient = new GridFTPClient(contactInfo.hostName, contactInfo.port);
-            ftpClient.setAuthorization(new HostAuthorization("host"));
-            ftpClient.authenticate(gsCredential);
-            ftpClient.setDataChannelAuthentication(DataChannelAuthentication.SELF);
-
-            log.info("Uploading file");
-
-            ftpClient.put(remoteFile, new DataSourceStream(io), new MarkerListener() {
-                public void markerArrived(Marker marker) {
-                }
-            });
-
-            log.info("Upload file to:" + remoteFile + " is done");
-
-        } catch (ServerException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } catch (ClientException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } finally {
-            if (ftpClient != null) {
-                try {
-                    ftpClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Upload file to remote location
-     *
-     * @param destURI Name of the file to be uploaded.
-     * @param gsCredential Credentials used to upload the file.
-     * @param localFile Local file to be uploaded.
-     */
-    public void updateFile(URI destURI, GSSCredential gsCredential, File localFile) throws Exception {
-        GridFTPClient ftpClient = null;
-        GridFTPContactInfo contactInfo = new GridFTPContactInfo(destURI.getHost(), destURI.getPort());
-        try {
-
-            String remoteFile = destURI.getPath();
-
-            log.info("The local temp file is " + localFile);
-            log.info("the remote file is " + remoteFile);
-
-            log.info("Setup GridFTP Client");
-
-            ftpClient = new GridFTPClient(contactInfo.hostName, contactInfo.port);
-            ftpClient.setAuthorization(new HostAuthorization("host"));
-            ftpClient.authenticate(gsCredential);
-            ftpClient.setDataChannelAuthentication(DataChannelAuthentication.SELF);
-
-            log.info("Uploading file");
-
-            ftpClient.put(localFile, remoteFile, false);
-
-
-            log.info("Upload file to:" + remoteFile + " is done");
-
-        } catch (ServerException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } catch (ClientException e) {
-            throw new Exception("Cannot upload file to GridFTP:" + contactInfo.toString(), e);
-        } finally {
-            if (ftpClient != null) {
-                try {
-                    ftpClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Download File from remote location
-     *
-     * @param destURI  File to be downloaded.
-     * @param gsCredential To authenticate user to remote machine.
-     * @param localFile The downloaded file name.
-     */
-    public void downloadFile(URI destURI, GSSCredential gsCredential, File localFile) throws Exception {
-        GridFTPClient ftpClient = null;
-        GridFTPContactInfo contactInfo = new GridFTPContactInfo(destURI.getHost(), destURI.getPort());
-        try {
-            String remoteFile = destURI.getPath();
-
-            log.info("The local temp file is " + localFile);
-            log.info("the remote file is " + remoteFile);
-
-            log.info("Setup GridFTP Client");
-
-            ftpClient = new GridFTPClient(contactInfo.hostName, contactInfo.port);
-            ftpClient.setAuthorization(new HostAuthorization("host"));
-            ftpClient.authenticate(gsCredential);
-            ftpClient.setDataChannelAuthentication(DataChannelAuthentication.SELF);
-
-            log.info("Downloading file");
-
-            ftpClient.get(remoteFile, localFile);
-
-            log.info("Download file to:" + remoteFile + " is done");
-
-        } catch (ServerException e) {
-            throw new Exception("Cannot download file from GridFTP:" + contactInfo.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot download file from GridFTP:" + contactInfo.toString(), e);
-        } catch (ClientException e) {
-            throw new Exception("Cannot download file from GridFTP:" + contactInfo.toString(), e);
-        } finally {
-            if (ftpClient != null) {
-                try {
-                    ftpClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Checks whether files exists.
-     *
-     * @param destURI Name of the file to check existence.
-     * @param gsCredential Credentials to authenticate user.
-     */
-    public boolean exists(URI destURI, GSSCredential gsCredential) throws Exception {
-        GridFTPClient ftpClient = null;
-        GridFTPContactInfo contactInfo = new GridFTPContactInfo(destURI.getHost(), destURI.getPort());
-        try {
-            String remoteFile = destURI.getPath();
-
-            log.info("the remote file is " + remoteFile);
-
-            log.info("Setup GridFTP Client");
-
-            ftpClient = new GridFTPClient(contactInfo.hostName, contactInfo.port);
-            ftpClient.setAuthorization(new HostAuthorization("host"));
-            ftpClient.authenticate(gsCredential);
-            ftpClient.setDataChannelAuthentication(DataChannelAuthentication.SELF);
-
-            log.info("Checking whether file exists");
-
-            return ftpClient.exists(destURI.getPath());
-
-        } catch (ServerException e) {
-            throw new Exception("Cannot download file from GridFTP:" + contactInfo.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot download file from GridFTP:" + contactInfo.toString(), e);
-        } finally {
-            if (ftpClient != null) {
-                try {
-                    ftpClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Stream remote file
-     *
-     * @param destURI Remote file to be read.
-     * @param gsCredential Credentials to authenticate user.
-     * @param localFile Downloaded local file name.
-     * @return  The content of the downloaded file.
-     */
-    public String readRemoteFile(URI destURI, GSSCredential gsCredential, File localFile) throws Exception {
-        BufferedReader instream = null;
-        File localTempfile = null;
-        try {
-
-            if (localFile == null) {
-                localTempfile = File.createTempFile("stderr", "err");
-            } else {
-                localTempfile = localFile;
-            }
-
-            log.info("Loca temporary file:" + localTempfile);
-
-            downloadFile(destURI, gsCredential, localTempfile);
-
-            instream = new BufferedReader(new FileReader(localTempfile));
-            StringBuffer buff = new StringBuffer();
-            String temp = null;
-            while ((temp = instream.readLine()) != null) {
-                buff.append(temp);
-                buff.append(System.getProperty("line.separator"));
-            }
-
-            log.info("finish read file:" + localTempfile);
-
-            return buff.toString();
-        } catch (FileNotFoundException e) {
-            throw new Exception("Cannot read localfile file:" + localTempfile, e);
-        } catch (IOException e) {
-            throw new Exception("Cannot read localfile file:" + localTempfile, e);
-        } finally {
-            if (instream != null) {
-                try {
-                    instream.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection");
-                }
-            }
-        }
-    }
-
-    /**
-     * Transfer data from one GridFTp Endpoint to another GridFTP Endpoint
-     *
-     * @param srchost Source file and host.
-     * @param desthost Destination file and host.
-     * @param gssCred Credentials to be authenticate user.
-     * @param srcActive Tells source to be active. i.e. asking src to connect destination.
-     * @throws ServerException If an error occurred while transferring data.
-     * @throws ClientException If an error occurred while transferring data.
-     * @throws IOException If an error occurred while transferring data.
-     */
-    public void transfer(URI srchost, URI desthost, GSSCredential gssCred, boolean srcActive) throws Exception {
-        GridFTPClient destClient = null;
-        GridFTPClient srcClient = null;
-
-        try {
-            destClient = new GridFTPClient(desthost.getHost(), desthost.getPort());
-            destClient.setAuthorization(new HostAuthorization("host"));
-            destClient.authenticate(gssCred);
-            destClient.setType(Session.TYPE_IMAGE);
-
-            srcClient = new GridFTPClient(srchost.getHost(), srchost.getPort());
-            srcClient.setAuthorization(new HostAuthorization("host"));
-            srcClient.authenticate(gssCred);
-            srcClient.setType(Session.TYPE_IMAGE);
-
-            if (srcActive) {
-                log.info("Set src active");
-                HostPort hp = destClient.setPassive();
-                srcClient.setActive(hp);
-            } else {
-                log.info("Set dst active");
-                HostPort hp = srcClient.setPassive();
-                destClient.setActive(hp);
-            }
-
-            log.info("Start transfer file from GridFTP:" + srchost.toString() + " to " + desthost.toString());
-
-            /**
-             * Transfer a file. The transfer() function blocks until the transfer is complete.
-             */
-            srcClient.transfer(srchost.getPath(), destClient, desthost.getPath(), false, null);
-            if (srcClient.getSize(srchost.getPath()) == destClient.getSize(desthost.getPath())) {
-                log.info("CHECK SUM OK");
-            } else {
-                log.info("****CHECK SUM FAILED****");
-            }
-
-        } catch (ServerException e) {
-            throw new Exception("Cannot transfer file from GridFTP:" + srchost.toString() + " to "
-                    + desthost.toString(), e);
-        } catch (IOException e) {
-            throw new Exception("Cannot transfer file from GridFTP:" + srchost.toString() + " to "
-                    + desthost.toString(), e);
-        } catch (ClientException e) {
-            throw new Exception("Cannot transfer file from GridFTP:" + srchost.toString() + " to "
-                    + desthost.toString(), e);
-        } finally {
-            if (destClient != null) {
-                try {
-                    destClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection at Desitnation:" + desthost.toString());
-                }
-            }
-            if (srcClient != null) {
-                try {
-                    srcClient.close();
-                } catch (Exception e) {
-                    log.info("Cannot close GridFTP client connection at Source:" + srchost.toString());
-                }
-            }
-        }
-    }
-
-    public static URI createGsiftpURI(String host, String localPath) throws URISyntaxException {
-        StringBuffer buf = new StringBuffer();
-        if (!host.startsWith("gsiftp://"))
-            buf.append("gsiftp://");
-        buf.append(host);
-        if (!host.endsWith("/"))
-            buf.append("/");
-        buf.append(localPath);
-        return new URI(buf.toString());
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPConstants.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPConstants.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPConstants.java
deleted file mode 100644
index 5e00df0..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPConstants.java
+++ /dev/null
@@ -1,45 +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.file.manager.core.remote.client.gridftp;
-
-public class GridFTPConstants {
-
-    public static final String MYPROXY_SERVER = "myproxyServer";
-    public static final String MYPROXY_PORT = "myproxyPort";
-    public static final String MYPROXY_LIFETIME = "myproxy_lifetime";
-    public static final String MYPROXY_USERNAME = "myproxyUserName";
-    public static final String MYPROXY_PASSWD = "myproxyPasswd";
-    public static final String TRUSTED_CERTS_FILE = "trustedCertsFile";
-    public static final String HOSTCERTS_KEY_FILE = "hostcertsKeyFile";
-
-    public static final String TESTINGHOST = "testing.host";
-
-    public static final String LONESTARGRIDFTPEPR = "lonestar.gridftp.endpoint";
-    public static final String RANGERGRIDFTPEPR = "ranger.gridftp.endpoint";
-    public static final String TRESTLESGRIDFTPEPR = "trestles.gridftp.endpoint";
-
-    public static final String GRIDFTPSERVERSOURCE = "gridftpserverSource";
-    public static final String GRIDFTPSOURCEPATH = "gridftpSourcePath";
-    public static final String GRIDFTPSERVERDEST = "gridftpserverDest";
-    public static final String GRIDFTPDESTPATH = "gridftpDestPath";
-    public static final String UPLOADING_FILE_PATH = "gridftpUploadingFilePath";
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPContactInfo.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPContactInfo.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPContactInfo.java
deleted file mode 100644
index 060f015..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/GridFTPContactInfo.java
+++ /dev/null
@@ -1,60 +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.file.manager.core.remote.client.gridftp;
-
-/**
-* Class represents GridFTP Endpoint
-*
-*/
-public class GridFTPContactInfo {
-    public static final int DEFAULT_GSI_FTP_PORT = 2811;
-    public String hostName;
-    public int port;
-
-    public GridFTPContactInfo(String hostName, int port) {
-        if (port <= 0 || port == 80) {
-            port = DEFAULT_GSI_FTP_PORT;
-        }
-        this.hostName = hostName;
-        this.port = port;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (obj instanceof GridFTPContactInfo) {
-            return hostName.equals(((GridFTPContactInfo) obj).hostName) && port == ((GridFTPContactInfo) obj).port;
-        } else {
-            return false;
-        }
-    }
-
-    @Override
-    public int hashCode() {
-        return hostName.hashCode();
-    }
-
-    @Override
-    public String toString() {
-        StringBuffer buf = new StringBuffer();
-        buf.append(hostName).append(":").append(port);
-        return buf.toString();
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/CertificateManager.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/CertificateManager.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/CertificateManager.java
deleted file mode 100644
index 00d9343..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/CertificateManager.java
+++ /dev/null
@@ -1,87 +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.file.manager.core.remote.client.gridftp.myproxy;
-
-import java.io.InputStream;
-import java.security.GeneralSecurityException;
-import java.security.cert.X509Certificate;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.globus.gsi.util.CertificateLoadUtil;
-import org.globus.util.ClassLoaderUtils;
-
-public class CertificateManager {
-
-    private static X509Certificate[] trustedCertificates;
-
-    /**
-     * Load CA certificates from a file included in the XBaya jar.
-     *
-     * @return The trusted certificates.
-     */
-    public static X509Certificate[] getTrustedCertificate(String certificate) {
-        if (trustedCertificates != null) {
-            return trustedCertificates;
-        }
-
-        List<X509Certificate> extremeTrustedCertificates = getTrustedCertificates(certificate);
-
-        List<X509Certificate> allTrustedCertificates = new ArrayList<X509Certificate>();
-        allTrustedCertificates.addAll(extremeTrustedCertificates);
-
-        trustedCertificates = allTrustedCertificates.toArray(new X509Certificate[allTrustedCertificates.size()]);
-        return trustedCertificates;
-    }
-
-    private static List<X509Certificate> getTrustedCertificates(String pass) {
-        // ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); //**
-        // InputStream stream = classLoader.getResourceAsStream(pass); //**
-        InputStream stream = ClassLoaderUtils.getResourceAsStream(pass); // **
-        if (stream == null) {
-            throw new RuntimeException("Failed to get InputStream to " + pass);
-        }
-        return readTrustedCertificates(stream);
-    }
-
-    /**
-     * @param stream
-     * @return List of X509Certificate
-     */
-    public static List<X509Certificate> readTrustedCertificates(InputStream stream) {
-        ArrayList<X509Certificate> certificates = new ArrayList<X509Certificate>();
-        while (true) {
-            X509Certificate certificate;
-            try {
-                certificate = CertificateLoadUtil.loadCertificate(stream);
-            } catch (GeneralSecurityException e) {
-                String message = "Certificates are invalid";
-                throw new RuntimeException(message, e);
-            }
-            if (certificate == null) {
-                break;
-            }
-            certificates.add(certificate);
-        }
-        return certificates;
-    }
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/MyProxyCredentials.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/MyProxyCredentials.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/MyProxyCredentials.java
deleted file mode 100644
index 23dfd5e..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/MyProxyCredentials.java
+++ /dev/null
@@ -1,296 +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.file.manager.core.remote.client.gridftp.myproxy;
-
-import java.io.*;
-import java.security.PrivateKey;
-import java.security.cert.X509Certificate;
-
-import org.apache.log4j.Logger;
-import org.globus.gsi.X509Credential;
-import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
-import org.globus.myproxy.GetParams;
-import org.globus.myproxy.MyProxy;
-import org.ietf.jgss.GSSCredential;
-
-/**
- * Class to manipulate my proxy credentials. Responsible for retrieving, creating
- * my proxy credentials.
- */
-public class MyProxyCredentials implements Serializable {
-
-    private static final long serialVersionUID = -2471014486509046212L;
-    protected String myProxyHostname;
-    protected String myProxyUserName;
-    protected String myProxyPassword;
-    protected int myProxyPortNumber;
-    protected int myProxyLifeTime = 14400;
-    protected String trustedCertificatePath;
-
-    private static final Logger log = Logger.getLogger(MyProxyCredentials.class);
-
-    /**
-     * Default constructor.
-     */
-    public MyProxyCredentials() {
-    }
-
-    /**
-     * Constructor.
-     * @param myProxyServer Ip address of the my proxy server.
-     * @param myProxyPort Port which my proxy server is running.
-     * @param myProxyUsername User name to connect to my proxy server.
-     * @param myProxyPassPhrase Password for my proxy authentication.
-     * @param myProxyLifetime Lifetime of the retrieving credentials.
-     * @param trustedCerts Trusted certificate location for SSL communication.
-     */
-    public MyProxyCredentials(String myProxyServer, int myProxyPort, String myProxyUsername, String myProxyPassPhrase,
-                              int myProxyLifetime, String trustedCerts) {
-
-        this.myProxyHostname = myProxyServer;
-        this.myProxyPortNumber = myProxyPort;
-        this.myProxyUserName = myProxyUsername;
-        this.myProxyPassword = myProxyPassPhrase;
-        this.myProxyLifeTime = myProxyLifetime;
-        this.trustedCertificatePath = trustedCerts;
-
-        init();
-
-    }
-
-    /**
-     * Gets the default proxy certificate.
-     * @return Default my proxy credentials.
-     * @throws Exception If an error occurred while retrieving credentials.
-     */
-    public GSSCredential getDefaultCredentials() throws Exception {
-        MyProxy myproxy = new MyProxy(this.myProxyHostname, this.myProxyPortNumber);
-        return myproxy.get(this.myProxyUserName, this.myProxyPassword, this.myProxyLifeTime);
-    }
-
-    /**
-     * Gets a new proxy certificate given current credentials.
-     * @param credential The new proxy credentials.
-     * @return The short lived GSSCredentials
-     * @throws Exception If an error is occurred while retrieving credentials.
-     */
-    public GSSCredential getProxyCredentials(GSSCredential credential) throws Exception {
-
-        MyProxy myproxy = new MyProxy(this.myProxyHostname, this.myProxyPortNumber);
-        return myproxy.get(credential, this.myProxyUserName, this.myProxyPassword, this.myProxyLifeTime);
-    }
-
-    /**
-     * Renew GSSCredentials.
-     * @param credential Credentials to be renewed.
-     * @return  Renewed credentials.
-     * @throws Exception If an error occurred while renewing credentials.
-     */
-    public GSSCredential renewCredentials(GSSCredential credential) throws Exception {
-        MyProxy myproxy = new MyProxy(this.myProxyHostname, this.myProxyPortNumber);
-
-        GetParams getParams = new GetParams();
-        getParams.setAuthzCreds(credential);
-        getParams.setUserName(this.myProxyUserName);
-        getParams.setLifetime(this.getMyProxyLifeTime());
-
-        return myproxy.get(credential, getParams);
-    }
-
-    public GSSCredential createCredentials(X509Certificate[] x509Certificates, PrivateKey privateKey) throws Exception {
-        X509Credential newCredential = new X509Credential(privateKey,
-                x509Certificates);
-
-        return new GlobusGSSCredentialImpl(newCredential,
-                GSSCredential.INITIATE_AND_ACCEPT);
-
-    }
-
-    public GSSCredential createCredentials(X509Certificate x509Certificate, PrivateKey privateKey) throws Exception {
-
-        X509Certificate[] x509Certificates = new X509Certificate[1];
-        x509Certificates[0] = x509Certificate;
-
-        return createCredentials(x509Certificates, privateKey);
-
-    }
-
-    public void init() {
-        validateTrustedCertificatePath();
-    }
-
-    private void validateTrustedCertificatePath() {
-
-        File file = new File(this.trustedCertificatePath);
-
-        if (!file.exists() || !file.canRead()) {
-            File f = new File(".");
-            System.out.println("Current directory " + f.getAbsolutePath());
-            throw new RuntimeException("Cannot read trusted certificate path " + this.trustedCertificatePath);
-        } else {
-            System.setProperty("X509_CERT_DIR", file.getAbsolutePath());
-        }
-    }
-
-
-    /**
-     * @return the myProxyHostname
-     */
-    public String getMyProxyHostname() {
-        return myProxyHostname;
-    }
-
-    /**
-     * @param myProxyHostname the myProxyHostname to set
-     */
-    public void setMyProxyHostname(String myProxyHostname) {
-        this.myProxyHostname = myProxyHostname;
-    }
-
-    /**
-     * @return the myProxyUserName
-     */
-    public String getMyProxyUserName() {
-        return myProxyUserName;
-    }
-
-    /**
-     * @param myProxyUserName the myProxyUserName to set
-     */
-    public void setMyProxyUserName(String myProxyUserName) {
-        this.myProxyUserName = myProxyUserName;
-    }
-
-    /**
-     * @return the myProxyPassword
-     */
-    public String getMyProxyPassword() {
-        return myProxyPassword;
-    }
-
-    /**
-     * @param myProxyPassword the myProxyPassword to set
-     */
-    public void setMyProxyPassword(String myProxyPassword) {
-        this.myProxyPassword = myProxyPassword;
-    }
-
-    /**
-     * @return the myProxyLifeTime
-     */
-    public int getMyProxyLifeTime() {
-        return myProxyLifeTime;
-    }
-
-    /**
-     * @param myProxyLifeTime the myProxyLifeTime to set
-     */
-    public void setMyProxyLifeTime(int myProxyLifeTime) {
-        this.myProxyLifeTime = myProxyLifeTime;
-    }
-
-    /**
-     * @return the myProxyPortNumber
-     */
-    public int getMyProxyPortNumber() {
-        return myProxyPortNumber;
-    }
-
-    /**
-     * @param myProxyPortNumber the myProxyPortNumber to set
-     */
-    public void setMyProxyPortNumber(int myProxyPortNumber) {
-        this.myProxyPortNumber = myProxyPortNumber;
-    }
-
-    public String getTrustedCertificatePath() {
-        return trustedCertificatePath;
-    }
-
-    public void setTrustedCertificatePath(String trustedCertificatePath) {
-        this.trustedCertificatePath = trustedCertificatePath;
-    }
-
-    /**
-     * @return the portalUserName
-     */
-    /*public String getPortalUserName() {
-        return portalUserName;
-    }*/
-
-    /**
-     * @param portalUserName
-     *            the portalUserName to set
-     */
-    /*public void setPortalUserName(String portalUserName) {
-        this.portalUserName = portalUserName;
-    }*/
-
-    /**
-     * Returns the initialized.
-     *
-     * @return The initialized
-     */
-    /*public boolean isInitialized() {
-        return this.initialized;
-    }*/
-
-    /**
-     * Sets initialized.
-     *
-     * @param initialized
-     *            The initialized to set.
-     */
-   /* public void setInitialized(boolean initialized) {
-        this.initialized = initialized;
-    }*/
-
-    /**
-     * @param hostcertsKeyFile
-     *            the hostcertsKeyFile to set
-     */
-    /*public void setHostcertsKeyFile(String hostcertsKeyFile) {
-        this.hostcertsKeyFile = hostcertsKeyFile;
-    }*/
-
-    /**
-     * @return the hostcertsKeyFile
-     */
-    /*public String getHostcertsKeyFile() {
-        return hostcertsKeyFile;
-    }*/
-
-    /**
-     * @param trustedCertsFile
-     *            the trustedCertsFile to set
-     */
-    /*public void setTrustedCertsFile(String trustedCertsFile) {
-        this.trustedCertsFile = trustedCertsFile;
-    }*/
-
-    /**
-     * @return the trustedCertsFile
-     */
-    /*public String getTrustedCertsFile() {
-        return trustedCertsFile;
-    }*/
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/SecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/SecurityContext.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/SecurityContext.java
deleted file mode 100644
index eb1a541..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/gridftp/myproxy/SecurityContext.java
+++ /dev/null
@@ -1,211 +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.file.manager.core.remote.client.gridftp.myproxy;
-
-import java.io.File;
-import java.io.InputStream;
-import java.util.Properties;
-
-import org.apache.airavata.file.manager.core.remote.client.gridftp.GridFTPConstants;
-import org.apache.log4j.Logger;
-import org.globus.myproxy.MyProxy;
-import org.ietf.jgss.GSSCredential;
-
-public class SecurityContext {
-
-    /**
-     *
-     */
-    public static final String GRIDFTP_CLIENT_PROPERTY = "gridftp-client.properties";
-    private Properties properties;
-    protected GSSCredential gssCredential;
-
-    private MyProxyCredentials myProxyCredentials;
-    private static final Logger log = Logger.getLogger(SecurityContext.class);
-
-    private String userName = null;
-    private String password = null;
-
-    /**
-     *
-     * Constructs a ApplicationGlobalContext.
-     *
-     * @throws Exception
-     */
-
-    public SecurityContext() throws Exception {
-        log.setLevel(org.apache.log4j.Level.INFO);
-        loadConfiguration();
-
-    }
-
-    public SecurityContext(String user, String pwd) throws Exception {
-
-        this.userName = user;
-        this.password = pwd;
-
-        log.setLevel(org.apache.log4j.Level.INFO);
-        loadConfiguration();
-
-    }
-
-    /**
-     *
-     * @throws Exception
-     */
-    public void login() throws Exception {
-        gssCredential = myProxyCredentials.getDefaultCredentials();
-    }
-
-    public GSSCredential getProxyCredentials(GSSCredential credential) throws Exception {
-        return myProxyCredentials.getProxyCredentials(credential);
-    }
-
-    public GSSCredential renewCredentials(GSSCredential credential) throws Exception {
-        return myProxyCredentials.renewCredentials(credential);
-    }
-
-    public static String getProperty(String name) {
-        try {
-            SecurityContext context = new SecurityContext();
-            return context.getProperties().getProperty(name);
-        } catch (Exception e) {
-            e.printStackTrace();
-            return null;
-        }
-
-    }
-
-    /**
-     * Load the configration file
-     *
-     * @throws Exception
-     */
-    private void loadConfiguration() throws Exception {
-        try {
-
-            System.out.println("In the load configurations method .....");
-
-            if (properties == null) {
-                ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
-
-                InputStream propertyStream = classLoader.getResourceAsStream(GRIDFTP_CLIENT_PROPERTY);
-                properties = new Properties();
-                if (myProxyCredentials == null) {
-                    this.myProxyCredentials = new MyProxyCredentials();
-                }
-                if (propertyStream != null) {
-                    properties.load(propertyStream);
-                    String myproxyServerTmp = properties.getProperty(GridFTPConstants.MYPROXY_SERVER);
-                    if (myproxyServerTmp != null) {
-                        this.myProxyCredentials.setMyProxyHostname(myproxyServerTmp.trim());
-                    }
-                    String myproxyPortTemp = properties.getProperty(GridFTPConstants.MYPROXY_PORT);
-                    if (myproxyPortTemp != null && myproxyPortTemp.trim().length() > 0) {
-                        this.myProxyCredentials.setMyProxyPortNumber(Integer.parseInt(myproxyPortTemp.trim()));
-                    } else {
-                        this.myProxyCredentials.setMyProxyPortNumber(MyProxy.DEFAULT_PORT);
-                    }
-
-                    this.myProxyCredentials.setMyProxyUserName(userName);
-                    this.myProxyCredentials.setMyProxyPassword(password);
-
-                    String myproxytime = properties.getProperty(GridFTPConstants.MYPROXY_LIFETIME);
-                    if (myproxytime != null) {
-                        this.myProxyCredentials.setMyProxyLifeTime(Integer.parseInt(myproxytime));
-                    }
-
-                    String currentDirectory = System.getProperty("projectDirectory");
-                    String certificatePath = currentDirectory + File.separatorChar
-                            + properties.getProperty(GridFTPConstants.TRUSTED_CERTS_FILE);
-
-                    this.myProxyCredentials.setTrustedCertificatePath(certificatePath);
-
-                    System.out.println("Certificate path - " + certificatePath);
-
-                    this.myProxyCredentials.init();
-                }
-            }
-
-        } catch (Exception e) {
-            e.printStackTrace();
-            log.error(e.getLocalizedMessage());
-            throw new Exception(e);
-        }
-
-    }
-
-    /**
-     * @return the properties
-     */
-    public Properties getProperties() {
-        return properties;
-    }
-
-    /**
-     * @param properties
-     *            the properties to set
-     */
-    public void setProperties(Properties properties) {
-        this.properties = properties;
-    }
-
-    /**
-     * Returns the raw gssCredential, without creating a proxy.
-     *
-     * @return The gssCredential
-     */
-    public GSSCredential getRawCredential() throws Exception{
-
-        return gssCredential;
-    }
-
-    /**
-     * Returns the gssCredential.
-     *
-     * @return The gssCredential
-     */
-    public GSSCredential getGssCredential() throws Exception{
-
-        if (this.gssCredential == null)
-            return null;
-
-        return renewCredentials(gssCredential);
-    }
-
-    /**
-     * Sets gssCredential.
-     *
-     * @param gssCredential
-     *            The gssCredential to set.
-     */
-    public void setGssCredential(GSSCredential gssCredential) {
-        this.gssCredential = gssCredential;
-    }
-
-    public MyProxyCredentials getMyProxyCredentials() {
-        return myProxyCredentials;
-    }
-
-    public void setMyProxyCredentials(MyProxyCredentials myProxyCredentials) {
-        this.myProxyCredentials = myProxyCredentials;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/http/HTTPStorageClient.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/http/HTTPStorageClient.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/http/HTTPStorageClient.java
deleted file mode 100644
index e829c3b..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/http/HTTPStorageClient.java
+++ /dev/null
@@ -1,215 +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.file.manager.core.remote.client.http;
-
-import org.apache.airavata.file.manager.core.remote.client.RemoteStorageClient;
-import org.apache.airavata.model.file.transfer.LSEntryModel;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.net.ssl.HttpsURLConnection;
-import javax.net.ssl.SSLContext;
-import javax.net.ssl.TrustManager;
-import javax.net.ssl.X509TrustManager;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.nio.channels.Channels;
-import java.nio.channels.ReadableByteChannel;
-import java.security.KeyManagementException;
-import java.security.NoSuchAlgorithmException;
-import java.util.List;
-import java.util.UUID;
-
-public class HTTPStorageClient implements RemoteStorageClient {
-    private final static Logger logger = LoggerFactory.getLogger(HTTPStorageClient.class);
-
-    public static enum Protocol {
-        HTTP, HTTPS
-    }
-
-    private String host;
-    private int port;
-    private Protocol protocol;
-
-    public HTTPStorageClient(Protocol protocol, String host, int port) throws KeyManagementException, NoSuchAlgorithmException {
-        this.protocol = protocol;
-        this.host = host;
-        this.port = port;
-
-        // Create a new trust manager that trust all certificates
-        TrustManager[] trustAllCerts = new TrustManager[]{
-                new X509TrustManager() {
-                    public java.security.cert.X509Certificate[] getAcceptedIssuers() {
-                        return null;
-                    }
-
-                    public void checkClientTrusted(
-                            java.security.cert.X509Certificate[] certs, String authType) {
-                    }
-
-                    public void checkServerTrusted(
-                            java.security.cert.X509Certificate[] certs, String authType) {
-                    }
-                }
-        };
-
-        // Activate the new trust manager
-        SSLContext sc = SSLContext.getInstance("SSL");
-        sc.init(null, trustAllCerts, new java.security.SecureRandom());
-        HttpsURLConnection.setDefaultSSLSocketFactory(sc.getSocketFactory());
-    }
-
-    /**
-     * Reads a remote file, write it to local temporary directory and returns a file pointer to it
-     *
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    @Override
-    public File readFile(String filePath) throws Exception {
-        String url = "";
-        if (protocol == Protocol.HTTP)
-            url += "http://";
-        else
-            url += "https://";
-        url += host + ":" + port;
-        if (!filePath.startsWith("/"))
-            filePath += "/" + filePath;
-        url += filePath;
-
-        URL fileUrl = new URL(url);
-        URLConnection urlConnection = fileUrl.openConnection();
-        ReadableByteChannel rbc = Channels.newChannel(urlConnection.getInputStream());
-        String localFilePath = System.getProperty("java.io.tmpdir") + File.separator + UUID.randomUUID().toString();
-        FileOutputStream fos = new FileOutputStream(localFilePath);
-        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
-
-        return new File(localFilePath);
-    }
-
-    /**
-     * Writes the source file in the local storage to specified path in the remote storage
-     *
-     * @param sourceFile
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    @Override
-    public void writeFile(File sourceFile, String filePath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Returns a directory listing of the specified directory
-     *
-     * @param directoryPath
-     * @return
-     * @throws Exception
-     */
-    @Override
-    public List<LSEntryModel> getDirectoryListing(String directoryPath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Move the specified file from source to destination within the same storage resource
-     *
-     * @param currentPath
-     * @param newPath
-     * @throws Exception
-     */
-    @Override
-    public void moveFile(String currentPath, String newPath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * @param sourcePath
-     * @param destinationPath
-     * @throws Exception
-     */
-    @Override
-    public void copyFile(String sourcePath, String destinationPath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Rename file with the given name
-     *
-     * @param filePath
-     * @param newFileName
-     * @throws Exception
-     */
-    @Override
-    public void renameFile(String filePath, String newFileName) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Delete the specified file
-     *
-     * @param filePath
-     * @throws Exception
-     */
-    @Override
-    public void deleteFile(String filePath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Create new directory in the specified file
-     *
-     * @param newDirPath
-     * @throws Exception
-     */
-    @Override
-    public void mkdir(String newDirPath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Checks whether specified file exists in the remote storage system
-     *
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    @Override
-    public boolean checkFileExists(String filePath) throws Exception {
-        throw new UnsupportedOperationException();
-    }
-
-    /**
-     * Checks whether the given path is a directory
-     *
-     * @param filePath
-     * @return
-     * @throws Exception
-     */
-    @Override
-    public boolean checkIsDirectory(String filePath) throws Exception {
-        return false;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/CommandOutput.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/CommandOutput.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/CommandOutput.java
deleted file mode 100644
index 5fd2b52..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/CommandOutput.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.file.manager.core.remote.client.scp;
-
-import com.jcraft.jsch.Channel;
-import java.io.OutputStream;
-
-public interface CommandOutput {
-    void onOutput(Channel var1);
-
-    OutputStream getStandardError();
-
-    void exitCode(int var1);
-
-    int getExitCode();
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/1ad9ae5d/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/SCPApiException.java
----------------------------------------------------------------------
diff --git a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/SCPApiException.java b/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/SCPApiException.java
deleted file mode 100644
index 0f07707..0000000
--- a/modules/file-manager/file-manager-core/src/main/java/org/apache/airavata/file/manager/core/remote/client/scp/SCPApiException.java
+++ /dev/null
@@ -1,33 +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.file.manager.core.remote.client.scp;
-
-public class SCPApiException extends Exception {
-
-    public SCPApiException(String message) {
-        super(message);
-    }
-
-    public SCPApiException(String message, Exception e) {
-        super(message, e);
-    }
-
-}