edu.umn.msi.tropix.webgui.server.ExportServiceImpl.java Source code

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/*******************************************************************************
 * Copyright 2009 Regents of the University of Minnesota. All rights
 * reserved.
 * Copyright 2009 Mayo Foundation for Medical Education and Research.
 * All rights reserved.
 *
 * This program is made available under the terms of the Eclipse
 * Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * 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 INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS
 * OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A
 * PARTICULAR PURPOSE.  See the License for the specific language
 * governing permissions and limitations under the License.
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 ******************************************************************************/

package edu.umn.msi.tropix.webgui.server;

import java.util.List;

import javax.annotation.ManagedBean;
import javax.inject.Inject;

import org.apache.commons.io.FilenameUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import com.google.common.collect.Lists;

import edu.umn.msi.tropix.client.galaxy.GalaxyExportOptions;
import edu.umn.msi.tropix.client.galaxy.GalaxyExporter;
import edu.umn.msi.tropix.files.PersistentModelStorageDataFactory;
import edu.umn.msi.tropix.grid.credentials.Credential;
import edu.umn.msi.tropix.grid.gridftp.GridFtpClient;
import edu.umn.msi.tropix.grid.gridftp.GridFtpClientUtils;
import edu.umn.msi.tropix.grid.gridftp.GridFtpFactory;
import edu.umn.msi.tropix.models.TropixFile;
import edu.umn.msi.tropix.models.TropixObject;
import edu.umn.msi.tropix.persistence.service.FileService;
import edu.umn.msi.tropix.persistence.service.TropixObjectService;
import edu.umn.msi.tropix.storage.client.StorageData;
import edu.umn.msi.tropix.webgui.server.aop.ServiceMethod;
import edu.umn.msi.tropix.webgui.server.security.UserSession;
import edu.umn.msi.tropix.webgui.services.object.ExportService;

@ManagedBean
public class ExportServiceImpl implements ExportService {
    private static final Log LOG = LogFactory.getLog(ExportServiceImpl.class);
    private final FileService fileService;
    private final UserSession userSession;
    private final PersistentModelStorageDataFactory storageDataFactory;
    private final GridFtpFactory gridFtpFactory;
    private final GalaxyExporter galaxyExporter;
    private final TropixObjectService tropixObjectService;

    @Inject
    public ExportServiceImpl(final FileService fileService, final UserSession userSession,
            final PersistentModelStorageDataFactory storageDataFactory, final GridFtpFactory gridFtpFactory,
            final GalaxyExporter galaxyExporter, final TropixObjectService tropixObjectService) {
        this.fileService = fileService;
        this.userSession = userSession;
        this.storageDataFactory = storageDataFactory;
        this.gridFtpFactory = gridFtpFactory;
        this.galaxyExporter = galaxyExporter;
        this.tropixObjectService = tropixObjectService;
    }

    @ServiceMethod()
    public void export(final String[] ids, final GridFtpServerOptions gridFtpOptions) {
        final TropixFile[] tropixFiles = fileService.getFiles(userSession.getGridId(), ids);
        final String host = gridFtpOptions.getHostname();
        final int port = gridFtpOptions.getPort();
        final Credential credential = userSession.getProxy();
        LOG.info("GridFTP request to host and port " + host + " " + port);
        final GridFtpClient gridFtpClient = gridFtpFactory.getClient(host, port, credential);

        final String path = FilenameUtils.normalizeNoEndSeparator(gridFtpOptions.getPath());
        try {
            LOG.debug("Attempting to create path " + path);
            gridFtpClient.makeDir(path);
        } catch (final RuntimeException e) {
            LOG.warn("Failed to make directory with path " + path
                    + " proceeding anyway in case directory already exists.", e);
        }
        for (final TropixFile tropixFile : tropixFiles) {
            final StorageData data = storageDataFactory.getStorageData(tropixFile, credential);
            final String name = FilenameUtils.getBaseName(tropixFile.getName());
            LOG.debug("Attempting to transfer file wit id " + tropixFile.getFileId() + " and name " + name);
            data.getDownloadContext().get(GridFtpClientUtils.getOutputContext(gridFtpClient, path + "/" + name));
        }
    }

    @ServiceMethod()
    public void exportGalaxy(GalaxyExportOptions galaxyExportOptions) {
        galaxyExporter.uploadFiles(userSession.getGridId(), galaxyExportOptions);
    }

    @ServiceMethod()
    public void exportRawGalaxy(GalaxyExportOptions galaxyExportOptions, List<String> peakListIds) {
        galaxyExporter.uploadFiles(userSession.getGridId(),
                populateAssociations(galaxyExportOptions, peakListIds, "source"));
    }

    @ServiceMethod()
    public void exportMzXMLGalaxy(GalaxyExportOptions galaxyExportOptions, List<String> peakListIds) {
        galaxyExporter.uploadFiles(userSession.getGridId(),
                populateAssociations(galaxyExportOptions, peakListIds, "mzxml"));
    }

    private GalaxyExportOptions populateAssociations(final GalaxyExportOptions galaxyExportOptions,
            final List<String> objectIds, final String associationName) {
        galaxyExportOptions.setFileObjectIds(Lists.<String>newArrayList());
        for (final String objectId : objectIds) {
            TropixObject fileObject = tropixObjectService.getAssociation(userSession.getGridId(), objectId,
                    associationName);
            galaxyExportOptions.getFileObjectIds().add(fileObject.getId());
        }
        return galaxyExportOptions;
    }
}