OMEROGateway.java

/*
 *------------------------------------------------------------------------------
 *  Copyright (C) 2006-2015 University of Dundee. All rights reserved.
 *
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along
 *  with this program; if not, write to the Free Software Foundation, Inc.,
 *  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 *------------------------------------------------------------------------------
 */

package org.openmicroscopy.shoola.env.data;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.ResourceBundle;
import java.util.Set;
import java.util.Map.Entry;
import java.util.concurrent.ExecutionException;

import org.apache.commons.collections.CollectionUtils;
import org.openmicroscopy.shoola.util.CommonsLangUtils;

import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;

import org.openmicroscopy.shoola.env.data.login.UserCredentials;
import org.openmicroscopy.shoola.env.data.model.AdminObject;
import org.openmicroscopy.shoola.env.data.model.EnumerationObject;
import org.openmicroscopy.shoola.env.data.model.ImportableObject;
import org.openmicroscopy.shoola.env.data.model.MovieExportParam;
import org.openmicroscopy.shoola.env.data.model.FigureParam;
import org.openmicroscopy.shoola.env.data.model.SaveAsParam;
import org.openmicroscopy.shoola.env.data.model.ScriptObject;
import org.openmicroscopy.shoola.env.data.model.TableParameters;
import org.openmicroscopy.shoola.env.data.util.ModelMapper;

import omero.gateway.util.PojoMapper;

import org.openmicroscopy.shoola.env.data.util.SearchDataContext;

import omero.gateway.Gateway;
import omero.gateway.LoginCredentials;
import omero.gateway.SecurityContext;
import omero.gateway.exception.DSAccessException;
import omero.gateway.exception.DSOutOfServiceException;
import omero.gateway.exception.RenderingServiceException;
import omero.gateway.facility.BrowseFacility;
import omero.gateway.facility.DataManagerFacility;
import omero.gateway.facility.ROIFacility;
import omero.gateway.facility.SearchFacility;
import omero.gateway.model.ROIResult;
import omero.gateway.model.SearchResultCollection;
import omero.gateway.model.SearchParameters;
import omero.gateway.model.TableResult;
import omero.gateway.util.Requests;

import org.openmicroscopy.shoola.env.data.util.StatusLabel;
import org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory;
import org.openmicroscopy.shoola.env.rnd.RndProxyDef;
import org.openmicroscopy.shoola.util.ui.UIUtilities;

import omero.ResourceError;
import ome.formats.OMEROMetadataStoreClient;
import ome.formats.importer.ImportCandidates;
import ome.formats.importer.ImportConfig;
import ome.formats.importer.ImportContainer;
import ome.formats.importer.ImportEvent;
import ome.formats.importer.ImportLibrary;
import ome.formats.importer.OMEROWrapper;
import ome.formats.importer.util.ProportionalTimeEstimatorImpl;
import ome.formats.importer.util.TimeEstimator;
import ome.system.UpgradeCheck;
import ome.util.checksum.ChecksumProvider;
import ome.util.checksum.ChecksumProviderFactory;
import ome.util.checksum.ChecksumProviderFactoryImpl;
import ome.util.checksum.ChecksumType;
import omero.ApiUsageException;
import omero.AuthenticationException;
import omero.ChecksumValidationException;
import omero.ConcurrencyException;
import omero.InternalException;
import omero.LockTimeout;
import omero.MissingPyramidException;
import omero.RLong;
import omero.RString;
import omero.RType;
import omero.SecurityViolation;
import omero.ServerError;
import omero.SessionException;
import omero.ValidationException;
import omero.rtypes;
import omero.api.ExporterPrx;
import omero.api.IAdminPrx;
import omero.api.IContainerPrx;
import omero.api.IMetadataPrx;
import omero.api.IPixelsPrx;
import omero.api.IProjectionPrx;
import omero.api.IQueryPrx;
import omero.api.IRenderingSettingsPrx;
import omero.api.IRepositoryInfoPrx;
import omero.api.IRoiPrx;
import omero.api.IScriptPrx;
import omero.api.IUpdatePrx;
import omero.api.RawFileStorePrx;
import omero.api.RawPixelsStorePrx;
import omero.api.RenderingEnginePrx;
import omero.api.RoiOptions;
import omero.api.Save;
import omero.api.SearchPrx;
import omero.api.StatefulServiceInterfacePrx;
import omero.api.ThumbnailStorePrx;
import omero.cmd.Chmod2;
import omero.cmd.CmdCallbackI;
import omero.cmd.HandlePrx;
import omero.cmd.Request;
import omero.constants.projection.ProjectionType;
import omero.grid.BoolColumn;
import omero.grid.Column;
import omero.grid.Data;
import omero.grid.DoubleColumn;
import omero.grid.ImageColumn;
import omero.grid.ImportProcessPrx;
import omero.grid.ImportRequest;
import omero.grid.LongColumn;
import omero.grid.ProcessCallbackI;
import omero.grid.RepositoryMap;
import omero.grid.RepositoryPrx;
import omero.grid.RoiColumn;
import omero.grid.SharedResourcesPrx;
import omero.grid.StringColumn;
import omero.grid.TablePrx;
import omero.grid.WellColumn;
import omero.model.ChecksumAlgorithm;
import omero.model.ChecksumAlgorithmI;
import omero.model.Dataset;
import omero.model.DatasetI;
import omero.model.Details;
import omero.model.DetailsI;
import omero.model.EllipseI;
import omero.model.Experimenter;
import omero.model.ExperimenterGroup;
import omero.model.ExperimenterGroupI;
import omero.model.FileAnnotation;
import omero.model.Fileset;
import omero.model.FilesetEntry;
import omero.model.GroupExperimenterMap;
import omero.model.IObject;
import omero.model.Image;
import omero.model.ImageI;
import omero.model.Instrument;
import omero.model.LabelI;
import omero.model.Laser;
import omero.model.LogicalChannel;
import omero.model.MaskI;
import omero.model.OriginalFile;
import omero.model.OriginalFileI;
import omero.model.Permissions;
import omero.model.PermissionsI;
import omero.model.Pixels;
import omero.model.PixelsType;
import omero.model.Plate;
import omero.model.PlateAcquisition;
import omero.model.PlateAcquisitionI;
import omero.model.PlateI;
import omero.model.PointI;
import omero.model.PolygonI;
import omero.model.PolylineI;
import omero.model.Project;
import omero.model.ProjectI;
import omero.model.RectangleI;
import omero.model.RenderingDef;
import omero.model.Screen;
import omero.model.ScreenI;
import omero.model.TagAnnotation;
import omero.model.TagAnnotationI;
import omero.model.Well;
import omero.model.WellSample;
import omero.model.WellSampleI;
import omero.model.enums.ChecksumAlgorithmSHA1160;
import omero.sys.Parameters;
import omero.sys.ParametersI;
import omero.sys.Roles;
import omero.gateway.model.AnnotationData;
import omero.gateway.model.BooleanAnnotationData;
import omero.gateway.model.ChannelAcquisitionData;
import omero.gateway.model.DataObject;
import omero.gateway.model.DatasetData;
import omero.gateway.model.EllipseData;
import omero.gateway.model.ExperimenterData;
import omero.gateway.model.FileAnnotationData;
import omero.gateway.model.FileData;
import omero.gateway.model.FilesetData;
import omero.gateway.model.GroupData;
import omero.gateway.model.ImageAcquisitionData;
import omero.gateway.model.ImageData;
import omero.gateway.model.InstrumentData;
import omero.gateway.model.LightSourceData;
import omero.gateway.model.LongAnnotationData;
import omero.gateway.model.MapAnnotationData;
import omero.gateway.model.MaskData;
import omero.gateway.model.PlateAcquisitionData;
import omero.gateway.model.PlateData;
import omero.gateway.model.PointData;
import omero.gateway.model.PolygonData;
import omero.gateway.model.PolylineData;
import omero.gateway.model.ProjectData;
import omero.gateway.model.ROIData;
import omero.gateway.model.RatingAnnotationData;
import omero.gateway.model.RectangleData;
import omero.gateway.model.ScreenData;
import omero.gateway.model.TagAnnotationData;
import omero.gateway.model.TermAnnotationData;
import omero.gateway.model.TextData;
import omero.gateway.model.TextualAnnotationData;
import omero.gateway.model.TimeAnnotationData;
import omero.gateway.model.WellData;
import omero.gateway.model.WellSampleData;


/**
 * Unified access point to the various <i>OMERO</i> services.
 *
 * @author Jean-Marie Burel &nbsp;&nbsp;&nbsp;&nbsp;
 * <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
 * @author <br>Andrea Falconi &nbsp;&nbsp;&nbsp;&nbsp;
 * <a href="mailto:a.falconi@dundee.ac.uk">a.falconi@dundee.ac.uk</a>
 * @version 2.2
 * @since OME2.2
 */
@SuppressWarnings({"rawtypes", "unchecked"})
class OMEROGateway
{

	/** Identifies the fileset as root. */
	private static final String REF_FILESET = "/Fileset";

	/** Identifies the image as root. */
	private static final String REF_IMAGE = "/Image";

	/** Identifies the dataset as root. */
	private static final String REF_DATASET = "/Dataset";

	/** Identifies the project as root. */
	private static final String REF_PROJECT = "/Project";

	/** Identifies the screen as root. */
	private static final String REF_SCREEN = "/Screen";

	/** Identifies the plate as root. */
	private static final String REF_PLATE = "/Plate";

	/** Identifies the ROI as root. */
	private static final String REF_ROI = "/Roi";

	/** Identifies the PlateAcquisition as root. */
	private static final String REF_PLATE_ACQUISITION = "/PlateAcquisition";

	/** Identifies the PlateAcquisition as root. */
	private static final String REF_WELL = "/Well";

	/** Identifies the Tag. */
	private static final String REF_ANNOTATION = "/Annotation";

	/** Identifies the Tag. */
	private static final String REF_TAG = "/TagAnnotation";

	/** Identifies the Term. */
	private static final String REF_TERM = "/TermAnnotation";

	/** Identifies the File. */
	private static final String REF_FILE= "/FileAnnotation";

	/** Identifies the group. */
	private static final String REF_GROUP = "/ExperimenterGroup";

	/** Indicates to keep a certain type of annotations. */
	static final String KEEP = "KEEP";

	/** The default MIME type. */
	private static final String				DEFAULT_MIMETYPE =
		"application/octet-stream";

	/** String used to identify the overlays. */
	private static final String				OVERLAYS = "Overlays";

	/** Maximum size of pixels read at once. */
	private static final int				INC = 262144;//256000;

	/**
	 * The maximum number of thumbnails retrieved before restarting the
	 * thumbnails service.
	 */
	static final int						MAX_RETRIEVAL = 50;//100;

	/** Maximum number of rows to retrieve at one time from a table. */
	private static final int				MAX_TABLE_ROW_RETRIEVAL = 100000;

	/** The collection of escaping characters we allow in the search. */
	private static final List<Character>	SUPPORTED_SPECIAL_CHAR;

	/** The collection of escaping characters we allow in the search. */
	private static final List<String>		WILD_CARDS;

	/** The collection of scripts that have a UI available. */
	private static final List<String>		SCRIPTS_UI_AVAILABLE;

	/** The collection of scripts that have a UI available. */
	private static final List<String>		SCRIPTS_NOT_AVAILABLE_TO_USER;

	/* checksum provider factory for verifying file integrity in upload */
	private static final ChecksumProviderFactory checksumProviderFactory = new ChecksumProviderFactoryImpl();

	static {
		SUPPORTED_SPECIAL_CHAR = new ArrayList<Character>();
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('-'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('+'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('['));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf(']'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf(')'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('('));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf(':'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('|'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('!'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('{'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('}'));
		SUPPORTED_SPECIAL_CHAR.add(Character.valueOf('^'));
		WILD_CARDS = new ArrayList<String>();
		WILD_CARDS.add("*");
		WILD_CARDS.add("?");
		WILD_CARDS.add("~");

		//script w/ a UI.
		SCRIPTS_UI_AVAILABLE = new ArrayList<String>();

		SCRIPTS_UI_AVAILABLE.add(FigureParam.ROI_SCRIPT);
		SCRIPTS_UI_AVAILABLE.add(FigureParam.THUMBNAIL_SCRIPT);
		SCRIPTS_UI_AVAILABLE.add(FigureParam.MOVIE_SCRIPT);
		SCRIPTS_UI_AVAILABLE.add(FigureParam.SPLIT_VIEW_SCRIPT);
		SCRIPTS_UI_AVAILABLE.add(MovieExportParam.MOVIE_SCRIPT);

		SCRIPTS_NOT_AVAILABLE_TO_USER = new ArrayList<String>();
		SCRIPTS_NOT_AVAILABLE_TO_USER.add(
				ScriptObject.IMPORT_PATH+"Populate_ROI.py");
		SCRIPTS_NOT_AVAILABLE_TO_USER.add(
				ScriptObject.ANALYSIS_PATH+"FLIM.py");
		SCRIPTS_NOT_AVAILABLE_TO_USER.add(
				ScriptObject.ANALYSIS_PATH+"flim-omero.py");
		SCRIPTS_NOT_AVAILABLE_TO_USER.add(
				ScriptObject.SETUP_PATH+"FLIM_initialise.py");
	}

	/**
	 * Used whenever a broken link is detected to get the Login Service and
	 * try re-establishing a valid link to <i>OMERO</i>.
	 */
	private DataServicesFactory dsFactory;

	/** Map hosting the enumeration required for metadata. */
	private Map<String, List<EnumerationObject>> enumerations;

	/** Keep track of the file system view. */
	private Map<Long, FSFileSystemView> fsViews;
	
	private Gateway gw;
	
	/**
	 * Creates the query to load the file set corresponding to a given image.
	 *
	 * @return See above.
	 */
	private String createFileSetQuery()
	{
		StringBuffer buffer = new StringBuffer();
		buffer.append("select fs from Fileset as fs ");
		buffer.append("join fetch fs.images as image ");
		buffer.append("left outer join fetch fs.usedFiles as usedFile ");
		buffer.append("join fetch usedFile.originalFile as f ");
		buffer.append("join fetch f.hasher ");
		buffer.append("where image.id in (:imageIds)");
		return buffer.toString();
	}

    /**
     * Logs the information.
     */
    private void log(String msg)
    {
    	dsFactory.getLogger().debug(this, msg);
    }


	/**
	 * Returns <code>true</code> if the server is running.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 */
	boolean isServerRunning(SecurityContext ctx)
	{
		if (!gw.isConnected()) 
		    return false;
		try {
            return null != gw.getConnector(ctx, true, true);
        } catch (Throwable t) {
            return false;
        }
	}

	/**
	 * Creates the permissions corresponding to the specified level.
	 *
	 * @param level The level to handle.
	 * @return
	 */
	private Permissions createPermissions(int level)
	{
		String perms = "rw----"; //private group
		switch (level) {
			case GroupData.PERMISSIONS_GROUP_READ:
				perms = "rwr---";
				break;
			case GroupData.PERMISSIONS_GROUP_READ_LINK:
				perms = "rwra--";
				break;
			case GroupData.PERMISSIONS_GROUP_READ_WRITE:
				perms = "rwrw--";
				break;
			case GroupData.PERMISSIONS_PUBLIC_READ:
				perms = "rwrwr-";
		}
		return new PermissionsI(perms);
	}

	/**
	 * Returns the identifier of the specified script.
	 *
	 * @param ctx The security context.
	 * @param name The name of the script.
	 * @param message The error message.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException       If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	private long getScriptID(SecurityContext ctx, String name, String message)
		throws DSOutOfServiceException, DSAccessException
	{
		IScriptPrx svc = getScriptService(ctx);
		try {
			return svc.getScriptID(name);
		} catch (Exception e) {
			handleException(e, message);
		}
		return -1;
	}

	/**
	 * Returns the specified script.
	 *
	 * @param ctx The security context.
	 * @param scriptID The identifier of the script to run.
	 * @param parameters The parameters to pass to the script.
	 * @return See above.
	 * @throws ProcessException If an error occurred while running the script.
	 */
	private ScriptCallback runScript(SecurityContext ctx, long scriptID,
			Map<String, RType> parameters)
		throws ProcessException
	{
		ScriptCallback cb = null;
		try {
		    
		    ProcessCallbackI pcb = gw.runScript(ctx, scriptID, parameters);
	         cb = new ScriptCallback(scriptID, pcb);
		} catch (Exception e) {
			handleConnectionException(e);
			throw new ProcessException("Cannot run script with ID:"+scriptID,
					e);
		}
		return cb;
	}
	
	/**
	 * Closes the specified service.
	 *
	 * @param ctx The security context.
	 * @param svc The service to close.
	 */
	void closeService(SecurityContext ctx,
            StatefulServiceInterfacePrx svc)
    {
        if (ctx == null || svc == null) return;
        gw.closeService(ctx, svc);
    }

	/**
	 * Creates a table with the overlays.
	 *
	 * @param imageID The id of the image.
	 * @param table   The table to handle.
	 * @return See above
	 * @throws DSAccessException If an error occurred while trying to
	 *                           retrieve data from OMEDS service.
	 */
	private TableResult createOverlay(long imageID, TablePrx table)
		throws DSAccessException
	{
		if (table == null) return null;
		try {
			Column[] cols = table.getHeaders();
			int imageIndex = -1;
			int roiIndex = -1;
			int colorIndex = -1;
			int size = 0;
			for (int i = 0; i < cols.length; i++) {
				if (cols[i] instanceof ImageColumn) {
					imageIndex = i;
					size++;
				} else if (cols[i] instanceof RoiColumn) {
					roiIndex = i;
					size++;
				} else if (cols[i] instanceof LongColumn) {
					if ("Color".equals(cols[i].name)) {
						colorIndex = i;
						size++;
					}
				}
			}
			if (imageIndex == -1 || roiIndex == -1) return null;;
			String[] headers = new String[size];
			String[] headersDescriptions = new String[size];
			headers[0] = cols[imageIndex].name;
			headersDescriptions[0] = cols[imageIndex].description;

			headers[1] = cols[roiIndex].name;
			headersDescriptions[1] = cols[roiIndex].description;

			headers[1] = cols[roiIndex].name;
			headersDescriptions[1] = cols[roiIndex].description;

			int n = (int) table.getNumberOfRows();
			Data d;
			Column column;
			long[] a = {imageIndex, roiIndex, colorIndex};
			long[] b = new long[0];

			d = table.slice(a, b);
			List<Integer> rows = new ArrayList<Integer>();
			column = d.columns[imageIndex];
			Long value;
			if (column instanceof ImageColumn) {
				for (int j = 0; j < n; j++) {
					value = ((ImageColumn) column).values[j];
					if (value == imageID)
						rows.add(j);
				}
			}

			Integer row;
			Object[][] data = new Object[rows.size()][size];
			int k = 0;
			Iterator<Integer> r = rows.iterator();
			column = d.columns[roiIndex];
			Column columnColor = null;
			if (colorIndex != -1) columnColor = d.columns[colorIndex];
			while (r.hasNext()) {
				row = r.next();
				data[k][0] = row;
				data[k][1] = ((RoiColumn) column).values[row];
				if (columnColor != null)
					data[k][2] = ((LongColumn) columnColor).values[row];
				k++;
			}
			table.close();
			return new TableResult(data, headers);
		} catch (Exception e) {
			try {
				if (table != null) table.close();
			} catch (Exception ex) {
				//Digest exception
			}
			throw new DSAccessException("Unable to read the table.");
		}
	}

	/**
	 * Translates a set of table results into an array.
	 * @param src Source data from the table.
	 * @param dst Destination array.
	 * @param offset Offset within the destination array from which to copy
	 * data into.
	 * @param length Number of rows of data to be copied.
	 */
	private void translateTableResult(Data src, Object[][] dst, int offset,
	                                  int length, Map<Integer, Integer> indexes)
	{
		Column[] cols = src.columns;
		Column column;
		for (int i = 0; i < cols.length; i++) {
			column = cols[i];
			if (column instanceof LongColumn) {
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((LongColumn) column).values[j];
				}
			} else if (column instanceof DoubleColumn) {
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((DoubleColumn) column).values[j];
				}
			} else if (column instanceof StringColumn) {
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((StringColumn) column).values[j];
				}
			} else if (column instanceof BoolColumn) {
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((BoolColumn) column).values[j];
				}
			} else if (column instanceof RoiColumn) {
				indexes.put(TableResult.ROI_COLUMN_INDEX, i);
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((RoiColumn) column).values[j];
				}
			} else if (column instanceof ImageColumn) {
				indexes.put(TableResult.IMAGE_COLUMN_INDEX, i);
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((ImageColumn) column).values[j];
				}
			} else if (column instanceof WellColumn) {
				indexes.put(TableResult.WELL_COLUMN_INDEX, i);
				for (int j = 0; j < length; j++) {
					dst[j + offset][i] =
						((WellColumn) column).values[j];
				}
			}
		}
	}

	/**
	 * Transforms a set of rows for the passed table.
	 *
	 * @param table The table to convert.
	 * @param rows The rows of the table to convert.
	 * @return See above
	 * @throws DSAccessException If an error occurred while trying to
	 *                           retrieve data from OMEDS service.
	 */
	private TableResult createTableResult(TablePrx table, long[] rows)
		throws DSAccessException
	{
		if (table == null) return null;
		try {
			Column[] cols = table.getHeaders();
			String[] headers = new String[cols.length];
			String[] headersDescriptions = new String[cols.length];
			for (int i = 0; i < cols.length; i++) {
				headers[i] = cols[i].name;
				headersDescriptions[i] = cols[i].description;
			}
			int totalRowCount = rows.length;
			Object[][] data = new Object[totalRowCount][cols.length];
			Data d;
			long[] columns = new long[cols.length];
			for (int i = 0; i < cols.length; i++) {
				columns[i] = i;
			}

			int rowOffset = 0;
			int rowCount = 0;
			int rowsToGo = totalRowCount;
			long[] rowSubset;
			Map<Integer, Integer> indexes = new HashMap<Integer, Integer>();
			while (rowsToGo > 0) {
				rowCount = (int) Math.min(MAX_TABLE_ROW_RETRIEVAL,
				                          totalRowCount - rowOffset);
				rowSubset = new long[rowCount];
				System.arraycopy(rows, rowOffset, rowSubset, 0, rowCount);
				d = table.slice(columns, rowSubset);
				for (int i = 0; i < cols.length; i++) {
					translateTableResult(d, data, rowOffset, rowCount, indexes);
				}
				rowOffset += rowCount;
				rowsToGo -= rowCount;
			}
			table.close();
			TableResult tr = new TableResult(data, headers);
			tr.setIndexes(indexes);
			return tr;
		} catch (Exception e) {
			try {
				if (table != null) table.close();
			} catch (Exception ex) {
				//Digest exception
			}
			throw new DSAccessException("Unable to read the table.", e);
		}
	}

	/**
	 * Helper method to handle exceptions thrown by the connection library.
	 * Methods in this class are required to fill in a meaningful context
	 * message.
	 * This method is not supposed to be used in this class' constructor or in
	 * the login/logout methods.
	 *
	 * @param t     	The exception.
	 * @param message	The context message.
	 * @throws DSOutOfServiceException  A connection problem.
	 * @throws DSAccessException    A server-side error.
	 */
	private void handleException(Throwable t, String message)
		throws DSOutOfServiceException, DSAccessException
	{
		boolean b = handleConnectionException(t);
		if (!b) return;
		if (!gw.isConnected()) return;
		Throwable cause = t.getCause();
		if (cause instanceof SecurityViolation) {
			String s = "For security reasons, cannot access data. \n";
			throw new DSAccessException(s+message, cause);
		} else if (cause instanceof SessionException) {
			String s = "Session is not valid. \n";
			throw new DSOutOfServiceException(s+message, cause);
		} else if (cause instanceof AuthenticationException) {
			String s = "Cannot initialize the session. \n";
			throw new DSOutOfServiceException(s+message, cause);
		} else if (cause instanceof ResourceError) {
			String s = "Fatal error. Please contact the administrator. \n";
			throw new DSOutOfServiceException(s+message, t);
		}
		throw new DSAccessException("Cannot access data. \n"+message, t);
	}

	/**
	 * Helper method to handle exceptions thrown by the connection library.
	 * Depending on the specified exception, the user will be asked to
	 * reconnect or to exit the application.
	 *
	 * @param e The exception to handle.
	 * @return <code>true</code> to continue handling the error,
	 * <code>false</code> otherwise.
	 */
	boolean handleConnectionException(Throwable e)
	{
		ConnectionExceptionHandler handler = new ConnectionExceptionHandler();
		int index = handler.handleConnectionException(e);
		if (index < 0) return true;
		dsFactory.sessionExpiredExit(index, e);
		return false;
	}

	/**
	 * Helper method to handle exceptions thrown by the connection library.
	 * Methods in this class are required to fill in a meaningful context
	 * message.
	 * This method is not supposed to be used in this class' constructor or in
	 * the login/logout methods.
	 *
	 * @param t The exception.
	 * @param message The context message.
	 * @throws FSAccessException A server-side error.
	 */
	private void handleFSException(Throwable t, String message)
		throws FSAccessException
	{
		boolean b = handleConnectionException(t);
		if (!b) return;
		if (!gw.isConnected()) return;
		Throwable cause = t.getCause();
		String s = "\nImage not ready. Please try again later.";
		if (cause instanceof ConcurrencyException) {
			ConcurrencyException mpe = (ConcurrencyException) cause;
			//s += ", ready in approximately ";
			//s += UIUtilities.calculateHMSFromMilliseconds(mpe.backOff);
			FSAccessException fsa = new FSAccessException(message+s, cause);
			if (mpe instanceof MissingPyramidException ||
					mpe instanceof LockTimeout)
				fsa.setIndex(FSAccessException.PYRAMID);
			fsa.setBackOffTime(mpe.backOff);
			throw fsa;
		} else if (t instanceof ConcurrencyException) {
			ConcurrencyException mpe = (ConcurrencyException) t;
			s += UIUtilities.calculateHMSFromMilliseconds(mpe.backOff);
			FSAccessException fsa = new FSAccessException(message+s, t);
			if (mpe instanceof MissingPyramidException ||
					mpe instanceof LockTimeout)
				fsa.setIndex(FSAccessException.PYRAMID);
			fsa.setBackOffTime(mpe.backOff);
			throw fsa;
		}
	}

	/**
	 * Utility method to print the error message
	 *
	 * @param e The exception to handle.
	 * @return  See above.
	 */
	private String printErrorText(Throwable e)
	{
		return UIUtilities.printErrorText(e);
	}

	/**
	 * Handles the result of the search.
	 *
	 * @param type 	The supported type.
	 * @param r		The collection to fill.
	 * @param svc	Helper reference to the service.
	 * @return See above.
	 * @throws ServerError If an error occurs while reading the results.
	 */
    private Object handleSearchResult(String type, Collection r, SearchPrx svc)
		throws ServerError
	{
		//First get object of a given type.
		boolean hasNext = false;
		try {
			hasNext = svc.hasNext();
		} catch (Exception e) {
			int size = 0;
			if (e instanceof InternalException) size = -1;
			else svc.getBatchSize();
			return Integer.valueOf(size);
		}
		if (!hasNext) return r;
		List l = svc.results();
		Iterator k = l.iterator();
		IObject object;
		long id;
		while (k.hasNext()) {
			object = (IObject) k.next();
			if (type.equals(object.getClass().getName())) {
				id = object.getId().getValue();
				if (!r.contains(id))
					r.add(id); //Retrieve the object of a given type.
			}
		}
		return r;
	}

	/**
	 * Formats the elements of the passed array. Adds the
	 * passed field in front of each term.
	 *
	 * @param terms	The terms to format.
	 * @param field	The string to add in front of the terms.
	 * @return See above.
	 */
	private List<String> formatText(List<String> terms, String field)
	{
		if (CollectionUtils.isEmpty(terms)) return null;
		if (CommonsLangUtils.isBlank(field)) return terms;
		List<String> formatted = new ArrayList<String>(terms.size());
		Iterator<String> j = terms.iterator();
		while (j.hasNext())
			formatted.add(field+":"+j.next());

		return formatted;
	}

	/**
	 * Formats the elements of the passed array. Adds the
	 * passed field in front of each term.
	 * @param terms			The terms to format.
	 * @param firstField	The string to add in front of the terms.
	 * @param sep			Separator used to join, exclude etc.
	 * @param secondField	The string to add in front of the terms.
	 * @return See above.
	 */
	private List<String> formatText(List<String> terms, String firstField,
								String sep, String secondField)
	{
		if (CollectionUtils.isEmpty(terms)) return null;
		List<String> formatted = new ArrayList<String>(terms.size());
		String value;
		Iterator<String> j = terms.iterator();
		String v;
		while (j.hasNext()) {
			v = j.next();
			value = firstField+":"+v+" "+sep+" "+secondField+":"+v;
			formatted.add(value);
		}
		return formatted;
	}

	/**
	 * Determines the table name corresponding to the specified class.
	 *
	 * @param klass The class to analyze.
	 * @return See above.
	 */
	private String getTableForLink(Class klass)
	{
		String table = null;
		if (Dataset.class.equals(klass)) table = "DatasetImageLink";
		else if (DatasetI.class.equals(klass)) table = "DatasetImageLink";
		else if (Project.class.equals(klass)) table = "ProjectDatasetLink";
		else if (ProjectI.class.equals(klass)) table = "ProjectDatasetLink";
		else if (Screen.class.equals(klass)) table = "ScreenPlateLink";
		else if (ScreenI.class.equals(klass)) table = "ScreenPlateLink";
		else if (PlateAcquisition.class.equals(klass))
			table = "PlateAcquisitionWellSampleLink";
		else if (PlateAcquisitionI.class.equals(klass))
			table = "PlateAcquisitionWellSampleLink";
		else if (TagAnnotation.class.equals(klass))
			table = "AnnotationAnnotationLink";
		else if (TagAnnotationI.class.equals(klass))
			table = "AnnotationAnnotationLink";
		return table;
	}

	/**
	 * Determines the table name corresponding to the specified class.
	 *
	 * @param klass The class to analyze.
	 * @return See above.
	 */
	private String getAnnotationTableLink(Class klass)
	{
		String table = null;
		if (Dataset.class.equals(klass) ||
		        DatasetI.class.equals(klass) ||
			DatasetData.class.equals(klass))
			table = "DatasetAnnotationLink";
		else if (Project.class.equals(klass) ||
		        ProjectI.class.equals(klass) ||
				ProjectData.class.equals(klass))
			table = "ProjectAnnotationLink";
		else if (Image.class.equals(klass) ||
		        ImageI.class.equals(klass) ||
				ImageData.class.equals(klass)) 
		    table = "ImageAnnotationLink";
		else if (Screen.class.equals(klass) ||
		        ScreenI.class.equals(klass) ||
				ScreenData.class.equals(klass))
			table = "ScreenAnnotationLink";
		else if (Plate.class.equals(klass) ||
		        PlateI.class.equals(klass) ||
				PlateData.class.equals(klass))
			table = "PlateAnnotationLink";
		else if (PlateAcquisition.class.equals(klass) ||
		        PlateAcquisitionI.class.equals(klass) ||
				PlateAcquisitionData.class.equals(klass))
			table = "PlateAcquisitionAnnotationLink";
		else if (WellSample.class.equals(klass) ||
		        WellSampleI.class.equals(klass) ||
				WellSampleData.class.equals(klass))
			table = "ScreenAnnotationLink";
		else if (RectangleData.class.equals(klass) || RectangleI.class.equals(klass) ||
		        EllipseData.class.equals(klass) ||  EllipseI.class.equals(klass) ||
		        PointData.class.equals(klass) || PointI.class.equals(klass) ||
		        PolygonData.class.equals(klass) || PolygonI.class.equals(klass) ||
		        PolylineData.class.equals(klass) || PolylineI.class.equals(klass) ||
		        TextData.class.equals(klass) || LabelI.class.equals(klass) ||
		        MaskData.class.equals(klass) || MaskI.class.equals(klass)) {
		    table = "ShapeAnnotationLink";
		} else if (ROIData.class.equals(klass)) {
		    table = "RoiAnnotationLink";
		}
		else table = "AnnotationAnnotationLink";
		return table;
	}

	/**
	 * Determines the table name corresponding to the specified class.
	 *
	 * @param klass The class to analyze.
	 * @return See above.
	 */
	private String getTableForClass(Class klass)
	{
		if (DatasetData.class.equals(klass)) return "Dataset";
		else if (ProjectData.class.equals(klass)) return "Project";
		else if (ImageData.class.equals(klass)) return "Image";
		else if (ScreenData.class.equals(klass)) return "Screen";
		else if (PlateData.class.equals(klass)) return "Plate";
		else if (PlateAcquisitionData.class.equals(klass))
			return "PlateAcquisition";
		return null;
	}

	/**
	 * Transforms the specified <code>property</code> into the
	 * corresponding server value.
	 * The transformation depends on the specified class.
	 *
	 * @param nodeType The type of node this property corresponds to.
	 * @param property The name of the property.
	 * @return See above.
	 */
	private String convertProperty(Class nodeType, String property)
	{
		if (nodeType.equals(DatasetData.class)) {
			if (property.equals(OmeroDataService.IMAGES_PROPERTY))
				return DatasetData.IMAGE_LINKS;
		}  else throw new IllegalArgumentException("NodeType or " +
				"property not supported");
		return null;
	}

	/**
	 * Loads the links.
	 *
	 * @param ctx The security context.
	 * @param table The table's link.
	 * @param childID The annotation's identifier
	 * @param userID The user's identifier.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private List loadLinks(SecurityContext ctx, String table, long childID,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			if (table == null) return new ArrayList();
			ParametersI param = new ParametersI();
			param.map.put("id", omero.rtypes.rlong(childID));
			StringBuffer sb = new StringBuffer();
			sb.append("select link from "+table+" as link ");
			sb.append("left outer join fetch link.child as child ");
			sb.append("left outer join fetch link.parent parent ");
			if (childID >= 0) {
				sb.append("where link.child.id = :id");
				param.addId(childID);
				if (userID >= 0) {
					sb.append(" and link.details.owner.id = :userID");
					param.map.put("userID", omero.rtypes.rlong(userID));
				}
			} else {
				if (userID >= 0) {
					sb.append("where link.details.owner.id = :userID");
					param.map.put("userID", omero.rtypes.rlong(userID));
				}
			}

			return service.findAllByQuery(sb.toString(), param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
					"child ID: "+childID);
		}
		return new ArrayList();
	}

	/**
	 * Returns the {@link SharedResourcesPrx} service.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private SharedResourcesPrx getSharedResources(SecurityContext ctx)
		throws DSAccessException, DSOutOfServiceException
	{
	    return gw.getSharedResources(ctx);
	}

	/**
	 * Returns the {@link IRenderingSettingsPrx} service.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private IRenderingSettingsPrx getRenderingSettingsService(
			SecurityContext ctx)
		throws DSAccessException, DSOutOfServiceException
	{
	    return gw.getRenderingSettingsService(ctx);
	}

	/**
	 * Creates or recycles the import store.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private OMEROMetadataStoreClient getImportStore(SecurityContext ctx,
			String userName)
		throws DSAccessException, DSOutOfServiceException
	{
		return gw.getImportStore(ctx, userName);
	}

	/**
	 * Returns the {@link IScriptPrx} service.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private IScriptPrx getScriptService(SecurityContext ctx)
		throws DSAccessException, DSOutOfServiceException
	{
		return gw.getScriptService(ctx);
	}

	
	/**
	 * Checks if some default rendering settings have to be created
	 * for the specified set of pixels.
	 *
	 * @param pixelsID	The pixels ID.
	 * @param prx The rendering engine to load or thumbnail store.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private void needDefault(long pixelsID, Object prx)
		throws DSAccessException, DSOutOfServiceException
	{
		try {
			if (prx instanceof ThumbnailStorePrx) {
				ThumbnailStorePrx service = (ThumbnailStorePrx) prx;
				if (!(service.setPixelsId(pixelsID))) {
				}
			} else if (prx instanceof RenderingEnginePrx) {
				RenderingEnginePrx re = (RenderingEnginePrx) prx;
				if (!re.lookupRenderingDef(pixelsID)) {
					re.resetDefaultSettings(true);
					re.lookupRenderingDef(pixelsID);
				}
			}
		} catch (Throwable e) {
			handleConnectionException(e);
			handleException(e, "Cannot set the rendering defaults.");
		}
	}

	/**
	 * Formats the terms to search for.
	 *
	 * @param terms		The terms to search for.
	 * @param service	The search service.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private List<String> prepareTextSearch(String[] terms, SearchPrx service)
		throws DSAccessException, DSOutOfServiceException
	{
		if (terms == null || terms.length == 0) return null;
		String value;
		int n;
		char[] arr;
		String v;
		List<String> formattedTerms = new ArrayList<String>(terms.length);
		String formatted;
		try {
			for (int j = 0; j < terms.length; j++) {
				value = terms[j];
				if (startWithWildCard(value))
					service.setAllowLeadingWildcard(true);
				//format string
				n = value.length();
				arr = new char[n];
				v = "";
				value.getChars(0, n, arr, 0);
				for (int i = 0; i < arr.length; i++) {
					if (SUPPORTED_SPECIAL_CHAR.contains(arr[i]))
						v += "\\"+arr[i];
					else v += arr[i];
				}
				if (value.contains(" "))
					formatted = "\""+v.toLowerCase()+"\"";
				else formatted = v.toLowerCase();
				formattedTerms.add(formatted);
			}
		} catch (Throwable e) {
			handleException(e, "Cannot format text for search.");
		}
		return formattedTerms;
	}

	/**
	 * Formats the terms to search for.
	 *
	 * @param terms		The terms to search for.
	 * @param service	The search service.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private List<String> prepareTextSearch(Collection<String> terms,
			SearchPrx service)
		throws DSAccessException, DSOutOfServiceException
	{
		if (CollectionUtils.isEmpty(terms)) return null;
		String[] values = new String[terms.size()];
		Iterator<String> i = terms.iterator();
		int index = 0;
		while (i.hasNext()) {
			values[index] = i.next();
			index++;
		}
		return prepareTextSearch(values, service);
	}

	/**
	 * Returns <code>true</code> if the specified value starts with a wild card,
	 * <code>false</code> otherwise.
	 *
	 * @param value The value to handle.
	 * @return See above.
	 */
	private boolean startWithWildCard(String value)
	{
		if (CommonsLangUtils.isBlank(value)) return false;
		Iterator<String> i = WILD_CARDS.iterator();
		String card = null;
		while (i.hasNext()) {
			card = i.next();
			if (value.startsWith(card)) {
				return true;
			}
		}
		return false;
	}

	/**
	 * Converts the class to the specified model string.
	 *
	 * @param pojo The class to convert.
	 * @return See above.
	 */
	private String convertAnnotation(Class pojo)
	{
		if (TextualAnnotationData.class.equals(pojo))
			return "ome.model.annotations.CommentAnnotation";
		else if (TagAnnotationData.class.equals(pojo))
			return "ome.model.annotations.TagAnnotation";
		else if (RatingAnnotationData.class.equals(pojo))
			return "ome.model.annotations.LongAnnotation";
		else if (LongAnnotationData.class.equals(pojo))
			return "ome.model.annotations.LongAnnotation";
		else if (FileAnnotationData.class.equals(pojo))
			return "ome.model.annotations.FileAnnotation";
		else if (TermAnnotationData.class.equals(pojo))
			return "ome.model.annotations.UriAnnotation";
		else if (TimeAnnotationData.class.equals(pojo))
			return "ome.model.annotations.TimeAnnotation";
		else if (BooleanAnnotationData.class.equals(pojo))
			return "ome.model.annotations.BooleanAnnotation";
		return null;
	}


	/**
	 * Creates a new instance.
	 *
	 * @param dsFactory 	A reference to the factory. Used whenever a broken
	 * 						link is detected to get the Login Service and try
	 *                  	reestablishing a valid link to <i>OMERO</i>.
	 *                  	Mustn't be <code>null</code>.
	 */
	OMEROGateway(DataServicesFactory dsFactory)
	{
		if (dsFactory == null)
			throw new IllegalArgumentException("No Data service factory.");
		this.dsFactory = dsFactory;
		enumerations = new HashMap<String, List<EnumerationObject>>();
		
		this.gw = new Gateway(dsFactory.getLogger());
	}

	public Gateway getGateway() {
	    return this.gw;
	}
	
	/**
	 * Creates the string corresponding to the object to delete.
	 *
	 * @param data The object to handle.
	 * @return See above.
	 */
	String createDeleteCommand(String data)
	{
		if (ImageData.class.getName().equals(data)) return REF_IMAGE;
		else if (DatasetData.class.getName().equals(data)) return REF_DATASET;
		else if (ProjectData.class.getName().equals(data)) return REF_PROJECT;
		else if (ScreenData.class.getName().equals(data)) return REF_SCREEN;
		else if (PlateData.class.getName().equals(data)) return REF_PLATE;
		else if (ROIData.class.getName().equals(data)) return REF_ROI;
		else if (PlateAcquisitionData.class.getName().equals(data))
			return REF_PLATE_ACQUISITION;
		else if (FilesetData.class.getName().equals(data)) return REF_FILESET;
		else if (WellData.class.getName().equals(data))
			return REF_WELL;
		else if (PlateAcquisitionData.class.getName().equals(data))
			return REF_PLATE_ACQUISITION;
		else if (TagAnnotationData.class.getName().equals(data) ||
				TermAnnotationData.class.getName().equals(data) ||
				FileAnnotationData.class.getName().equals(data) ||
				TextualAnnotationData.class.getName().equals(data) ||
				MapAnnotationData.class.getName().equals(data))
			return REF_ANNOTATION;
		throw new IllegalArgumentException("Cannot delete the speficied type.");
	}

	/**
	 * Creates the string corresponding to the object to delete.
	 *
	 * @param data The object to handle.
	 * @return See above.
	 */
	String createDeleteOption(String data)
	{
		if (TagAnnotationData.class.getName().equals(data))
			return REF_TAG;
		else if (TermAnnotationData.class.getName().equals(data))
			return REF_TERM;
		else if (FileAnnotationData.class.getName().equals(data))
			return REF_FILE;
		throw new IllegalArgumentException("Cannot delete the speficied type.");
	}

	/**
	 * Tells whether the communication channel to <i>OMERO</i> is currently
	 * connected.
	 * This means that we have established a connection and have successfully
	 * logged in.
	 *
	 * @return  <code>true</code> if connected, <code>false</code> otherwise.
	 */
	boolean isConnected() { return gw.isConnected(); }

	/**
	 * Retrieves the details on the current user and maps the result calling
	 * {@link PojoMapper#asDataObjects(Map)}.
	 *
	 * @param ctx The security context.
	 * @param name  The user's name.
	 * @param connectionError Pass <code>true</code> to handle the connection
	 * error, <code>false</code> otherwise.
	 * @return The {@link ExperimenterData} of the current user.
	 * @throws DSOutOfServiceException If the connection is broken, or
	 * logged in.
	 * @see IPojosPrx#getUserDetails(Set, Map)
	 */
	ExperimenterData getUserDetails(SecurityContext ctx, String name,
			boolean connectionError)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IAdminPrx service = gw.getAdminService(ctx);
			return (ExperimenterData)
				PojoMapper.asDataObject(service.lookupExperimenter(name));
		} catch (Exception e) {
			if (connectionError) handleConnectionException(e);
			throw new DSOutOfServiceException("Cannot retrieve user's data " +
					printErrorText(e), e);
		}
	}

	/**
	 * Returns <code>true</code> if an upgrade is required, <code>false</code>
	 * otherwise.
	 *
	 * @param name The name of the agent.
	 * @return See above.
	 */
	boolean isUpgradeRequired(String name)
	{
	    ResourceBundle bundle = ResourceBundle.getBundle("omero");
	    String version = bundle.getString("omero.version");
	    String url = bundle.getString("omero.upgrades.url");
	    //Strip the "OMERO" part of the string
	    if (CommonsLangUtils.isBlank(name)) {
	        name = "insight";
	    }
	    if (name.startsWith("OMERO.")) {
	        name = name.substring("OMERO.".length());
	    }
	    UpgradeCheck check = new UpgradeCheck(url, version, name);
	    check.run();
	    return check.isUpgradeNeeded();
	}

	/**
	 * Connects to the server and returns details about the logged in user.
	 *
	 * @param c The logging credentials.
	 * @return
	 * @throws DSOutOfServiceException
	 */
	ExperimenterData connect(LoginCredentials c) throws DSOutOfServiceException {
	    return gw.connect(c);
	}

	/**
	 * Returns the current session id for the given user.
	 *
	 * @param user The user to handle.
	 * @return See above.
	 */
	String getSessionId(ExperimenterData user) {
	    return gw.getSessionId(user);
	}
	
    /**
     * Get the omero client properties from the server
     * @param The groupId for the {@link SecurityContext}
     * @return See above.
     * @throws DSAccessException
     * @throws DSOutOfServiceException
     */
    Map<String, String> getOmeroClientProperties(long groupId)
            throws DSOutOfServiceException, DSAccessException {
        if (isConnected()) {
            try {
                return gw.getConfigService(new SecurityContext(groupId)).getClientConfigValues();
            } catch (Exception e) {
                handleException(e, "Cannot access config service. ");
            }
        }
        return null;
    }

	/**
	 * Retrieves the system view hosting the repositories.
	 *
	 * @param ctx The security context.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in.
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	FSFileSystemView getFSRepositories(SecurityContext ctx, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		if (fsViews == null) fsViews = new HashMap<Long, FSFileSystemView>();
		if (fsViews.containsKey(userID)) return fsViews.get(userID);
		//Review that code
		FSFileSystemView view = null;
		try {
			RepositoryMap m = getSharedResources(ctx).repositories();
			List proxys = m.proxies;
			List names = m.descriptions;
			Iterator i = names.iterator();
			int index = 0;
			FileData f;
			RepositoryPrx proxy;
			Map<FileData, RepositoryPrx>
				repositories = new HashMap<FileData, RepositoryPrx>();
			while (i.hasNext()) {
				f = new FileData((OriginalFile) i.next(), true);
				if (!f.getName().contains("Tmp")) {
					proxy = (RepositoryPrx) proxys.get(index);
					repositories.put(f, proxy);
				}
				index++;
			}
			view = new FSFileSystemView(userID, repositories);
		} catch (Throwable e) {
			handleException(e, "Cannot load the repositories");
		}
		if (view != null) fsViews.put(userID, view);
		return view;
	}

	/**
	 * Changes the default group of the currently logged in user.
	 *
	 * @param ctx The security context.
	 * @param exp The experimenter to handle
	 * @param groupID The id of the group.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in.
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void changeCurrentGroup(SecurityContext ctx, ExperimenterData exp,
			long groupID)
		throws DSOutOfServiceException, DSAccessException
	{
		List<GroupData> groups = exp.getGroups();
		Iterator<GroupData> i = groups.iterator();
		GroupData group = null;
		boolean in = false;
		while (i.hasNext()) {
			group = i.next();
			if (group.getId() == groupID) {
				in = true;
				break;
			}
		}
		if (in) {
		    try {
		        IAdminPrx svc = gw.getAdminService(ctx);
		        svc.setDefaultGroup(exp.asExperimenter(),
	                    new ExperimenterGroupI(groupID, false));
            } catch (Exception e) {
               handleException(e, "Can't modify the current group for user:"
            +exp.getId());
            }
		}

		String s = "Can't modify the current group.\n\n";
		if (!in) {
			throw new DSOutOfServiceException(s);
		}
	}


	/**
	 * Returns the version of the server.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in.
	 */
	String getServerVersion()
		throws DSOutOfServiceException
	{
		try {
			return gw.getServerVersion();
		} catch (Exception e) {
			handleConnectionException(e);
			String s = "Can't retrieve the server version.\n\n";
			s += printErrorText(e);
			throw new DSOutOfServiceException(s, e);
		}
	}

	/**
	 * Returns the LDAP details or an empty string.
	 *
	 * @param ctx The security context.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection can't be established
	 *                                  or the credentials are invalid.
	 */
	String lookupLdapAuthExperimenter(SecurityContext ctx, long userID)
		throws DSOutOfServiceException
	{
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			return svc.lookupLdapAuthExperimenter(userID);
		} catch (Throwable e) {
			handleConnectionException(e);
			String s = "Can't find the LDAP information.\n\n";
			s += printErrorText(e);
			throw new DSOutOfServiceException(s, e);
		}
	}

	/**
	 * Returns the rendering engines to re-activate.
	 *
	 * @return See above.
	 */
	Map<SecurityContext, Set<Long>> getRenderingEngines()
	{
		return gw.getRenderingEngines();
	}

	boolean joinSession() {
	    return gw.joinSession();
	}

	void logout() {
	    gw.disconnect();
	}

	/**
	 * Retrieves hierarchy trees rooted by a given node.
	 * i.e. the requested node as root and all of its descendants.
	 * The annotation for the current user is also linked to the object.
	 * Annotations are currently possible only for Image and Dataset.
	 * Wraps the call to the
	 * {@link IPojos#loadContainerHierarchy(Class, List, Map)}
	 * and maps the result calling {@link PojoMapper#asDataObjects(Set)}.
	 *
	 * @param ctx The security context, necessary to determine the service.
	 * @param rootType  The top-most type which will be searched for
	 *                  Can be <code>Project</code>.
	 *                  Mustn't be <code>null</code>.
	 * @param rootIDs   A set of the IDs of top-most containers.
	 *                  Passed <code>null</code> to retrieve all container
	 *                  of the type specified by the rootNodetype parameter.
	 * @param options   The Options to retrieve the data.
	 * @return  A set of hierarchy trees.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#loadContainerHierarchy(Class, List, Map)
	 */
	Set loadContainerHierarchy(SecurityContext ctx, Class rootType,
			List rootIDs, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
	    try {
            BrowseFacility f = gw.getFacility(BrowseFacility.class);
            // TODO: tmp solution, should be changed to Collection<DataObject> throughout
           return new HashSet(f.loadHierarchy(ctx, rootType,
                    rootIDs, options));
        } catch (Throwable e) {
            handleException(e, "Cannot load hierarchy for "+rootType+".");
        }

        return new HashSet();
	}

	/**
	 * Retrieves hierarchy trees in various hierarchies that
	 * contain the specified Images.
	 * The annotation for the current user is also linked to the object.
	 * Annotations are currently possible only for Image and Dataset.
	 * Wraps the call to the
	 * {@link IPojos#findContainerHierarchies(Class, List, Map)}
	 * and maps the result calling {@link PojoMapper#asDataObjects(Set)}.
	 *
	 * @param ctx The security context, necessary to determine the service.
	 * @param rootNodeType  top-most type which will be searched for
	 *                      Can be <code>Project</code>
	 *                      Mustn't be <code>null</code>.
	 * @param leavesIDs     Set of identifiers of the Images that sit at the
	 * 						bottom of the trees. Mustn't be <code>null</code>.
	 * @param options Options to retrieve the data.
	 * @return A <code>Set</code> with all root nodes that were found.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#findContainerHierarchies(Class, List, Map)
	 */
	Set findContainerHierarchy(SecurityContext ctx, Class rootNodeType,
			List leavesIDs, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			return PojoMapper.asDataObjects(service.findContainerHierarchies(
					PojoMapper.getModelType(rootNodeType).getName(), leavesIDs, options));
		} catch (Throwable t) {
			handleException(t, "Cannot find hierarchy for "+rootNodeType+".");
		}
		return new HashSet();
	}

	/**
	 * Loads all the annotations that have been attached to the specified
	 * <code>rootNodes</code>. This method looks for all the <i>valid</i>
	 * annotations that have been attached to each of the specified objects. It
	 * then maps each <code>rootNodeID</code> onto the set of all annotations
	 * that were found for that node. If no annotations were found for that
	 * node, then the entry will be <code>null</code>. Otherwise it will be a
	 * <code>Set</code> containing <code>Annotation</code> objects.
	 * Wraps the call to the
	 * {@link IMetadataPrx#loadAnnotations(String, List, List, List)}
	 * and maps the result calling {@link PojoMapper#asDataObjects(Parameters)}.
	 *
	 * @param ctx The security context.
	 * @param nodeType      The type of the rootNodes.
	 *                      Mustn't be <code>null</code>.
	 * @param nodeIDs       TheIds of the objects of type
	 *                      <code>rootNodeType</code>.
	 *                      Mustn't be <code>null</code>.
	 * @param annotationTypes The collection of annotations to retrieve or
	 * 						  passed an empty list if we retrieve all the
	 * 						  annotations.
	 * @param annotatorIDs  The identifiers of the users for whom annotations
	 * 						should be retrieved. If <code>null</code>,
	 * 						all annotations are returned.
	 * @param options       Options to retrieve the data.
	 * @return A map whose key is rootNodeID and value the <code>Set</code> of
	 *         all annotations for that node or <code>null</code>.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#findAnnotations(Class, List, List, Map)
	 */
	Map loadAnnotations(SecurityContext ctx, Class nodeType, List nodeIDs,
			List<Class> annotationTypes, List annotatorIDs, Parameters options)
	throws DSOutOfServiceException, DSAccessException
	{
		List<String> types = new ArrayList<String>();
		if (annotationTypes != null && annotationTypes.size() > 0) {
			types = new ArrayList<String>(annotationTypes.size());
			Iterator<Class> i = annotationTypes.iterator();
			String k;
			while (i.hasNext()) {
				k = convertAnnotation(i.next());
				if (k != null)
					types.add(k);
			}
		}
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			return PojoMapper.asDataObjects(
					service.loadAnnotations(PojoMapper.getModelType(nodeType).getName(),
							nodeIDs, types, annotatorIDs, options));
		} catch (Throwable t) {
			handleException(t, "Cannot find annotations for "+nodeType+".");
		}
		return new HashMap();
	}

	/**
	 * Loads the specified annotations.
	 *
	 * @param ctx The security context.
	 * @param annotationIds The annotation to load.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.s
	 */
	Set<DataObject> loadAnnotation(SecurityContext ctx,
			List<Long> annotationIds)
		throws DSOutOfServiceException, DSAccessException
	{
		if (annotationIds == null || annotationIds.size() == 0)
			return new HashSet<DataObject>();

		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			return PojoMapper.asDataObjects(
					service.loadAnnotation(annotationIds));
		} catch (Throwable t) {
			handleException(t, "Cannot find the annotations.");
		}
		return new HashSet<DataObject>();
	}

	/**
	 * Finds the links if any between the specified parent and child.
	 *
	 * @param ctx The security context.
	 * @param type    The type of parent to handle.
	 * @param userID  The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Collection findAllAnnotations(SecurityContext ctx, Class type, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getAnnotationTableLink(type);
			if (table == null) return null;
			String sql = "select link from "+table+" as link";
			sql +=" left outer join link.child as child";
			Parameters p = new ParametersI();
			p.map = new HashMap<String, RType>();
			p.map.put("uid", omero.rtypes.rlong(userID));
			sql += " where link.details.owner.id = :uid";
			return service.findAllByQuery(sql, p);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
					"userID: "+userID);
		}
		return new ArrayList();
	}

	/**
	 * Retrieves the images contained in containers specified by the
	 * node type.
	 * Wraps the call to the {@link IPojos#getImages(Class, List, Parameters)}
	 * and maps the result calling {@link PojoMapper#asDataObjects(Set)}.
	 *
	 * @param ctx The security context.
	 * @param nodeType  The type of container. Can be either Project, Dataset.
	 * @param nodeIDs   Set of containers' IDS.
	 * @param options   Options to retrieve the data.
	 * @return A <code>Set</code> of retrieved images.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#getImages(Class, List, Map)
	 */
	Set getContainerImages(SecurityContext ctx, Class nodeType, List nodeIDs,
			Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			return PojoMapper.asDataObjects(service.getImages(
					PojoMapper.getModelType(nodeType).getName(), nodeIDs, options));
		} catch (Throwable t) {
			handleException(t, "Cannot find images for "+nodeType+".");
		}
		return new HashSet();
	}

    /**
     * Retrieves the images imported by the current user. Wraps the call to the
     * {@link IPojos#getUserImages(Parameters)} and maps the result calling
     * {@link PojoMapper#asDataObjects(Set)}.
     *
     * @param ctx
     *            The security context.
     * @param userID
     *            The id of the user.
     * @param orphan
     *            Indicates to load the images not in any container
     * @return A <code>Collection</code> of retrieved images.
     * @throws DSOutOfServiceException
     *             If the connection is broken, or logged in
     * @throws DSAccessException
     *             If an error occurred while trying to retrieve data from OMERO
     *             service.
     * @see IPojos#getUserImages(Map)
     */
    Collection<ImageData> getUserImages(SecurityContext ctx, long userID, boolean orphan)
            throws DSOutOfServiceException, DSAccessException {
        try {
            BrowseFacility browse = gw.getFacility(BrowseFacility.class);
            if (!orphan)
                return browse.getUserImages(ctx);
            else
                return browse.getOrphanedImages(ctx, userID);
        } catch (Throwable t) {
            handleException(t, "Cannot find user images.");
        }
        return new HashSet();
    }

	/**
	 * Counts the number of items in a collection for a given object.
	 * Returns a map which key is the passed rootNodeID and the value is
	 * the number of items contained in this object and
	 * maps the result calling {@link PojoMapper#asDataObjects(Map)}.
	 *
	 * @param ctx The security context.
	 * @param rootNodeType 	The type of container.
	 * @param property		One of the properties defined by this class.
	 * @param ids           The identifiers of the objects.
	 * @param options		Options to retrieve the data.
	 * @param rootNodeIDs	Set of root node IDs.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#getCollectionCount(String, String, List, Map)
	 */
	Map getCollectionCount(SecurityContext ctx, Class rootNodeType,
			String property, List ids, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		      IMetadataPrx service = gw.getMetadataService(ctx);
		        IContainerPrx svc = gw.getPojosService(ctx);
			if (TagAnnotationData.class.equals(rootNodeType)) {
				return service.getTaggedObjectsCount(ids, options);
			}
			String p = convertProperty(rootNodeType, property);
			if (p == null) return null;
			return PojoMapper.asDataObjects(svc.getCollectionCount(
					PojoMapper.getModelType(rootNodeType).getName(), p, ids, options));
		} catch (Throwable t) {
			handleException(t, "Cannot count the collection.");
		}
		return new HashMap();
	}

	/**
	 * Creates the specified object.
	 *
	 * @param ctx The security context.
	 * @param object The object to create.
	 * @param options Options to create the data.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#createDataObject(IObject, Map)
	 */
	IObject createObject(SecurityContext ctx, IObject object)
		throws DSOutOfServiceException, DSAccessException
	{
		return createObject(ctx, object, null);
	}

	/**
	 * Creates the specified object.
	 *
	 * @param ctx The security context.
	 * @param object The object to create.
	 * @param options Options to create the data.
	 * @param userName The name of the user to create data for.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#createDataObject(IObject, Map)
	 */
	IObject createObject(SecurityContext ctx, IObject object, String userName)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
			return saveAndReturnObject(ctx, object, null, userName);
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return null;
	}

	/**
	 * Creates the specified objects.
	 *
	 * @param ctx The security context.
	 * @param objects The objects to create.
	 * @param options Options to create the data.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#createDataObjects(IObject[], Map)
	 */
	List<IObject> createObjects(SecurityContext ctx, List<IObject> objects)
		throws DSOutOfServiceException, DSAccessException
	{
		return createObjects(ctx, objects, null);
	}

	/**
	 * Creates the specified objects.
	 *
	 * @param ctx The security context.
	 * @param objects The objects to create.
	 * @param options Options to create the data.
	 * @param userName The name of the user.s
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#createDataObjects(IObject[], Map)
	 */
	List<IObject> createObjects(SecurityContext ctx, List<IObject> objects,
			String userName)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
			return saveAndReturnObject(ctx, objects, null, userName);
		} catch (Throwable t) {
			handleException(t, "Cannot create the objects.");
		}
		return new ArrayList<IObject>();
	}

	/**
	 * Deletes the specified object.
	 *
	 * @param ctx The security context.
	 * @param object    The object to delete.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void deleteObject(SecurityContext ctx, IObject object)
		throws DSOutOfServiceException, DSAccessException
	{
	    deleteObjects(ctx, Collections.singletonList(object));
	}

	/**
	 * Deletes the specified objects.
	 *
	 * @param ctx The security context.
	 * @param objects                  The objects to delete.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException       If an error occurred while trying to
	 *                                 retrieve data from OMERO service.
	 */
	void deleteObjects(SecurityContext ctx, List<IObject> objects)
		throws DSOutOfServiceException, DSAccessException
	{
        try {
            DataManagerFacility dmf = gw.getFacility(DataManagerFacility.class);
            CmdCallbackI cb = dmf.delete(ctx, objects);
            cb.loop(100, 250);
        } catch (Throwable t) {
            handleException(t, "Cannot delete the object.");
        }
	}

	/**
	 * Updates the specified object.
	 *
	 * @param ctx The security context.
	 * @param object The object to update.
	 * @param options Options to update the data.
	 * @return The updated object.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#updateDataObject(IObject, Map)
	 */
	IObject saveAndReturnObject(SecurityContext ctx, IObject object,
			Map options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IUpdatePrx service = gw.getUpdateService(ctx);
			if (options == null) return service.saveAndReturnObject(object);
			return service.saveAndReturnObject(object, options);
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return null;
	}

	/**
	 * Updates the specified object.
	 *
	 * @param ctx The security context.
	 * @param object The object to update.
	 * @param options Options to update the data.
	 * @param userName The name of the user to create the data for.
	 * @return The updated object.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#updateDataObject(IObject, Map)
	 */
	IObject saveAndReturnObject(SecurityContext ctx, IObject object,
			Map options, String userName)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
            IUpdatePrx service = gw.getUpdateService(ctx, userName);

			if (options == null) return service.saveAndReturnObject(object);
			return service.saveAndReturnObject(object, options);
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return null;
	}

	/**
	 * Updates the specified object.
	 *
	 * @param ctx The security context.
	 * @param objects The objects to update.
	 * @param options Options to update the data.
	 * @return The updated object.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#updateDataObject(IObject, Map)
	 */
	List<IObject> saveAndReturnObject(SecurityContext ctx,
			List<IObject> objects, Map options, String userName)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
	        IUpdatePrx service = gw.getUpdateService(ctx, userName);
			return service.saveAndReturnArray(objects);
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return new ArrayList<IObject>();
	}

	/**
	 * Updates the specified object.
	 *
	 * @param ctx The security context.
	 * @param object The object to update.
	 * @param options Options to update the data.
	 * @return The updated object.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#updateDataObject(IObject, Map)
	 */
	IObject updateObject(SecurityContext ctx, IObject object,
			Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			IObject r = service.updateDataObject(object, options);
			return findIObject(ctx, r);
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return null;
	}

	/**
	 * Updates the specified <code>IObject</code>s and returned the
	 * updated <code>IObject</code>s.
	 *
	 * @param ctx The security context.
	 * @param objects The array of objects to update.
	 * @param options Options to update the data.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @see IPojos#updateDataObjects(IObject[], Map)
	 */
	List<IObject> updateObjects(SecurityContext ctx, List<IObject> objects,
			Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			List<IObject> l = service.updateDataObjects(objects, options);
			if (l == null) return l;
			Iterator<IObject> i = l.iterator();
			List<IObject> r = new ArrayList<IObject>(l.size());
			IObject io;
			while (i.hasNext()) {
				io = findIObject(ctx, i.next());
				if (io != null) r.add(io);
			}
			return r;
		} catch (Throwable t) {
			handleException(t, "Cannot update the object.");
		}
		return new ArrayList<IObject>();
	}

	/**
	 * Retrieves the dimensions in microns of the specified pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The pixels set ID.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Pixels getPixels(SecurityContext ctx, long pixelsID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IPixelsPrx service = gw.getPixelsService(ctx);
			return service.retrievePixDescription(pixelsID);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the pixels set for "+pixelsID);
		}
		return null;
	}

	/**
	 * Retrieves the thumbnail for the passed set of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set the thumbnail is for.
	 * @param sizeX The size of the thumbnail along the X-axis.
	 * @param sizeY The size of the thumbnail along the Y-axis.
	 * @param userID The id of the user the thumbnail is for.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	byte[] getThumbnail(SecurityContext ctx, long pixelsID,
			int sizeX, int sizeY, long userID)
		throws RenderingServiceException, DSOutOfServiceException
	{
		return retrieveThumbnail(ctx, pixelsID, sizeX, sizeY, userID);
	}

	/**
	 * Retrieves the thumbnail for the passed set of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set the thumbnail is for.
	 * @param sizeX The size of the thumbnail along the X-axis.
	 * @param sizeY The size of the thumbnail along the Y-axis.
	 * @param userID The id of the user the thumbnail is for.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	private byte[] retrieveThumbnail(SecurityContext ctx,
			long pixelsID, int sizeX, int sizeY, long userID)
		throws RenderingServiceException, DSOutOfServiceException
	{
	    ThumbnailStorePrx service = null;
		try {
		    service = gw.getThumbnailService(ctx);
			needDefault(pixelsID, service);
			//getRendering Def for a given pixels set.
			if (userID >= 0) {
				RenderingDef def = getRenderingDef(ctx, pixelsID, userID);
				if (def != null) service.setRenderingDefId(
						def.getId().getValue());
			}
			return service.getThumbnail(omero.rtypes.rint(sizeX),
					omero.rtypes.rint(sizeY));
		} catch (Throwable t) {
			handleConnectionException(t);
			if (t instanceof ServerError) {
				throw new DSOutOfServiceException(
						"Thumbnail service null for pixelsID: "+pixelsID, t);
			}
			throw new RenderingServiceException("Cannot get thumbnail", t);
		} finally {
		    if (service != null) gw.closeService(ctx, service);
		}
	}

	/**
	 * Retrieves the thumbnail for the passed set of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set the thumbnail is for.
	 * @param maxLength The maximum length of the thumbnail width or height
	 * 					depending on the pixel size.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	byte[] getThumbnailByLongestSide(SecurityContext ctx, long pixelsID,
			int maxLength)
		throws RenderingServiceException, DSOutOfServiceException
	{
		return retrieveThumbnailByLongestSide(ctx, pixelsID, maxLength);
	}

	/**
	 * Retrieves the thumbnail for the passed set of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set the thumbnail is for.
	 * @param maxLength The maximum length of the thumbnail width or height
	 * 					depending on the pixel size.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	private byte[] retrieveThumbnailByLongestSide(
			SecurityContext ctx, long pixelsID, int maxLength)
		throws RenderingServiceException, DSOutOfServiceException
	{
		ThumbnailStorePrx service = null;
		try {
		    service = gw.getThumbnailService(ctx);
			// No need to call setPixelsID if using set method?
			return service.getThumbnailByLongestSide(
					omero.rtypes.rint(maxLength));
		} catch (Throwable t) {
			handleConnectionException(t);
			if (t instanceof ServerError) {
				throw new DSOutOfServiceException(
						"Thumbnail service null for pixelsID: "+pixelsID, t);
			}
			throw new RenderingServiceException("Cannot get thumbnail", t);
		} finally {
		    if (service != null) 
		        gw.closeService(ctx, service);
		}
	}

	/**
	 * Retrieves the thumbnail for the passed collection of pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The collection of pixels set.
	 * @param maxLength The maximum length of the thumbnail width or height
	 * 					depending on the pixel size.
	 * @param reset Pass <code>true</code> to reset the thumbnail store,
	 *              <code>false</code> otherwise.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	Map getThumbnailSet(SecurityContext ctx, List<Long> pixelsID,
			int maxLength, boolean reset)
		throws RenderingServiceException, DSOutOfServiceException
	{
		return retrieveThumbnailSet(ctx, pixelsID, maxLength, reset);
	}

	/**
	 * Retrieves the thumbnail for the passed collection of pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The collection of pixels set.
	 * @param maxLength The maximum length of the thumbnail width or height
	 * 					depending on the pixel size.
	 * @param reset Pass <code>true</code> to reset the thumbnail store,
	 *              <code>false</code> otherwise.
	 * @return See above.
	 * @throws RenderingServiceException If an error occurred while trying to
	 *              retrieve data from the service.
	 * @throws DSOutOfServiceException If the connection is broken.
	 */
	private Map retrieveThumbnailSet(SecurityContext ctx,
			List<Long> pixelsID, int maxLength, boolean reset)
		throws RenderingServiceException, DSOutOfServiceException
	{
		ThumbnailStorePrx service = null;
		try {
		    service = gw.getThumbnailService(ctx);
			return service.getThumbnailByLongestSideSet(
					omero.rtypes.rint(maxLength), pixelsID);
		} catch (Throwable t) {
			handleConnectionException(t);
			if (t instanceof ServerError) {
				throw new DSOutOfServiceException(
						"Thumbnail service null for pixelsID: "+pixelsID, t);
			}
			throw new RenderingServiceException("Cannot get thumbnail", t);
		} finally {
		    gw.closeService(ctx, service);
		}
	}

	/**
	 * Creates a new rendering service for the specified pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The pixels set ID.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @throws FSAccessException If an error occurred when trying to build a
	 * pyramid or access file not available.
	 */
	RenderingEnginePrx createRenderingEngine(SecurityContext ctx,
			long pixelsID)
		throws DSOutOfServiceException, DSAccessException, FSAccessException
	{
		return generateRenderingEngine(ctx, pixelsID);
	}

	/**
	 * Creates a new rendering service for the specified pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The pixels set ID.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 * @throws FSAccessException If an error occurred when trying to build a
	 * pyramid or access file not available.
	 */
	private RenderingEnginePrx generateRenderingEngine(
			SecurityContext ctx, long pixelsID)
		throws DSOutOfServiceException, DSAccessException, FSAccessException
	{
	    RenderingEnginePrx service = null;
		try {
		    service = gw.getRenderingService(ctx, pixelsID);
			service.lookupPixels(pixelsID);
			needDefault(pixelsID, service);
			service.load();
			return service;
		} catch (Throwable t) {
		    log(t.getMessage());
		    gw.closeService(ctx, service);
			String s = "Cannot start the Rendering Engine.";
			handleFSException(t, s);
			handleException(t, s);
		}
		return null;
	}
	/**
	 * Finds the link if any between the specified parent and child.
	 *
	 * @param ctx The security context.
	 * @param type The type of annotation to handle.
	 * @param parentID The id of the parent.
	 * @param childID The id of the child, or <code>-1</code> if no
	 *                child specified.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	IObject findAnnotationLink(SecurityContext ctx, Class type, long parentID,
			long childID, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getAnnotationTableLink(type);
			if (table == null) return null;
			StringBuffer buffer = new StringBuffer();

			buffer.append("select link from "+table+" as link ");
			buffer.append("left outer join fetch link.details.owner ");
			buffer.append("where link.parent.id = :parentID");
			Parameters p = new ParametersI();
			p.map = new HashMap<String, RType>();
			p.map.put("parentID", omero.rtypes.rlong(parentID));
			if (userID >= 0) {
				buffer.append(" and link.details.owner.id = :userID");
				p.map.put("userID", omero.rtypes.rlong(userID));
			}
			if (childID >= 0) {
				buffer.append(" and link.child.id = :childID");
				p.map.put("childID", omero.rtypes.rlong(childID));
			}

			return service.findByQuery(buffer.toString(), p);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
					"parent ID: "+parentID+" and child " +
					"ID: "+childID);
		}
		return null;
	}

	/**
	 * Finds the link if any between the specified parent and child.
	 *
	 * @param ctx The security context.
	 * @param parentType The type of parent to handle.
	 * @param parentID The id of the parent to handle.
	 * @param children Collection of the identifiers.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List findAnnotationLinks(SecurityContext ctx, Class parentType,
			long parentID, List<Long> children)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getAnnotationTableLink(parentType);
			if (table == null) return null;
			StringBuffer sb = new StringBuffer();
			sb.append("select link from "+table+" as link");
			sb.append(" left outer join fetch link.details.owner as owner");
			sb.append(" left outer join fetch link.child as child");
			sb.append(" left outer join fetch link.parent as parent");
			ParametersI p = new ParametersI();
			if (parentID > 0) {
				sb.append(" where link.parent.id = :parentID");
				if (children != null && children.size() > 0) {
					sb.append(" and link.child.id in (:childIDs)");
					p.addLongs("childIDs", children);
				}
				p.map.put("parentID", omero.rtypes.rlong(parentID));
			} else {
				if (children != null && children.size() > 0) {
					sb.append(" where link.child.id in (:childIDs)");
					p.addLongs("childIDs", children);
				}
			}
			return service.findAllByQuery(sb.toString(), p);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the annotation links for "+
					"parent ID: "+parentID);
		}
		return new ArrayList();
	}

	/**
	 * Finds the link if any between the specified parent and child.
	 *
	 * @param ctx The security context.
	 * @param parent The parent.
	 * @param child The child.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	IObject findLink(SecurityContext ctx, IObject parent, IObject child)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getTableForLink(parent.getClass());
			if (table == null) return null;
			String sql = "select link from "+table+" as link where " +
			"link.parent.id = :parentID and link.child.id = :childID";

			ParametersI param = new ParametersI();
			param.map = new HashMap<String, RType>();
			param.map.put("parentID", parent.getId());
			param.map.put("childID", child.getId());
			return service.findByQuery(sql, param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
					"parent ID: "+parent.getId()+" and child " +
					"ID: "+child.getId());
		}
		return null;
	}

	/**
	 * Finds the links if any between the specified parent and children.
	 *
	 * @param ctx The security context.
	 * @param parent The parent.
	 * @param children Collection of children as identifiers.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List findLinks(SecurityContext ctx, IObject parent, List children)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getTableForLink(parent.getClass());
			if (table == null) return null;

			ParametersI param = new ParametersI();
			param.map.put("parentID", parent.getId());

			String sql = "select link from "+table+" as link where " +
			"link.parent.id = :parentID";
			if (children != null && children.size() > 0) {
				sql += " and link.child.id in (:childIDs)";
				param.addLongs("childIDs", children);

			}
			return service.findAllByQuery(sql, param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
					"parent ID: "+parent.getId());
		}
		return new ArrayList();
	}

	/**
	 * Finds the links if any between the specified parent and children.
	 *
	 * @param ctx The security context.
	 * @param parentClass The parent.
	 * @param children Collection of children as identifiers.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List findLinks(SecurityContext ctx, Class parentClass, List children,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getTableForLink(parentClass);
			if (table == null) return null;
			String sql = "select link from "+table+" as link where " +
			"link.child.id in (:childIDs)";
			ParametersI param = new ParametersI();
			param.addLongs("childIDs", children);

			if (userID >= 0) {
				sql += " and link.details.owner.id = :userID";
				param.map.put("userID", omero.rtypes.rlong(userID));
			}
			return service.findAllByQuery(sql, param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
			"the specified children");
		}
		return new ArrayList();
	}
	
	/**
	 * Finds all DatasetImageLinks for a given list of image ids
	 * @param ctx The security context.
	 * @param children A list of image ids.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException
	 * @throws DSAccessException
	 */
        List findDatasetLinks(SecurityContext ctx, List children, long userID) throws DSOutOfServiceException,
                DSAccessException {
            try {
                IQueryPrx service = gw.getQueryService(ctx);
                // have to fetch the Dataset, too; otherwise Dataset.name won't be initialized
                String sql = "SELECT link FROM DatasetImageLink AS link LEFT JOIN FETCH link.parent dataset WHERE "
                        + "link.child.id IN (:childIDs)";
                ParametersI param = new ParametersI();
                param.addLongs("childIDs", children);
    
                if (userID >= 0) {
                    sql += " and link.details.owner.id = :userID";
                    param.map.put("userID", omero.rtypes.rlong(userID));
                }
                return service.findAllByQuery(sql, param);
            } catch (Throwable t) {
                handleException(t, "Cannot retrieve the requested datasets for "
                        + "the specified children");
            }
            return new ArrayList();
        }

	/**
	 * Finds all the links.
	 *
	 * @param ctx The security context.
	 * @param node The type of node to handle.
	 * @param nodeID The id of the node if any.
	 * @param children The collection of annotations' identifiers
	 * @param userID The user's identifier or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List findAnnotationLinks(SecurityContext ctx, Class node, long nodeID,
			List children, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			String table = getAnnotationTableLink(node);
			if (table == null) return null;
			StringBuffer sb = new StringBuffer();
			sb.append("select link from "+table+" as link ");
			sb.append("left outer join fetch link.child child ");
			sb.append("left outer join fetch link.parent parent ");
			sb.append("left outer join fetch parent.details.owner ");
			sb.append("left outer join fetch child.details.owner ");
			sb.append("left outer join fetch link.details.owner ");
			sb.append("where link.child.id in (:childIDs)");

			ParametersI param = new ParametersI();
			param.addLongs("childIDs", children);
			if (nodeID > 0) {
				sb.append(" and link.parent.id = :parentID");
				param.map.put("parentID", omero.rtypes.rlong(nodeID));
			}
			if (userID >= 0) {
				sb.append(" and link.details.owner.id = :userID");
				param.map.put("userID", omero.rtypes.rlong(userID));
			}
			return service.findAllByQuery(sb.toString(), param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested link for "+
			"the specified children");
		}
		return new ArrayList();
	}

	/**
	 * Returns the annotations links.
	 *
	 * @param ctx The security context.
     * @param node The type of node to handle.
     * @param nodeIDs The id of the nodes if any.
     * @param children The collection of annotations' identifiers
     * @param userID The user's identifier or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
     * @throws DSAccessException If an error occurred while trying to
     *                           retrieve data from OMERO service.
	 */
	Multimap<Long, IObject> findAnnotationLinks(SecurityContext ctx,
	        Class<?> node, List<Long> nodeIDs,
            List<Long> children, long userID)
        throws DSOutOfServiceException, DSAccessException
    {
        Multimap<Long, IObject> map = ArrayListMultimap.create();
        try {
            IQueryPrx service = gw.getQueryService(ctx);
            String table = getAnnotationTableLink(node);
            if (table == null) return null;
            StringBuffer sb = new StringBuffer();
            sb.append("select link from "+table+" as link ");
            sb.append("left outer join fetch link.child child ");
            sb.append("left outer join fetch link.parent parent ");
            sb.append("left outer join fetch parent.details.owner ");
            sb.append("left outer join fetch child.details.owner ");
            sb.append("left outer join fetch link.details.owner ");
            sb.append("where link.child.id in (:childIDs)");

            ParametersI param = new ParametersI();
            param.addLongs("childIDs", children);
            sb.append(" and link.parent.id in (:parentIDs)");
            param.addLongs("parentIDs", nodeIDs);
            if (userID >= 0) {
                sb.append(" and link.details.owner.id = :userID");
                param.map.put("userID", omero.rtypes.rlong(userID));
            }
            List<IObject> list = service.findAllByQuery(sb.toString(), param);
            if (CollectionUtils.isNotEmpty(list)) {
                Iterator<IObject> j = list.iterator();
                IObject link;
                while (j.hasNext()) {
                    link = (IObject) j.next();
                    IObject p = ModelMapper.getParentFromLink(link);
                    map.put(p.getId().getValue(), link);
                }
            }
            return map;
        } catch (Throwable t) {
            handleException(t, "Cannot retrieve the requested link for "+
            "the specified children");
        }
        return map;
    }
	
	/**
	 * Finds the links if any between the specified parent and children.
	 *
	 * @param ctx The security context.
	 * @param parentClass The parent.
	 * @param childID The id of the child.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List findLinks(SecurityContext ctx, Class parentClass, long childID,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		if (FileAnnotation.class.equals(parentClass)) {
			List results = new ArrayList();
			results.addAll(loadLinks(ctx, "ProjectAnnotationLink", childID,
					userID));
			results.addAll(loadLinks(ctx, "DatasetAnnotationLink", childID,
					userID));
			results.addAll(loadLinks(ctx, "ImageAnnotationLink", childID,
					userID));
			results.addAll(loadLinks(ctx, "ScreenAnnotationLink", childID,
                    userID));
			results.addAll(loadLinks(ctx, "PlateAnnotationLink", childID,
                    userID));
			results.addAll(loadLinks(ctx, "WellAnnotationLink", childID,
                    userID));
			results.addAll(loadLinks(ctx, "PlateAcquisitionAnnotationLink", childID,
                    userID));
			return results;
		}
		return loadLinks(ctx, getTableForLink(parentClass), childID, userID);
	}

	/**
	 * Finds the links if any between the specified parent and children.
	 *
	 * @param ctx The security context.
	 * @param childID The id of the child.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Set<DataObject> findPlateFromImage(SecurityContext ctx, long childID,
			long userID)
	throws DSOutOfServiceException, DSAccessException
	{
		Set<DataObject> data = new HashSet<DataObject>();
		List<Long> ids = new ArrayList<Long>();
		ParametersI param = new ParametersI();
		param.addLong("imageID", childID);

		StringBuilder sb = new StringBuilder();

		sb.append("select well from Well as well ");
		sb.append("left outer join fetch well.plate as pt ");
		sb.append("left outer join fetch well.wellSamples as ws ");
		sb.append("left outer join fetch ws.image as img ");
        sb.append("where img.id = :imageID");

        try {
            IQueryPrx service = gw.getQueryService(ctx);
            List results = service.findAllByQuery(sb.toString(), param);
    		Iterator i = results.iterator();
    		Well well;
    		Plate plate;
    		long id;
    		while (i.hasNext()) {
    			well = (Well) i.next();
    			plate = well.getPlate();
    			id = plate.getId().getValue();
    			if (!ids.contains(id)) {
    				data.add(PojoMapper.asDataObject(plate));
    				ids.add(id);
    			}
    		}
		} catch (Throwable t) {
			handleException(t, "Cannot find the plates containing the image.");
		}

		return data;
	}

	/**
     * Finds the links if any between the specified parent and children.
     *
     * @param ctx The security context.
     * @param childID The id of the child.
     * @param userID The id of the user.
     * @return See above.
     * @throws DSOutOfServiceException If the connection is broken, or logged in
     * @throws DSAccessException If an error occurred while trying to
     * retrieve data from OMERO service.
     */
    Set<DataObject> findPlateFromRun(SecurityContext ctx, long childID,
            long userID)
    throws DSOutOfServiceException, DSAccessException
    {
        Set<DataObject> data = new HashSet<DataObject>();
        List<Long> ids = new ArrayList<Long>();
        ParametersI param = new ParametersI();
        param.addLong("acqId", childID);

        StringBuilder sb = new StringBuilder();

        sb.append("select plate from Plate as plate where plate.id = (select acq.plate "
                + "from PlateAcquisition acq where acq.id = :acqId)");

        try {
            IQueryPrx service = gw.getQueryService(ctx);
            List results = service.findAllByQuery(sb.toString(), param);
            Iterator i = results.iterator();
            Plate plate;
            long id;
            while (i.hasNext()) {
                plate =  (Plate) i.next();
                id = plate.getId().getValue();
                if (!ids.contains(id)) {
                    data.add(PojoMapper.asDataObject(plate));
                    ids.add(id);
                }
            }
        } catch (Throwable t) {
            handleException(t, "Cannot find the plates containing the image.");
        }

        return data;
    }
    
    /**
     * Retrieves an updated version of the specified object.
     *
     * @param ctx The security context.
     * @param o The object to retrieve.
     * @return The last version of the object.
     * @throws DSOutOfServiceException If the connection is broken, or logged in
     * @throws DSAccessException If an error occurred while trying to
     * retrieve data from OMERO service.
     */
    IObject findIObject(SecurityContext ctx, IObject o)
        throws DSOutOfServiceException, DSAccessException
    {
        try {
            BrowseFacility browse = gw.getFacility(BrowseFacility.class);
            return browse.findIObject(ctx,o);
        } catch (ExecutionException e) {
            log("Can't get a BrowseFacility");
        }
        return null;
    }

	/**
	 * Retrieves an updated version of the specified object.
	 *
	 * @param ctx The security context.
	 * @param dataObjectThe object to retrieve.
	 * @param name The name of the object.
	 * @param
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	IObject findIObjectByName(SecurityContext ctx, Class dataObject,
			String name, long ownerID)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			ParametersI param = new ParametersI();
			param.map.put("name", rtypes.rstring(name));
			param.map.put("ownerID", rtypes.rlong(ownerID));
			String table = getTableForClass(dataObject);
			String sql = "select o from "+table+" as o";
			sql += " where o.name = :name";
			sql += " and o.details.owner.id = :ownerID";
			return service.findByQuery(sql, param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the requested object.");
		}
		return null;
	}

	/**
	 * Retrieves an updated version of the specified object.
	 *
	 * @param ctx The security context.
	 * @param klassName The type of object to retrieve.
	 * @param id The object's id.
	 * @return The last version of the object.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	IObject findIObject(SecurityContext ctx, String klassName, long id)
		throws DSOutOfServiceException, DSAccessException
	{
	    return findIObject(ctx, klassName, id, false);
	}
	
	/**
	 * Find an IObject by HQL query
	 * @param ctx The security context
	 * @param query The hql query string
	 * @param allGroups If true search for all groups, other just for
	 *   the SecurityContext's group
	 * @return The object, if found
	 * @throws DSOutOfServiceException
	 * @throws DSAccessException
	 */
	IObject findIObjectByQuery(SecurityContext ctx, String query, boolean allGroups)
                throws DSOutOfServiceException, DSAccessException
        {
                try {
                    Map<String, String> m = new HashMap<String, String>();
                    if(allGroups) {
                        m.put("omero.group", "-1");
                    }
                    else {
                        m.put("omero.group", ""+ctx.getGroupID());
                    }
                    
                    IQueryPrx service = gw.getQueryService(ctx);
                        return service.findByQuery(query, null, m);
                } catch (Throwable t) {
                        handleException(t, "Cannot retrieve the requested object with "+
                                        "query: "+query);
                }
                return null;
        }
	
	/**
         * Retrieves an updated version of the specified object.
         *
         * @param ctx The security context.
         * @param klassName The type of object to retrieve.
         * @param id The object's id.
         * @return The last version of the object.
         * @throws DSOutOfServiceException If the connection is broken, or logged in
         * @throws DSAccessException If an error occurred while trying to
         * retrieve data from OMERO service.
         */
        IObject findIObject(SecurityContext ctx, String klassName, long id, boolean allGroups)
                throws DSOutOfServiceException, DSAccessException
        {
                try {
                    BrowseFacility browse = gw.getFacility(BrowseFacility.class);
                    return browse.findIObject(ctx, klassName, id, allGroups);
                } catch (ExecutionException e) {
                    log("Can't get a BrowseFacility");
                }
                return null;
        }

	/**
	 * Retrieves the groups visible by the current experimenter.
	 *
	 * @param ctx The security context.
	 * @param loggedInUser The user currently logged in.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Set<GroupData> getAvailableGroups(SecurityContext ctx,
			ExperimenterData user)
		throws DSOutOfServiceException, DSAccessException
	{
		Set<GroupData> pojos = new HashSet<GroupData>();
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			//Need method server side.
			ParametersI p = new ParametersI();
			p.addId(user.getId());
			List<IObject> groups = service.findAllByQuery(
                    "select distinct g from ExperimenterGroup as g "
                    + "join fetch g.groupExperimenterMap as map "
                    + "join fetch map.parent e "
                    + "left outer join fetch map.child u "
                    + "left outer join fetch u.groupExperimenterMap m2 "
                    + "left outer join fetch m2.parent p "
                    + "where g.id in "
                    + "  (select m.parent from GroupExperimenterMap m "
                    + "  where m.child.id = :id )", p);
			ExperimenterGroup group;
			//GroupData pojoGroup;
			Iterator<IObject> i = groups.iterator();
			while (i.hasNext()) {
				group = (ExperimenterGroup) i.next();
				pojos.add((GroupData) PojoMapper.asDataObject(group));
			}
			return pojos;
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the available groups ");
		}
		return pojos;
	}

	/**
	 * Retrieves the archived files if any for the specified set of pixels.
	 *
	 * @param ctx The security context.
	 * @param file The location where to save the files.
	 * @param image The image to retrieve.
	 * @param keepOriginalPaths Pass <code>true</code> to preserve the original folder structure
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Map<Boolean, Object> getArchivedFiles(
			SecurityContext ctx, File file, ImageData image, boolean keepOriginalPaths)
		throws DSAccessException, DSOutOfServiceException
	{
		return retrieveArchivedFiles(ctx, file, image, keepOriginalPaths);
	}
	
	/**
	 * Retrieves the archived files if any for the specified set of pixels.
	 *
	 * @param ctx The security context.
	 * @param file The location where to save the files.
	 * @param image The image to retrieve.
	 * @param keepOriginalPaths Pass <code>true</code> to preserve the original folder
	 *               structure.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private Map<Boolean, Object> retrieveArchivedFiles(
			SecurityContext ctx, File file, ImageData image, boolean keepOriginalPaths)
		throws DSAccessException, DSOutOfServiceException
	{
		List<?> files = null;
		String query;
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			ParametersI param = new ParametersI();
			long id;
			if (image.isFSImage()) {
				id = image.getId();
				List<RType> l = new ArrayList<RType>();
				l.add(omero.rtypes.rlong(id));
				param.add("imageIds", omero.rtypes.rlist(l));
				query = createFileSetQuery();
			} else {//Prior to FS
				if (image.isArchived()) {
					StringBuffer buffer = new StringBuffer();
					id = image.getDefaultPixels().getId();
					buffer.append("select ofile from OriginalFile as ofile ");
					buffer.append("join fetch ofile.hasher ");
					buffer.append("left join ofile.pixelsFileMaps as pfm ");
					buffer.append("left join pfm.child as child ");
					buffer.append("where child.id = :id");
					param.map.put("id", omero.rtypes.rlong(id));
					query = buffer.toString();
				} else return null;
			}
			files = service.findAllByQuery(query, param);
		} catch (Exception e) {
			handleConnectionException(e);
			throw new DSAccessException("Cannot retrieve original file", e);
		}

		Map<Boolean, Object> result = new HashMap<Boolean, Object>();
		if (CollectionUtils.isEmpty(files)) return result;
		Iterator<?> i;
		Map<OriginalFile, Fileset> values = new HashMap<OriginalFile, Fileset>();
		if (image.isFSImage()) {
			i = files.iterator();
			Fileset set;
			List<FilesetEntry> entries;
			Iterator<FilesetEntry> j;
			while (i.hasNext()) {
				set = (Fileset) i.next();
				entries = set.copyUsedFiles();
				j = entries.iterator();
				while (j.hasNext()) {
					FilesetEntry fs = j.next();
					values.put(fs.getOriginalFile(), set);
				}
			}
		} else {
		    for(Object f : files)
		        values.put((OriginalFile)f, null);
		}

		RawFileStorePrx store = null;
		OriginalFile of;
		long size;
		FileOutputStream stream = null;
		long offset = 0;
		File f = null;
		List<File> results = new ArrayList<File>();
		List<String> notDownloaded = new ArrayList<String>();
		String folderPath = null;
		folderPath = file.getAbsolutePath();
		Iterator<Entry<OriginalFile, Fileset>> entries = values.entrySet().iterator();

		Map<Fileset, String> filesetPaths = new HashMap<Fileset, String>();
		
		while (entries.hasNext()) {
		    Entry<OriginalFile, Fileset> entry = entries.next();
		    
			of = entry.getKey();
			Fileset set = entry.getValue();
			
            String path = null;
            if (keepOriginalPaths && set != null && set.sizeOfUsedFiles() > 1) {
                // this will store multi file images within a subdirectory with
                // the same name as the main image file
                path = filesetPaths.get(set);
                if (path == null) {
                    path = folderPath.endsWith("/") ? folderPath : folderPath + "/";
                    String imgFilename = set.getFilesetEntry(0).getOriginalFile()
                            .getName().getValue();
                    path += imgFilename;
                    path = generateUniquePathname(path, false);
                    // path should now be in the form
                    // DOWNLOAD_FOLDER/IMAGE_NAME[(N)]
                    // where N is a consecutive number if the folder IMAGE_NAME
                    // already exists
                    filesetPaths.put(set, path);
                }
                String repoPath = set.getTemplatePrefix().getValue();
                path = path +"/"+ (of.getPath().getValue().replace(repoPath, ""));
                // path should now be in the form
                // DOWNLOAD_FOLDER/IMAGE_NAME[(N)]/X/Y/Z
                // where X, Y, Z are image specific subdirectories
                // for the single image/data files
                File origPath = new File(path);
                if (!origPath.exists())
                    origPath.mkdirs();
            } else {
                path = folderPath;
            }
			
			try {
			    store = gw.getRawFileService(ctx);
				store.setFileId(of.getId().getValue());
				
				if (path != null) 
				    f = new File(path, of.getName().getValue());
				else
				    f = file;
				
                if (f.exists()) {
                    String newFileName = generateUniquePathname(f.getPath(),
                            true);
                    f = new File(newFileName);
                }
				
				results.add(f);

				stream = new FileOutputStream(f);
				size = of.getSize().getValue();
				try {
					try {
						for (offset = 0; (offset+INC) < size;) {
							stream.write(store.read(offset, INC));
							offset += INC;
						}
					} finally {
						stream.write(store.read(offset, (int) (size-offset)));
						stream.close();
					}
				} catch (Exception e) {
					if (stream != null) stream.close();
					if (f != null) {
						f.delete();
						results.remove(f);
					}
					notDownloaded.add(of.getName().getValue());
					handleConnectionException(e);
				}
			} catch (IOException e) {
				if (f != null) {
					f.delete();
					results.remove(f);
				}
				notDownloaded.add(of.getName().getValue());
				throw new DSAccessException("Cannot create file in folderPath",
						e);
			} catch (ServerError sr) {
			    throw new DSAccessException("ServerError on retrieveArchived", sr);
			} finally {
			    gw.closeService(ctx, store);
			}
		}
		result.put(Boolean.valueOf(true), results);
		result.put(Boolean.valueOf(false), notDownloaded);
		return result;
	}
	
    /**
     * Checks if the given path already exists and if so, generates a new path
     * name path(N), where N is a consecutive number
     * 
     * @param path
     *            The path name to check
     * @param isFile
     *            Pass <code>true</code> if the path name represents a file
     * @return A unique path name based on the given path or the path itself if
     *         it doesn't exist yet
     */
    private String generateUniquePathname(String path, boolean isFile) {
        File tmp = new File(path);
        if (tmp.exists()) {
            String fileExt = null;
            if (isFile && path.matches(".+\\..+")) {
                fileExt = path.substring(path.lastIndexOf('.'), path.length());
                path = path.substring(0, path.lastIndexOf('.'));
            }
            if (path.matches(".+\\(\\d+\\)")) {
                int n = Integer.parseInt(path.substring(
                        path.lastIndexOf('(') + 1, path.lastIndexOf(')')));
                n++;
                path = path.substring(0, path.lastIndexOf('(')) + "(" + n + ")";
            } else {
                path += "(1)";
            }
            if (fileExt != null)
                path += fileExt;
            return generateUniquePathname(path, isFile);
        }
        return path;
    }

	/**
	 * Downloads a file previously uploaded to the server.
	 *
	 * @param ctx The security context.
	 * @param file The file to copy the data into.
	 * @param fileID The id of the file to download.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	File downloadFile(SecurityContext ctx, File file, long fileID)
		throws DSAccessException, DSOutOfServiceException
	{
		if (file == null) return null;
		return download(ctx, file, fileID);
	}

	/**
	 * Downloads a file previously uploaded to the server.
	 *
	 * @param ctx The security context.
	 * @param file The file to copy the data into.
	 * @param fileID The id of the file to download.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private File download(SecurityContext ctx, File file,
			long fileID)
		throws DSAccessException, DSOutOfServiceException
	{
		if (file == null) return null;
		OriginalFile of = getOriginalFile(ctx, fileID);
		if (of == null) return null;

		final String path = file.getAbsolutePath();

		RawFileStorePrx store = null;
		try {
		    store = gw.getRawFileService(ctx);
			store.setFileId(fileID);
		} catch (Throwable e) {
		    gw.closeService(ctx, store);
			handleException(e, "Cannot set the file's id.");
			return null; // Never reached.
		}

		try {
			long size = -1;
			long offset = 0;
			FileOutputStream stream = new FileOutputStream(file);
			try {
				try {
				    size = store.size();
					for (offset = 0; (offset+INC) < size;) {
						stream.write(store.read(offset, INC));
						offset += INC;
					}
				} finally {
					stream.write(store.read(offset, (int) (size-offset)));
					stream.close();
				}
			} catch (Exception e) {
				if (stream != null) stream.close();
				if (file != null) file.delete();
			}
		} catch (IOException e) {
			if (file != null) file.delete();
			gw.closeService(ctx, store);
			throw new DSAccessException("Cannot create file  " +path, e);
		} finally {
		    gw.closeService(ctx, store);
		}

		return file;
	}

	/**
	 * Returns the original file corresponding to the passed id.
	 *
	 * @param ctx The security context.
	 * @param id The id identifying the file.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	OriginalFile getOriginalFile(SecurityContext ctx, long id)
		throws DSAccessException, DSOutOfServiceException
	{
		OriginalFile of = null;
		try {
		    IQueryPrx svc = gw.getQueryService(ctx);
			ParametersI param = new ParametersI();
			param.map.put("id", omero.rtypes.rlong(id));
			of = (OriginalFile) svc.findByQuery(
					"select p from OriginalFile as p " +
					"where p.id = :id", param);
		} catch (Exception e) {
			handleException(e, "Cannot retrieve original file");
		}
		return of;
	}

	/**
	 * Returns the collection of original files related to the specified
	 * pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The ID of the pixels set.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List getOriginalFiles(SecurityContext ctx, long pixelsID)
		throws DSAccessException, DSOutOfServiceException
	{
		List files = null;
		try {
		    IQueryPrx svc = gw.getQueryService(ctx);
			ParametersI param = new ParametersI();
			param.map.put("id", omero.rtypes.rlong(pixelsID));
			files = svc.findAllByQuery(
					"select ofile from OriginalFile as ofile left join " +
					"ofile.pixelsFileMaps as pfm left join pfm.child as " +
					"child where child.id = :id", param);
		} catch (Exception e) {
			handleException(e, "Cannot retrieve original file");
		}
		return files;
	}

	/**
	 * Uploads the passed file to the server and returns the
	 * original file i.e. the server object.
	 *
	 * @param ctx The security context.
	 * @param file The file to upload.
	 * @param mimeType The mimeType of the file.
	 * @param originalFileID The id of the file or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	OriginalFile uploadFile(SecurityContext ctx, File file, String mimeType,
			long originalFileID)
		throws DSAccessException, DSOutOfServiceException
	{
		return upload(ctx, file, mimeType, originalFileID);
	}

	/**
	 * Uploads the passed file to the server and returns the
	 * original file i.e. the server object.
	 *
	 * @param ctx The security context.
	 * @param file The file to upload.
	 * @param mimeType The mimeType of the file.
	 * @param originalFileID The id of the file or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	private OriginalFile upload(SecurityContext ctx, File file,
			String mimeType, long originalFileID)
		throws DSAccessException, DSOutOfServiceException
	{
		if (file == null)
			throw new IllegalArgumentException("No file to upload");
		if (CommonsLangUtils.isBlank(mimeType))
			mimeType =  DEFAULT_MIMETYPE;

		boolean fileCreated = false;
        final ChecksumAlgorithm checksumAlgorithm = new ChecksumAlgorithmI();
        checksumAlgorithm.setValue(omero.rtypes.rstring(ChecksumAlgorithmSHA1160.value));
        OriginalFile save = null;
        Long fileId = null;

		try {
		    IUpdatePrx update = gw.getUpdateService(ctx, null);
			OriginalFile oFile;
			if (originalFileID <= 0) {
				oFile = new OriginalFileI();
				String name = file.getName();
				oFile.setName(omero.rtypes.rstring(name));
				String absolutePath = file.getAbsolutePath();
				String path = absolutePath.substring(0,
						absolutePath.length()-name.length());
				oFile.setPath(omero.rtypes.rstring(path));
				oFile.setSize(omero.rtypes.rlong(file.length()));
				//Need to be modified
				oFile.setMimetype(omero.rtypes.rstring(mimeType));
				oFile.setHasher(checksumAlgorithm);
				save =
					(OriginalFile) update.saveAndReturnObject(oFile);
				fileId = save.getId().getValue();
				fileCreated = true;
			} else {
				oFile = (OriginalFile) findIObject(ctx,
						OriginalFile.class.getName(), originalFileID);
				if (oFile == null) {
					oFile = new OriginalFileI();
					String name = file.getName();
					oFile.setName(omero.rtypes.rstring(name));
					String absolutePath = file.getAbsolutePath();
					String path = absolutePath.substring(0,
							absolutePath.length()-name.length());
					oFile.setPath(omero.rtypes.rstring(path));
					oFile.setSize(omero.rtypes.rlong(file.length()));
					//Need to be modified
					oFile.setMimetype(omero.rtypes.rstring(mimeType));
					oFile.setHasher(checksumAlgorithm);
					save = (OriginalFile) update.saveAndReturnObject(oFile);
					fileId = save.getId().getValue();
					fileCreated = true;
				} else {
					OriginalFile newFile = new OriginalFileI();
					newFile.setId(omero.rtypes.rlong(originalFileID));
					newFile.setName(omero.rtypes.rstring(file.getName()));
					newFile.setPath(omero.rtypes.rstring(
							file.getAbsolutePath()));
					newFile.setSize(omero.rtypes.rlong(file.length()));
					ChecksumAlgorithm oldHasher = oFile.getHasher();
					if (oldHasher == null) {
					    oldHasher = checksumAlgorithm;
					}
					newFile.setHasher(oldHasher);
					newFile.setMimetype(oFile.getMimetype());
					save = (OriginalFile) update.saveAndReturnObject(newFile);
					fileId = save.getId().getValue();
				}
			}
		} catch (Exception e) {
			handleException(e, "Cannot set the file's id.");
		}


		byte[] buf = new byte[INC];
		FileInputStream stream = null;
		final ChecksumProvider hasher = checksumProviderFactory.getProvider(
				ChecksumType.SHA1);
		RawFileStorePrx store = null;
		try {
		    store = gw.getRawFileService(ctx);
		    store.setFileId(fileId);
			stream = new FileInputStream(file);
			long pos = 0;
			int rlen;
			ByteBuffer bbuf;
			while ((rlen = stream.read(buf)) > 0) {
				store.write(buf, pos, rlen);
				pos += rlen;
				bbuf = ByteBuffer.wrap(buf);
				bbuf.limit(rlen);
				hasher.putBytes(bbuf);
			}
			stream.close();
			OriginalFile f = store.save();
			if (f != null) {
				save = f;
				final String clientHash = hasher.checksumAsString();
				final String serverHash = save.getHash().getValue();
				if (!clientHash.equals(serverHash)) {
				    throw new ImportException("file checksum mismatch on " +
				    		"upload: " + file +
				            " (client has " + clientHash + ", " +
				            		"server has " + serverHash + ")");
				}
			}

		} catch (Exception e) {
			try {
				if (fileCreated) deleteObject(ctx, save);
				if (stream != null) stream.close();
			} catch (Exception ex) {
			    log("Exception on upload cleanup: " + e);
			}
			handleConnectionException(e);
			throw new DSAccessException("Cannot upload the file with path " +
					file.getAbsolutePath(), e);
		} finally {
		    if (store != null) gw.closeService(ctx, store);
		}
		return save;
	}


	/**
	 * Modifies the password of the currently logged in user.
	 *
	 * @param ctx The security context.
	 * @param password	The new password.
	 * @param oldPassword The old password.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void changePassword(SecurityContext ctx, String password,
			String oldPassword)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx service = gw.getAdminService(ctx, true);
			service.changePasswordWithOldPassword(
					omero.rtypes.rstring(oldPassword),
					omero.rtypes.rstring(password));
		} catch (Throwable t) {
			handleException(t, "Cannot modify password. ");
		}
	}

	/**
	 * Updates the profile of the specified experimenter.
	 *
	 * @param ctx The security context.
	 * @param exp	The experimenter to handle.
	 * @param currentUserID The identifier of the user currently logged in.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void updateExperimenter(SecurityContext ctx, Experimenter exp,
			long currentUserID)
		throws DSOutOfServiceException, DSAccessException
	{
		if (exp == null) return;
		
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			if (exp.getId().getValue() == currentUserID)
				svc.updateSelf(exp);
			else svc.updateExperimenter(exp);
		} catch (Throwable t) {
			handleException(t, "Cannot update the user. ");
		}
	}

	/**
	 * Updates the group's permissions
	 * @param ctx The security context.
         * @param group The group to update.
         * @param permissions The new permissions.
	 * @return
	 * @throws DSOutOfServiceException
	 * @throws DSAccessException
	 */
        RequestCallback updateGroupPermissions(SecurityContext ctx,
                GroupData group, int permissions) throws DSOutOfServiceException,
                DSAccessException {
            if (group.getPermissions().getPermissionsLevel() != permissions
                    && permissions >= 0) {
                try {
                    String r = "rw----";
                    switch (permissions) {
                        case GroupData.PERMISSIONS_GROUP_READ:
                            r = "rwr---";
                            break;
                        case GroupData.PERMISSIONS_GROUP_READ_LINK:
                            r = "rwra--";
                            break;
                        case GroupData.PERMISSIONS_GROUP_READ_WRITE:
                            r = "rwrw--";
                            break;
                        case GroupData.PERMISSIONS_PUBLIC_READ:
                            r = "rwrwr-";
                    }
                    final Chmod2 chmod = Requests.chmod("ExperimenterGroup", group.getId(), r);
                    List<Request> l = new ArrayList<Request>();
                    l.add(chmod);
                    return new RequestCallback(gw.submit(ctx, l, null));
                } catch (Throwable e) {
                    handleException(e, "Cannot update the group's permissions. ");
                }
    
            }
            return null;
        }
	
	/**
	 * Updates the specified group.
	 *
	 * @param ctx The security context.
	 * @param group	The group to update.
	 * 
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void updateGroup(SecurityContext ctx, GroupData group)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			ExperimenterGroup g = group.asGroup();
			svc.updateGroup(g);
		} catch (Throwable t) {
			handleException(t, "Cannot update the group. ");
		}
	}

	/**
	 * Adds or removes the passed experimenters from the specified system group.
	 *
	 * @param ctx The security context.
	 * @param toAdd Pass <code>true</code> to add the experimenters as owners,
	 * 				<code>false</code> otherwise.
	 * @param experimenters The experimenters to add or remove.
	 * @param systemGroup	The roles to handle.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void modifyExperimentersRoles(SecurityContext ctx, boolean toAdd,
			List<ExperimenterData> experimenters, String systemGroup)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			if (toAdd) {
				Iterator<ExperimenterData> i = experimenters.iterator();
				ExperimenterData exp;
				List<GroupData> list;
				Iterator<GroupData> j;
				GroupData group;
				List<ExperimenterGroup> groups;
				boolean added = false;
				ExperimenterGroup gs = svc.lookupGroup(systemGroup);
				while (i.hasNext()) {
					exp = i.next();
					list = exp.getGroups();
					j = list.iterator();
					while (j.hasNext()) {
						group = j.next();
						if (dsFactory.getAdmin().isSecuritySystemGroup(
						        group.getId(), systemGroup))
							added = true;
					}
					if (!added) {
						groups = new ArrayList<ExperimenterGroup>();
						groups.add(gs);
						svc.addGroups(exp.asExperimenter(), groups);
					}
				}
			} else {
				Iterator<ExperimenterData> i = experimenters.iterator();
				ExperimenterData exp;
				List<GroupData> list;
				Iterator<GroupData> j;
				GroupData group;
				List<ExperimenterGroup> groups;
				while (i.hasNext()) {
					exp = i.next();
					list = exp.getGroups();
					groups = new ArrayList<ExperimenterGroup>();
					j = list.iterator();
					while (j.hasNext()) {
						group = j.next();
						if (dsFactory.getAdmin().isSecuritySystemGroup(
                                group.getId(), systemGroup)) {
							groups.add(group.asGroup());
						}
					}
					if (groups.size() > 0)
						svc.removeGroups(exp.asExperimenter(), groups);
				}
			}
		} catch (Throwable t) {
			handleException(t, "Cannot modify the roles of the experimenters.");
		}
	}

	/**
	 * Adds the passed experimenters as owner of the group if the flag is
	 * <code>true</code>, removes them otherwise.
	 *
	 * @param ctx The security context.
	 * @param toAdd Pass <code>true</code> to add the experimenters as owners,
	 * 				<code>false</code> otherwise.
	 * @param group	The group to handle.
	 * @param experimenters The experimenters to add or remove.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void handleGroupOwners(SecurityContext ctx, boolean toAdd,
			ExperimenterGroup group, List<Experimenter> experimenters)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			if (toAdd) svc.addGroupOwners(group, experimenters);
			else svc.removeGroupOwners(group, experimenters);
		} catch (Throwable t) {
			handleException(t, "Cannot handle the group ownership. ");
		}
	}

	/**
	 * Returns the XY-plane identified by the passed z-section, time-point
	 * and wavelength.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of pixels containing the requested plane.
	 * @param z The selected z-section.
	 * @param t The selected time-point.
	 * @param c The selected wavelength.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	byte[] getPlane(SecurityContext ctx, long pixelsID, int z, int t, int c)
		throws DSOutOfServiceException, DSAccessException, FSAccessException
	{
		return retrievePlane(ctx, pixelsID, z, t, c);
	}

	/**
	 * Returns the XY-plane identified by the passed z-section, time-point
	 * and wavelength.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of pixels containing the requested plane.
	 * @param z The selected z-section.
	 * @param t The selected time-point.
	 * @param c The selected wavelength.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	private byte[] retrievePlane(SecurityContext ctx,
			long pixelsID, int z, int t, int c)
		throws DSOutOfServiceException, DSAccessException, FSAccessException
	{
		RawPixelsStorePrx service = null;
		try {
		    service = gw.getPixelsStore(ctx);
			service.setPixelsId(pixelsID, false);
			byte[] plane = service.getPlane(z, c, t);
			return plane;
		} catch (Throwable e) {
			if (e instanceof ValidationException) return null;
			String s = "Cannot retrieve the plane " +
			"(z="+z+", t="+t+", c="+c+") for pixelsID: "+pixelsID;
			handleFSException(e, s);
			handleException(e, s);
		} finally {
		    if (service != null) gw.closeService(ctx, service);
		}
		return null;
	}
	/**
	 * Returns the free or available space (in Kilobytes) on the file system
	 * including nested sub-directories.
	 *
	 * @param ctx The security context.
	 * @param Either a group or a user.
	 * @param id The identifier of the user or group or <code>-1</code>
	 * 			 if not specified.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	long getFreeSpace(SecurityContext ctx, Class type, long id)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IRepositoryInfoPrx service = gw.getRepositoryService(ctx);
			return service.getFreeSpaceInKilobytes();
		} catch (Throwable e) {
			handleException(e, "Cannot retrieve the free space");
		}
		return -1;
	}

	/**
	 * Returns the used space (in Kilobytes) on the file system
	 * including nested sub-directories.
	 *
	 * @param ctx The security context.
	 * @param Either a group or a user.
	 * @param id The identifier of the user or group or <code>-1</code>
	 * 			 if not specified.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	long getUsedSpace(SecurityContext ctx, Class type, long id)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IRepositoryInfoPrx svc = gw.getRepositoryService(ctx);
	        IQueryPrx service = gw.getQueryService(ctx);
			if (id < 0)
				return svc.getUsedSpaceInKilobytes();
			StringBuffer buffer = new StringBuffer();
			buffer.append("select f from OriginalFile as f ");
			buffer.append("left outer join fetch f.details.owner as o ");
			buffer.append("where o.id = :userID");
			ParametersI param = new ParametersI();
			param.addLong("userID", id);
			List<IObject> result =
				service.findAllByQuery(buffer.toString(), param);
			if (result == null) return -1;
			Iterator<IObject> i = result.iterator();
			OriginalFile f;
			long count = 0;
			while (i.hasNext()) {
				f = (OriginalFile) i.next();
				if (f.getSize() != null) count += f.getSize().getValue();
			}
			return count;
		} catch (Throwable e) {
			handleException(e, "Cannot retrieve the free space");
		}
		return -1;
	}

	/**
	 * Retrieves the images specified by a set of parameters
	 * e.g. imported during a given period of time by a given user.
	 *
	 * @param ctx The security context.
	 * @param map The options.
	 * @param asDataObject Pass <code>true</code> to convert the
	 * 						<code>IObject</code>s into the corresponding
	 * 						<code>DataObject</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection getImages(SecurityContext ctx, Parameters map,
			boolean asDataObject)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			List result = service.getImagesByOptions(map);
			if (asDataObject) return PojoMapper.asDataObjects(result);
			return result;
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the images imported during " +
							"the specified period.");
		}
		return new HashSet();
	}

	/**
	 * Resets the rendering settings for the images contained in the
	 * specified node types.
	 * Resets the settings to the passed images if the type is
	 * <code>ImageData</code>.
	 * Returns <true> if the call was successful, <code>false</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param rootNodeType The type of nodes. Can either be
	 * 						<code>ImageData</code>, <code>DatasetData</code> or
	 * 						<code>PlateData</code>.
	 * @param nodes The nodes to apply settings to.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map resetRenderingSettings(SecurityContext ctx, Class rootNodeType,
			List nodes)
		throws DSOutOfServiceException, DSAccessException
	{
		List<Long> success = new ArrayList<Long>();
		List<Long> failure = new ArrayList<Long>();
		try {
		    IRenderingSettingsPrx service = getRenderingSettingsService(ctx);
			String klass = PojoMapper.getModelType(rootNodeType).getName();
			if (klass.equals(Image.class.getName())) failure.addAll(nodes);
			success = service.resetDefaultsInSet(klass, nodes);
		} catch (Exception e) {
			handleException(e, "Cannot reset the rendering settings.");
		}
		Iterator<Long> i = success.iterator();
		Long id;
		while (i.hasNext()) {
			id = i.next();
			if (failure.contains(id)) failure.remove(id);
		}
		Map<Boolean, List> result = new HashMap<Boolean, List>(2);
		result.put(Boolean.valueOf(true), success);
		result.put(Boolean.valueOf(false), failure);
		return result;
	}

	/**
	 * Resets the rendering settings for the images contained in the
	 * specified datasets if the rootType is <code>DatasetData</code>.
	 * Resets the settings to the passed images if the type is
	 * <code>ImageData</code>.
	 * Returns <true> if the call was successful, <code>false</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param rootNodeType The type of nodes. Can either be
	 * 						<code>ImageData</code>, <code>DatasetData</code>.
	 * @param nodes The nodes to apply settings to.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map setMinMaxSettings(SecurityContext ctx, Class rootNodeType, List nodes)
		throws DSOutOfServiceException, DSAccessException
	{
		List<Long> success = new ArrayList<Long>();
		List<Long> failure = new ArrayList<Long>();

		try {
		    IRenderingSettingsPrx service = getRenderingSettingsService(ctx);
			String klass = PojoMapper.getModelType(rootNodeType).getName();
			if (klass.equals(Image.class.getName())) failure.addAll(nodes);
			success = service.resetMinMaxInSet(klass, nodes);
		} catch (Exception e) {
			handleException(e, "Cannot reset the rendering settings.");
		}
		Iterator<Long> i = success.iterator();
		Long id;
		while (i.hasNext()) {
			id = i.next();
			if (failure.contains(id)) failure.remove(id);
		}
		Map<Boolean, List> result = new HashMap<Boolean, List>(2);
		result.put(Boolean.valueOf(true), success);
		result.put(Boolean.valueOf(false), failure);
		return result;
	}

	/**
	 * Resets the rendering settings, used by the owner of the images contained
	 * in the specified datasets if the rootType is <code>DatasetData</code>.
	 * Resets the settings to the passed images if the type is
	 * <code>ImageData</code>.
	 *
	 * Returns <true> if the call was successful, <code>false</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param rootNodeType The type of nodes. Can either be
	 * 						<code>ImageData</code>, <code>DatasetData</code>.
	 * @param nodes The nodes to apply settings to.
	 * @return <true> if the call was successful, <code>false</code> otherwise.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map setOwnerRenderingSettings(SecurityContext ctx, Class rootNodeType,
			List nodes)
		throws DSOutOfServiceException, DSAccessException
	{
		List<Long> success = new ArrayList<Long>();
		List<Long> failure = new ArrayList<Long>();
		try {
		    IRenderingSettingsPrx service = getRenderingSettingsService(ctx);
			String klass = PojoMapper.getModelType(rootNodeType).getName();
			if (klass.equals(Image.class.getName())) failure.addAll(nodes);
			success = service.resetDefaultsByOwnerInSet(klass, nodes);
		} catch (Exception e) {
			handleException(e, "Cannot reset the rendering settings.");
		}
		Iterator<Long> i = success.iterator();
		Long id;
		while (i.hasNext()) {
			id = i.next();
			if (failure.contains(id)) failure.remove(id);
		}
		Map<Boolean, List> result = new HashMap<Boolean, List>(2);
		result.put(Boolean.valueOf(true), success);
		result.put(Boolean.valueOf(false), failure);
		return result;
	}

	/**
	 * Applies the rendering settings associated to the passed pixels set
	 * to the images contained in the specified datasets or plate.
	 * if the rootType is <code>DatasetData</code> or <code>PlateData</code>.
	 * Applies the settings to the passed images if the type is
	 * <code>ImageData</code>.
	 *
	 * Returns <true> if the call was successful, <code>false</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set to copy the settings from.
	 * @param rootNodeType The type of nodes. Can either be
	 * 						<code>ImageData</code>, <code>DatasetData</code>.
	 * @param nodes The nodes to apply settings to.
	 * @return <true> if the call was successful, <code>false</code> otherwise.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map pasteRenderingSettings(SecurityContext ctx, long pixelsID,
			Class rootNodeType, List nodes)
		throws DSOutOfServiceException, DSAccessException
	{
		List<Long> success = new ArrayList<Long>();
		List<Long> failure = new ArrayList<Long>();
		try {
		    IRenderingSettingsPrx service = getRenderingSettingsService(ctx);
			Map m  = service.applySettingsToSet(pixelsID,
					PojoMapper.getModelType(rootNodeType).getName(),
					nodes);
			success = (List) m.get(Boolean.valueOf(true));
			failure = (List) m.get(Boolean.valueOf(false));
		} catch (Exception e) {
			handleException(e, "Cannot paste the rendering settings.");
		}
		Map<Boolean, List> result = new HashMap<Boolean, List>(2);
		result.put(Boolean.valueOf(true), success);
		result.put(Boolean.valueOf(false), failure);
		return result;
	}

	/**
	 * Retrieves all the rendering settings linked to the specified set
	 * of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The pixels ID.
	 * @param userID The id of the user.
	 * @return Map whose key is the experimenter who set the settings,
	 * 		  and the value is the rendering settings itself.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map<DataObject, Collection<RndProxyDef>> getRenderingSettings(
	        SecurityContext ctx, long pixelsID, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	    Multimap<DataObject, RndProxyDef> tmp = ArrayListMultimap.create();
		
		try {
		    IPixelsPrx service = gw.getPixelsService(ctx);
			List results = service.retrieveAllRndSettings(pixelsID, userID);
			if (CollectionUtils.isEmpty(results)) return tmp.asMap();
			Iterator i = results.iterator();
			RenderingDef rndDef;
			Experimenter exp;
			Map<Long, DataObject> users = new HashMap<Long, DataObject>();
			DataObject user;
			while (i.hasNext()) {
				rndDef = (RenderingDef) i.next();
				exp = rndDef.getDetails().getOwner();
				user = users.get(exp.getId().getValue());
				if (user == null) {
				    user = PojoMapper.asDataObject(exp);
				    users.put(exp.getId().getValue(), user);
				}
				tmp.put(user, PixelsServicesFactory.convert(rndDef));
			}
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the rendering settings " +
								"for: "+pixelsID);
		}
		return tmp.asMap();
	}

	/**
	 * Retrieves all the rendering settings linked to the specified set
	 * of pixels.
	 *
	 * @param ctx The security context.
	 * @param pixelsID	The pixels ID.
	 * @param userID	The id of the user.
	 * @param convert   Pass <code>true</code> to convert the object,
	 * 					<code>false</code> otherwise.
	 * @return Map whose key is the experimenter who set the settings,
	 * 		  and the value is the rendering settings itself.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<RndProxyDef> getRenderingSettingsFor(SecurityContext ctx,
			long pixelsID, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IPixelsPrx service = gw.getPixelsService(ctx);
			List results = service.retrieveAllRndSettings(pixelsID, userID);
			List<RndProxyDef> l = new ArrayList<RndProxyDef>();
			if (CollectionUtils.isEmpty(results)) return l;
			Iterator i = results.iterator();
			while (i.hasNext()) {
				l.add(PixelsServicesFactory.convert((RenderingDef) i.next()));
			}
			return l;
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the rendering settings " +
								"for: "+pixelsID);
		}
		return new ArrayList();
	}

	/**
	 * Retrieves the rendering settings for the specified pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The pixels ID.
	 * @param userID	The id of the user who set the rendering settings.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	RenderingDef getRenderingDef(SecurityContext ctx, long pixelsID,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IPixelsPrx service = gw.getPixelsService(ctx);
			return service.retrieveRndSettingsFor(pixelsID, userID);
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the rendering settings");
		}
		return null;
	}

	/**
	 * Retrieves the annotations of the passed type.
	 *
	 * @param ctx The security context.
	 * @param type The type of annotations to include.
	 * @param toInclude The collection of name space to include.
	 * @param toExclude The collection of name space to exclude.
	 * @param options The options.
	 * @return See above.
	 *@throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Set loadSpecificAnnotation(SecurityContext ctx, Class type,
			List<String> toInclude, List<String> toExclude, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			return PojoMapper.asDataObjects(
					service.loadSpecifiedAnnotations(
							PojoMapper.getModelType(type).getName(), toInclude,
							toExclude, options));
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the annotations");
		}
		return new HashSet();
	}

	/**
	 * Counts the annotations of the passed type.
	 *
	 * @param ctx The security context.
	 * @param type The type of annotations to include.
	 * @param toInclude The collection of name space to include.
	 * @param toExclude The collection of name space to exclude.
	 * @param options The options.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	long countSpecificAnnotation(SecurityContext ctx, Class type,
			List<String> toInclude, List<String> toExclude, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			RLong value = service.countSpecifiedAnnotations(
					PojoMapper.getModelType(type).getName(), toInclude,
					toExclude, options);
			if (value == null) return -1;
			return value.getValue();
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the annotations");
		}
		return -1;
	}

	/**
	 * Returns the number of annotations used by the passed user but not
	 * owned.
	 *
	 * @param ctx The security context.
	 * @param annotationType The type of annotation.
	 * @param userID The identifier of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	long countAnnotationsUsedNotOwned(SecurityContext ctx, Class annotationType,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		long count = 0;
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			RLong value = service.countAnnotationsUsedNotOwned(
					convertAnnotation(annotationType), userID);
			if (value != null) count = value.getValue();
			if (count < 0) count = 0;
		} catch (Exception e) {
			handleException(e, "Cannot count the type of annotation " +
					"used by the specified user");
		}
		return count;
	}

	/**
	 * Loads the tag Sets and the orphaned tags, if requested.
	 *
	 * @param ctx The security context.
	 * @param annotationType The type of annotation to retrieve.
	 * @param userID The identifier of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection loadAnnotationsUsedNotOwned(SecurityContext ctx,
			Class annotationType, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		Set result = new HashSet();
		
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			List<IObject> set = service.loadAnnotationsUsedNotOwned(
					convertAnnotation(annotationType), userID);
			Iterator<IObject> i = set.iterator();
			IObject o;
			while (i.hasNext()) {
				o = i.next();
				if (TagAnnotationData.class.equals(annotationType)) {
					result.add(new TagAnnotationData((TagAnnotation) o));
				}
			}
			return result;
		} catch (Exception e) {
			handleException(e, "Cannot find the Used Tags.");
		}
		return result;
	}

	/**
	 * Searches the images acquired or created during a given period of time.
	 *
	 * @param ctx The security context.
	 * @param context The context of the search.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Set searchByTime(SecurityContext ctx, SearchDataContext context)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		ParametersI param = new ParametersI();
		param.map = new HashMap<String, RType>();
		StringBuffer buf = new StringBuffer();
		buf.append("select img from Image as img ");
		buf.append("left outer join fetch img.pixels as pix ");
		buf.append("left outer join fetch pix.pixelsType as pt ");
		buf.append("left outer join fetch img.details.owner as owner ");
		boolean condition = false;
		Timestamp start = context.getStart();
		Timestamp end = context.getEnd();
		//Sets the time
		switch (context.getTimeIndex()) {
			case SearchDataContext.CREATION_TIME:
				if (start != null) {
					condition = true;
					buf.append("where img.acquisitionDate > :start ");
					param.map.put("start", omero.rtypes.rtime(start.getTime()));
					if (end != null) {
						param.map.put("end", omero.rtypes.rtime(end.getTime()));
						buf.append("and img.acquisitionDate < :end ");
					}
				} else {
					if (end != null) {
						condition = true;
						param.map.put("end", omero.rtypes.rtime(end.getTime()));
						buf.append("where img.acquisitionDate < :end ");
					}
				}
				break;
			case SearchDataContext.MODIFICATION_TIME:
				if (start != null) {
					condition = true;
					param.map.put("start", omero.rtypes.rtime(start.getTime()));
					buf.append("where img.details.creationEvent.time > :start ");
					if (end != null) {
						param.map.put("end", omero.rtypes.rtime(end.getTime()));
						buf.append("and img.details.creationEvent.time < :end ");
					}
				} else {
					if (end != null) {
						condition = true;
						param.map.put("end", omero.rtypes.rtime(end.getTime()));
						buf.append("where img.details.creationEvent.time < :end ");
					}
				}
				break;
			case SearchDataContext.ANNOTATION_TIME:
		}
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			List<ExperimenterData> l = context.getOwners();
			List<Long> ids = new ArrayList<Long>();
			if (l != null) {
				Iterator<ExperimenterData> i = l.iterator();
				while (i.hasNext()) {
					ids.add(i.next().getId());
				}
			}
			param.addLongs("ids", ids);
			if (condition) {
				buf.append(" and owner.id in (:ids)");
			} else
				buf.append("where owner.id in (:ids)");

			return PojoMapper.asDataObjects(
					service.findAllByQuery(buf.toString(), param));
		} catch (Throwable e) {
			handleException(e, "Cannot retrieve the images.");
		}

		return new HashSet();
	}

    /**
     * Searches for data.
     *
     * @param ctx
     *            The security context.
     * @param context
     *            The context of search (if context.groupId == -1 the scope of
     *            the search will be all groups, otherwise the scope of the
     *            search will be the group set in the security context)
     * @return The found objects.
     * @throws DSOutOfServiceException
     *             If the connection is broken, or logged in.
     * @throws DSAccessException
     *             If an error occurred while trying to retrieve data from OMEDS
     *             service.
     */
    SearchResultCollection search(SecurityContext ctx, SearchParameters context)
            throws DSOutOfServiceException, DSAccessException {
        try {
            SearchFacility search = gw.getFacility(SearchFacility.class);
            return search.search(ctx, context);
        } catch (ExecutionException e) {
            log("Can't get a SearchFacility");
        }
        return new SearchResultCollection();
    }
        
	/**
	 * Searches for data.
	 *
	 * @param ctx The security context.
	 * @param context The context of search.
	 * @return The found objects.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Object performSearch(SecurityContext ctx, SearchDataContext context)
		throws DSOutOfServiceException, DSAccessException
	{
		Map<Integer, Object> results = new HashMap<Integer, Object>();
		List<Class> types = context.getTypes();
		List<Integer> scopes = context.getScope();
		if (CollectionUtils.isEmpty(types)) return new HashMap();

		
		SearchPrx service = null;
		try {
		    service = gw.getSearchService(ctx);
			service.clearQueries();
			service.setAllowLeadingWildcard(true);
			service.setCaseSentivice(context.isCaseSensitive());
			Timestamp start = context.getStart();
			Timestamp end = context.getEnd();
			//Sets the time
			if (start != null || end != null) {
				switch (context.getTimeIndex()) {
					case SearchDataContext.CREATION_TIME:
						if (start != null && end != null)
							service.onlyCreatedBetween(
								omero.rtypes.rtime(start.getTime()),
								omero.rtypes.rtime(end.getTime()));
						else if (start != null && end == null)
							service.onlyCreatedBetween(
									omero.rtypes.rtime(start.getTime()),
									null);
						else if (start == null && end != null)
							service.onlyCreatedBetween(null,
									omero.rtypes.rtime(end.getTime()));
						break;
					case SearchDataContext.MODIFICATION_TIME:
						if (start != null && end != null)
							service.onlyModifiedBetween(
								omero.rtypes.rtime(start.getTime()),
								omero.rtypes.rtime(end.getTime()));
						else if (start != null && end == null)
							service.onlyModifiedBetween(
									omero.rtypes.rtime(start.getTime()),
									null);
						else if (start == null && end != null)
							service.onlyModifiedBetween(null,
									omero.rtypes.rtime(end.getTime()));
						break;
					case SearchDataContext.ANNOTATION_TIME:
						if (start != null && end != null)
							service.onlyAnnotatedBetween(
								omero.rtypes.rtime(start.getTime()),
								omero.rtypes.rtime(end.getTime()));
						else if (start != null && end == null)
							service.onlyAnnotatedBetween(
									omero.rtypes.rtime(start.getTime()),
									null);
						else if (start == null && end != null)
							service.onlyAnnotatedBetween(null,
									omero.rtypes.rtime(end.getTime()));
				}
			}
			List<ExperimenterData> users = context.getOwners();
			Iterator i;
			ExperimenterData exp;
			Details d;
			//owner
			List<Details> owners = new ArrayList<Details>();
			if (users != null && users.size() > 0) {
				i = users.iterator();
				while (i.hasNext()) {
					exp = (ExperimenterData) i.next();
					d = new DetailsI();
					d.setOwner(exp.asExperimenter());
			        owners.add(d);
				}
			}


			List<String> some = prepareTextSearch(context.getSome(), service);
			List<String> must = prepareTextSearch(context.getMust(), service);
			List<String> none = prepareTextSearch(context.getNone(), service);

			List<String> supportedTypes = new ArrayList<String>();
			i = types.iterator();
			while (i.hasNext())
				supportedTypes.add(PojoMapper.getModelType((Class) i.next()).getName());

			List rType;

			Object size;
			Integer key;
			i = scopes.iterator();
			while (i.hasNext())
				results.put((Integer) i.next(), new ArrayList());

			i = scopes.iterator();
			List<String> fSome = null, fMust = null, fNone = null;
			List<String> fSomeSec = null, fMustSec = null, fNoneSec = null;
			service.onlyType(Image.class.getName());
			while (i.hasNext()) {
				key = (Integer) i.next();
				rType = (List) results.get(key);
				size = null;
				if (key == SearchDataContext.TAGS) {
					fSome = formatText(some, "tag");
					fMust = formatText(must, "tag");
					fNone = formatText(none, "tag");
				} else if (key == SearchDataContext.NAME) {
					fSome = formatText(some, "name");
					fMust = formatText(must, "name");
					fNone = formatText(none, "name");
				} else if (key == SearchDataContext.DESCRIPTION) {
					fSome = formatText(some, "description");
					fMust = formatText(must, "description");
					fNone = formatText(none, "description");
				} else if (key == SearchDataContext.FILE_ANNOTATION) {
					fSome = formatText(some, "file.name");
					fMust = formatText(must, "file.name");
					fNone = formatText(none, "file.name");
					fSomeSec = formatText(some, "file.contents");
					fMustSec = formatText(must, "file.contents");
					fNoneSec = formatText(none, "file.contents");
				} else if (key == SearchDataContext.TEXT_ANNOTATION) {
					fSome = formatText(some, "annotation", "NOT", "tag");
					fMust = formatText(must, "annotation", "NOT", "tag");
					fNone = formatText(none, "annotation", "NOT", "tag");
				} else if (key == SearchDataContext.URL_ANNOTATION) {
					fSome = formatText(some, "url");
					fMust = formatText(must, "url");
					fNone = formatText(none, "url");
				} else if (key == SearchDataContext.ID) {
    				        fSome = formatText(some, "id");
    				        fMust = formatText(must, "id");
    				        fNone = formatText(none, "id");
				} else {
					fSome = formatText(some, "");
					fMust = formatText(must, "");
					fNone = formatText(none, "");
				}
					service.bySomeMustNone(fSome, fMust, fNone);
					size = handleSearchResult(
					        PojoMapper.convertTypeForSearch(Image.class), rType,
							service);
					if (size instanceof Integer)
						results.put(key, size);
					service.clearQueries();
					if (!(size instanceof Integer) && fSomeSec != null &&
							fSomeSec.size() > 0) {
						service.bySomeMustNone(fSomeSec, fMustSec,
								fNoneSec);
						size = handleSearchResult(
								PojoMapper.convertTypeForSearch(Image.class),
								rType, service);
						if (size instanceof Integer)
							results.put(key, size);
						service.clearQueries();
					}
				//}
				//}
			}
			return results;
		} catch (Throwable e) {
			handleException(e, "Cannot perform the search.");
		} finally {
		    if (service != null) gw.closeService(ctx, service);
		}
		return null;
	}

	/**
	 * Returns the collection of annotations of a given type.
	 *
	 * @param ctx The security context.
	 * @param annotationType	The type of annotation.
	 * @param terms				The terms to search for.
	 * @param start				The lower bound of the time interval
	 * 							or <code>null</code>.
	 * @param end				The lower bound of the time interval
	 * 							or <code>null</code>.
	 * @param exp				The experimenter who annotated the object.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List filterBy(SecurityContext ctx, Class annotationType, List<String> terms,
				Timestamp start, Timestamp end, ExperimenterData exp)
		throws DSOutOfServiceException, DSAccessException
	{
		
	    SearchPrx service = null;
		try {
		    service = gw.getSearchService(ctx);
			if (start != null && end != null)
				service.onlyAnnotatedBetween(
						omero.rtypes.rtime(start.getTime()),
						omero.rtypes.rtime(end.getTime()));
			if (exp != null) {
				Details d = new DetailsI();
				d.setOwner(exp.asExperimenter());
			}

			List<String> t = prepareTextSearch(terms, service);
			service.onlyType(PojoMapper.getModelType(annotationType).getName());
			List rType = new ArrayList();
			//service.bySomeMustNone(fSome, fMust, fNone);
			service.bySomeMustNone(t, null, null);
			Object size = handleSearchResult(
			        PojoMapper.convertTypeForSearch(annotationType), rType, service);
			if (size instanceof Integer) rType = new ArrayList();
			return rType;
		} catch (Exception e) {
			handleException(e, "Filtering by annotation not valid");
		} finally {
	        if (service != null) gw.closeService(ctx, service);
		}
		return new ArrayList();
	}

	/**
	 * Retrieves all containers of a given type.
	 * The containers are not linked to any of their children.
	 *
	 * @param ctx The security context.
	 * @param type		The type of container to retrieve.
	 * @param userID	The id of the owner of the container.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Set fetchContainers(SecurityContext ctx, Class type, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			Parameters p = new ParametersI();
			p.map = new HashMap<String, RType>();
			p.map.put("id", omero.rtypes.rlong(userID));
			String table = getTableForClass(type);
			return PojoMapper.asDataObjects(service.findAllByQuery(
	                "from "+table+" as p where p.details.owner.id = :id", p));
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the containers.");
		}
		return new HashSet();
	}

	/**
	 *
	 * @param ctx The security context.
	 * @param type
	 * @param annotationIds
	 * @param ownerIds
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Set getAnnotatedObjects(SecurityContext ctx, Class type,
			Set<Long> annotationIds, Set<Long> ownerIds)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			ParametersI param = new ParametersI();
			param.addLongs("ids", annotationIds);
			StringBuilder sb = new StringBuilder();

			if (type.equals(ImageData.class)) {
				sb.append("select img from Image as img ");
				sb.append("left outer join fetch "
	                    + "img.annotationLinksCountPerOwner img_a_c ");
				sb.append("left outer join fetch img.annotationLinks ail ");
				sb.append("left outer join fetch img.pixels as pix ");
	            sb.append("left outer join fetch pix.pixelsType as pt ");
	            sb.append("where ail.child.id in (:ids)");
	            if (ownerIds != null && ownerIds.size() > 0) {
	            	sb.append(" and img.details.owner.id in (:ownerIds)");
	            	param.addLongs("ownerIds", ownerIds);
	            }
	            return PojoMapper.asDataObjects(
	         			service.findAllByQuery(sb.toString(), param));
			}
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the annotated objects");
		}
		return new HashSet();
	}

	/**
	 * Returns the number of images related to a given tag.
	 *
	 * @param ctx The security context.
	 * @param rootNodeIDs The annotated objects.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map getDataObjectsTaggedCount(SecurityContext ctx, List rootNodeIDs)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			ParametersI param;
			StringBuilder sb = new StringBuilder();

			sb.append("select img from Image as img ");
			sb.append("left outer join fetch img.annotationLinks ail ");
            sb.append("where ail.child.id = :tagID");
            Iterator i = rootNodeIDs.iterator();
            Long id;
            Map<Long, Long> m = new HashMap<Long, Long>();
            //Image first
            List l;
            while (i.hasNext()) {
				id = (Long) i.next();
				param = new ParametersI();
				param.addLong("tagID", id);
				l = service.findAllByQuery(sb.toString(), param);
				if (l != null)
					m.put(id, Long.valueOf(l.size()));
			}
            //Dataset
            sb = new StringBuilder();
			sb.append("select d from Dataset as d ");
			sb.append("left outer join fetch d.annotationLinks ail ");
            sb.append("where ail.child.id = :tagID");
            i = rootNodeIDs.iterator();
            Long value;
            long r;
            while (i.hasNext()) {
				id = (Long) i.next();
				param = new ParametersI();
				param.addLong("tagID", id);
				value = m.get(id);
				l = service.findAllByQuery(sb.toString(), param);
				if (l != null) {
					r = l.size();
					if (value == null) value = r;
					else value += r;
				}
				m.put(id, value);
			}
            //Project
            sb = new StringBuilder();
			sb.append("select d from Project as d ");
			sb.append("left outer join fetch d.annotationLinks ail ");
            sb.append("where ail.child.id = :tagID");
            i = rootNodeIDs.iterator();
            while (i.hasNext()) {
				id = (Long) i.next();
				param = new ParametersI();
				param.addLong("tagID", id);
				value = m.get(id);
				l = service.findAllByQuery(sb.toString(), param);
				if (l != null) {
					r = l.size();
					if (value == null) value = r;
					else value += r;
				}
				m.put(id, value);
			}
			return m;
		} catch (Throwable t) {
			handleException(t, "Cannot count the collection.");
		}
		return new HashMap();
	}

	/**
	 * Projects the specified set of pixels according to the projection's
	 * parameters. Adds the created image to the passed dataset.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The id of the pixels set.
	 * @param startT	The time-point to start projecting from.
	 * @param endT		The time-point to end projecting.
	 * @param startZ    The first optical section.
	 * @param endZ      The last optical section.
	 * @param stepping  The stepping used to project. Default is <code>1</code>.
	 * @param algorithm The projection's algorithm.
	 * @param channels  The channels to project.
	 * @param datasets  The collection of datasets to add the image to.
	 * @param name      The name of the projected image.
	 * @param pixType   The destination Pixels type. If <code>null</code>, the
     * 					source Pixels set pixels type will be used.
	 * @return The newly created image.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	ImageData projectImage(SecurityContext ctx, long pixelsID, int startT,
			int endT, int startZ, int endZ, int stepping,
			ProjectionType algorithm, List<Integer> channels, String name,
			String pixType)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IProjectionPrx service = gw.getProjectionService(ctx);
			PixelsType type = null;
			if (pixType != null) {
				IQueryPrx svc = gw.getQueryService(ctx);
				List<IObject> l = svc.findAll(PixelsType.class.getName(), null);
				Iterator<IObject> i = l.iterator();
				PixelsType pt;
				String value;
				while (i.hasNext()) {
					pt = (PixelsType) i.next();
					value = pt.getValue().getValue();
					if (value.equals(pixType)) {
						type = pt;
						break;
					}
				}
			}
			long imageID = service.projectPixels(pixelsID, type, algorithm,
					startT, endT, channels, stepping, startZ, endZ, name);

			return getImage(ctx, imageID, new Parameters());
		} catch (Exception e) {
			handleException(e, "Cannot project the image.");
		}
		return null;
	}

	/**
	 * Returns the image and loaded pixels.
	 *
	 * @param ctx The security context.
	 * @param imageID The id of the image to load.
	 * @param options The options.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	ImageData getImage(SecurityContext ctx, long imageID, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
			Set result = getContainerImages(ctx, ImageData.class,
					Arrays.asList(imageID), options);
			if (result != null && result.size() == 1) {
				Iterator i = result.iterator();
				while (i.hasNext())
					return (ImageData) i.next();
			}
			return null;
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the image.");
		}
		return null;
	}

	/**
	 * Creates default rendering setting for the passed pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set to handle.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	RenderingDef createRenderingDef(SecurityContext ctx, long pixelsID)
		throws DSOutOfServiceException, DSAccessException
	{
		//TODO: add method to server so that we don't have to make 2 calls.
	   
		try {
		    IPixelsPrx svc = gw.getPixelsService(ctx);
			Pixels pixels = svc.retrievePixDescription(pixelsID);
			if (pixels == null) return null;
			IRenderingSettingsPrx service = getRenderingSettingsService(ctx);
			return service.createNewRenderingDef(pixels);
		} catch (Exception e) {
			handleException(e, "Cannot create settings for: "+pixelsID);
		}
		return null;
	}

	/**
	 * Returns the plate where the specified image has been imported.
	 *
	 * @param ctx The security context.
	 * @param imageID The identifier of the image.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	PlateData getImportedPlate(SecurityContext ctx, long imageID) // should be removed
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			List results = null;
			StringBuilder sb = new StringBuilder();
			ParametersI param = new ParametersI();
			param.addLong("imageID", imageID);
			sb.append("select plate from Plate as plate ");
			sb.append("left outer join fetch plate.wells as well ");
			sb.append("left outer join fetch well.wellSamples as ws ");
			sb.append("left outer join fetch ws.image as img ");
			sb.append("left outer join fetch img.pixels as pix ");
            sb.append("left outer join fetch pix.pixelsType as pt ");
            sb.append("where img.id = :imageID");
            results = service.findAllByQuery(sb.toString(), param);
            if (results.size() > 0) {
            	return new PlateData((Plate) results.get(0));
            }
		} catch (Exception e) {
			handleException(e, "Cannot load plate");
		}
		return null;
	}

	//TMP:
	Set loadPlateWells(SecurityContext ctx, long plateID, long acquisitionID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			List results = null;
			Set<DataObject> wells = new HashSet<DataObject>();
			Iterator i;

			//if no acquisition set. First try to see if we have a id.
			ParametersI param = new ParametersI();
			param.addLong("plateID", plateID);
			StringBuilder sb;
			if (acquisitionID < 0) {
				sb = new StringBuilder();
				sb.append("select pa from PlateAcquisition as pa ");
				sb.append("where pa.plate.id = :plateID");
				results = service.findAllByQuery(sb.toString(), param);
				if (results != null && results.size() > 0)
					acquisitionID =
						((PlateAcquisition) results.get(0)).getId().getValue();
			}

			sb = new StringBuilder();

			sb.append("select well from Well as well ");
			sb.append("left outer join fetch well.plate as pt ");
			sb.append("left outer join fetch well.wellSamples as ws ");
			sb.append("left outer join fetch ws.plateAcquisition as pa ");
			sb.append("left outer join fetch ws.image as img ");
			sb.append("left outer join fetch img.details.creationEvent as cre ");
			sb.append("left outer join fetch img.details.updateEvent as evt ");
			sb.append("left outer join fetch img.pixels as pix ");
            sb.append("left outer join fetch pix.pixelsType as pt ");
            sb.append("where well.plate.id = :plateID");
            if (acquisitionID > 0) {
            	sb.append(" and pa.id = :acquisitionID");
            	param.addLong("acquisitionID", acquisitionID);
            }
            results = service.findAllByQuery(sb.toString(), param);
			i = results.iterator();
			while (i.hasNext()) {
				wells.add((WellData) PojoMapper.asDataObject((Well) i.next()));
			}
			return wells;
		} catch (Exception e) {
			handleException(e, "Cannot load plate");
		}
		return new HashSet();
	}

	Set<WellData> loadPlateWells(SecurityContext ctx, List<Long> plateIDs)
			throws DSOutOfServiceException, DSAccessException
		{
	       
			try {
			    IQueryPrx service = gw.getQueryService(ctx);
				List<RType> ids = new ArrayList<RType>(plateIDs.size());
				Iterator<Long> j = plateIDs.iterator();
				while (j.hasNext())
					ids.add(omero.rtypes.rlong(j.next()));
				List results = null;
				Set<WellData> wells = new HashSet<WellData>();
				Iterator i;

				//if no acquisition set. First try to see if we have a id.
				ParametersI param = new ParametersI();
				param.add("plateIDs", omero.rtypes.rlist(ids));
				StringBuilder sb = new StringBuilder();

				sb.append("select well from Well as well ");
				sb.append("left outer join fetch well.plate as pt ");
				sb.append("left outer join fetch well.wellSamples as ws ");
				sb.append("left outer join fetch ws.plateAcquisition as pa ");
				sb.append("left outer join fetch ws.image as img ");
				sb.append("left outer join fetch img.details.creationEvent as cre ");
				sb.append("left outer join fetch img.details.updateEvent as evt ");
				sb.append("left outer join fetch img.pixels as pix ");
	            sb.append("left outer join fetch pix.pixelsType as pt ");
	            sb.append("where well.plate.id in (:plateIDs)");
	            results = service.findAllByQuery(sb.toString(), param);
				i = results.iterator();
				while (i.hasNext()) {
					wells.add((WellData)
							PojoMapper.asDataObject((Well) i.next()));
				}
				return wells;
			} catch (Exception e) {
				handleException(e, "Cannot load plate");
			}
			return new HashSet();
		}

	/**
	 * Loads the acquisition object related to the passed image.
	 * @param ctx The security context.
	 * @param imageID The id of image object to handle.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Object loadImageAcquisitionData(SecurityContext ctx, long imageID)
		throws DSOutOfServiceException, DSAccessException
	{
		ParametersI po = new ParametersI();
		po.acquisitionData();
		List<Long> ids = new ArrayList<Long>(1);
		ids.add(imageID);

		
        try {
            IContainerPrx service = gw.getPojosService(ctx);
        	List images = service.getImages(Image.class.getName(), ids, po);
        	if (images != null && images.size() == 1)
        		return new ImageAcquisitionData((Image) images.get(0));
		} catch (Exception e) {
			handleException(e, "Cannot load image acquisition data.");
		}
       return null;
	}

	/**
	 * Loads the acquisition metadata related to the specified channel.
	 *
	 * @param ctx The security context.
	 * @param channelID The id of the channel.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Object loadChannelAcquisitionData(SecurityContext ctx, long channelID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
	        IQueryPrx query = gw.getQueryService(ctx);
			List<Long> ids = new ArrayList<Long>(1);
			ids.add(channelID);
			List l = service.loadChannelAcquisitionData(ids);
			if (l != null && l.size() == 1) {
				LogicalChannel lc = (LogicalChannel) l.get(0);
				ChannelAcquisitionData data = new ChannelAcquisitionData(lc);
				LightSourceData src = data.getLightSource();
				if (src == null || src.isLoaded()) return data;
				//Not loaded so need to load
				IObject io = src.asIObject();
				if (io instanceof Laser) { //only case to handle.
					StringBuilder sb = new StringBuilder();
					sb.append("select l from Laser as l ");
					sb.append("left outer join fetch l.type ");
					sb.append("left outer join fetch l.laserMedium ");
					sb.append("left outer join fetch l.pulse as pulse ");
					sb.append("left outer join fetch l.pump as pump ");
					sb.append("left outer join fetch pump.type as pt ");
					sb.append("where l.id = :id");
					ParametersI param = new ParametersI();
					param.addId(src.getId());
					Laser laser = (Laser) query.findByQuery(
							sb.toString(), param);
					if (laser != null)
						data.setLightSource(new LightSourceData(laser));
				}
				return data;
			}
			return null;
		} catch (Exception e) {
			handleException(e, "Cannot load channel acquisition data.");
		}
		return null;
	}

	/**
	 * Returns the enumeration corresponding to the passed string or
	 * <code>null</code> if none found.
	 *
	 * @param ctx The security context.
	 * @param klass The class the enumeration is for.
	 * @param value The value of the enumeration.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	IObject getEnumeration(SecurityContext ctx, Class klass, String value)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			return service.findByString(klass.getName(), "value", value);
		} catch (Exception e) {
			handleException(e, "Cannot find the enumeration's value.");
		}
		return null;
	}

	/**
	 * Returns the enumerations corresponding to the passed type or
	 * <code>null</code> if none found.
	 *
	 * @param ctx The security context.
	 * @param klassName The name of the class the enumeration is for.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<EnumerationObject> getEnumerations(SecurityContext ctx,
			String klassName)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		List<EnumerationObject> r;
		try {
		    IPixelsPrx service = gw.getPixelsService(ctx);
			r = enumerations.get(klassName);
			if (r != null) return r;
			List<IObject> l = service.getAllEnumerations(klassName);
			r = new ArrayList<EnumerationObject>();
			if (l == null) return r;
			Iterator<IObject> i = l.iterator();
			while (i.hasNext()) {
				r.add(new EnumerationObject(i.next()));
			}
			enumerations.put(klassName, r);
			return r;
		} catch (Exception e) {
			handleException(e, "Cannot find the enumeration's value.");
		}
		return new ArrayList<EnumerationObject>();
	}

	/**
	 * Loads the tags.
	 *
	 * @param ctx The security context.
	 * @param id  The id of the tags.
	 * @param options
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection loadTags(SecurityContext ctx, Long id, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			List<Long> ids = new ArrayList<Long>(1);
			ids.add(id);
			Map m = service.loadTagContent(ids, options);
			if (m == null || m.size() == 0)
				return new ArrayList();
			return PojoMapper.asDataObjects((Collection) m.get(id));
		} catch (Exception e) {
			handleException(e, "Cannot find the Tags.");
		}
		return new ArrayList();
	}

	/**
	 * Loads the tag Sets and the orphaned tags, if requested.
	 *
	 * @param ctx The security context.
	 * @param options
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection loadTagSets(SecurityContext ctx, Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			return PojoMapper.asDataObjects(service.loadTagSets(options));
		} catch (Exception e) {
			handleException(e, "Cannot find the Tags.");
		}
		return new HashSet();
	}

	/**
	 * Returns the collection of plane info object related to the specified
	 * pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The id of the pixels set.
	 * @param z The selected z-section or <code>-1</code>.
     * @param t The selected time-point or <code>-1</code>.
     * @param channel The selected time-point or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<IObject> loadPlaneInfo(SecurityContext ctx, long pixelsID, int z,
			int t, int channel)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		StringBuilder sb;
		ParametersI param;
		sb = new StringBuilder();
		param = new ParametersI();
		sb.append("select info from PlaneInfo as info ");
        sb.append("where pixels.id = :id");
        param.addLong("id", pixelsID);
        if (z >= 0) {
        	 sb.append(" and info.theZ = :z");
        	 param.map.put("z", omero.rtypes.rint(z));
        }
        if (t >= 0) {
        	sb.append(" and info.theT = :t");
        	 param.map.put("t", omero.rtypes.rint(t));
        }
        if (channel >= 0) {
        	sb.append(" and info.theC = :c");
        	param.map.put("c", omero.rtypes.rint(channel));
        }
        try {
            IQueryPrx service = gw.getQueryService(ctx);
        	return service.findAllByQuery(sb.toString(), param);
		} catch (Exception e) {
			handleException(e,
					"Cannot load the plane info for pixels: "+pixelsID);
		}
		return new ArrayList<IObject>();
	}

	/**
	 * Fills the enumerations.
	 *
	 * @param ctx The security context.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	void fillEnumerations(SecurityContext ctx)
		throws DSOutOfServiceException, DSAccessException
	{
		getEnumerations(ctx, OmeroMetadataService.IMMERSION);
		getEnumerations(ctx, OmeroMetadataService.CORRECTION);
		getEnumerations(ctx, OmeroMetadataService.MEDIUM);
		getEnumerations(ctx, OmeroMetadataService.FORMAT);
		getEnumerations(ctx, OmeroMetadataService.DETECTOR_TYPE);
		getEnumerations(ctx, OmeroMetadataService.BINNING);
		getEnumerations(ctx, OmeroMetadataService.CONTRAST_METHOD);
		getEnumerations(ctx, OmeroMetadataService.ILLUMINATION_TYPE);
		getEnumerations(ctx, OmeroMetadataService.PHOTOMETRIC_INTERPRETATION);
		getEnumerations(ctx, OmeroMetadataService.ACQUISITION_MODE);
		getEnumerations(ctx, OmeroMetadataService.LASER_MEDIUM);
		getEnumerations(ctx, OmeroMetadataService.LASER_TYPE);
		getEnumerations(ctx, OmeroMetadataService.LASER_PULSE);
		getEnumerations(ctx, OmeroMetadataService.ARC_TYPE);
		getEnumerations(ctx, OmeroMetadataService.FILAMENT_TYPE);
		getEnumerations(ctx, OmeroMetadataService.FILTER_TYPE);
		getEnumerations(ctx, OmeroMetadataService.MICROSCOPE_TYPE);
	}

	/**
	 * Creates a movie. Returns the id of the annotation hosting the movie.
	 *
	 * @param ctx The security context.
	 * @param imageID 	The id of the image.
	 * @param pixelsID	The id of the pixels.
	 * @param userID	The id of the user.
     * @param channels 	The channels to map.
     * @param param 	The parameters to create the movie.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 * @throws ProcessException If an error occurred while running the script.
	 */
	ScriptCallback saveAs(SecurityContext ctx, long userID, SaveAsParam param)
		throws ProcessException, DSOutOfServiceException, DSAccessException
	{
		long id = getScriptID(ctx, SaveAsParam.SAVE_AS_SCRIPT,
				"Cannot start "+SaveAsParam.SAVE_AS_SCRIPT);
		if (id <= 0) return null;
		List<DataObject> objects = param.getObjects();
		List<RType> ids = new ArrayList<RType>();
		Iterator<DataObject> i = objects.iterator();
		String type = "Image";
		DataObject data;
		while (i.hasNext()) {
			data = i.next();
			if (data instanceof DatasetData) {
				type = "Dataset";
			}
			ids.add(omero.rtypes.rlong(data.getId()));
		}
		Map<String, RType> map = new HashMap<String, RType>();
		map.put("IDs", omero.rtypes.rlist(ids));
		map.put("Data_Type", omero.rtypes.rstring(type));
		map.put("Format", omero.rtypes.rstring(param.getIndexAsString()));
		if (CommonsLangUtils.isNotEmpty(param.getBatchExportFilename()))
			map.put("Folder_Name",
		omero.rtypes.rstring(param.getBatchExportFilename()));
		return runScript(ctx, id, map);
	}

	/**
	 * Creates a movie. Returns the id of the annotation hosting the movie.
	 *
	 * @param ctx The security context.
	 * @param imageID 	The id of the image.
	 * @param pixelsID	The id of the pixels.
	 * @param userID	The id of the user.
     * @param channels 	The channels to map.
     * @param param 	The parameters to create the movie.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 * @throws ProcessException If an error occurred while running the script.
	 */
	ScriptCallback createMovie(SecurityContext ctx, long imageID, long pixelsID,
			long userID, List<Integer> channels, MovieExportParam param)
		throws ProcessException, DSOutOfServiceException, DSAccessException
	{
		//TODO remove that code
		long id = getScriptID(ctx, param.getScriptName(),
				"Cannot start "+param.getScriptName());
		if (id <= 0) return null;
		List<RType> set = new ArrayList<RType>(channels.size());
		Iterator<Integer> i = channels.iterator();
		while (i.hasNext())
			set.add(omero.rtypes.rint(i.next()));

		RenderingDef def = null;
		int startZ = param.getStartZ();
		int endZ = param.getEndZ();
		if (!param.isZSectionSet()) {
			def = getRenderingDef(ctx, pixelsID, userID);
			startZ = def.getDefaultZ().getValue();
			endZ = def.getDefaultZ().getValue();
		}
		int startT = param.getStartT();
		int endT = param.getEndT();
		if (!param.isTimeIntervalSet()) {
			if (def == null) def = getRenderingDef(ctx, pixelsID, userID);
			startT = def.getDefaultT().getValue();
			endT = def.getDefaultT().getValue();
		}

		Map<String, RType> map = new HashMap<String, RType>();
		map.put("IDs", omero.rtypes.rlist(omero.rtypes.rlong(imageID)));
		map.put("Movie_Name", omero.rtypes.rstring(param.getName()));
		map.put("Z_Start", omero.rtypes.rint(startZ));
		map.put("Z_End", omero.rtypes.rint(endZ));
		map.put("T_Start", omero.rtypes.rint(startT));
		map.put("T_End", omero.rtypes.rint(endT));
		map.put("Channels", omero.rtypes.rlist(set));
		map.put("FPS", omero.rtypes.rint(param.getFps()));
		map.put("Show_Plane_Info",
				omero.rtypes.rbool(param.isLabelVisible()));
		map.put("Show_Time",
				omero.rtypes.rbool(param.isLabelVisible()));
		map.put("Split_View", omero.rtypes.rbool(false));
		map.put("Scalebar", omero.rtypes.rint(param.getScaleBar()));
		map.put("Format", omero.rtypes.rstring(param.getFormatAsString()));
		if (param.getColor() != null)
			map.put("Overlay_Colour", omero.rtypes.rstring(
					param.getColor()));
		return runScript(ctx, id, map);
	}

	/**
	 * Returns all the scripts that the user can run.
	 *
	 * @param ctx The security context.
	 * @param experimenter The experimenter or <code>null</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ScriptObject> loadRunnableScripts(SecurityContext ctx)
		throws DSOutOfServiceException, DSAccessException
	{
		List<ScriptObject> scripts = new ArrayList<ScriptObject>();
		try {
		    IScriptPrx svc = getScriptService(ctx);
			List<OriginalFile> storedScripts = svc.getScripts();

			if (CollectionUtils.isEmpty(storedScripts))
				return scripts;
			Iterator<OriginalFile> j = storedScripts.iterator();
			ScriptObject script;
			OriginalFile of;
			RString value;
			String v = null;
			while (j.hasNext()) {
				of = j.next();
				value = of.getName();
				v = of.getPath().getValue()+ value.getValue();
				if (!SCRIPTS_NOT_AVAILABLE_TO_USER.contains(v)
					&& !SCRIPTS_UI_AVAILABLE.contains(v)) {
					script = new ScriptObject(of.getId().getValue(),
							of.getPath().getValue(), of.getName().getValue());
					value = of.getMimetype();
					if (value != null) script.setMIMEType(value.getValue());
					scripts.add(script);
				}
			}
			storedScripts = svc.getUserScripts(new ArrayList());
			j = storedScripts.iterator();
			while (j.hasNext()) {
				of = j.next();
				value = of.getName();
				script = new ScriptObject(of.getId().getValue(),
						of.getPath().getValue(), of.getName().getValue());
				value = of.getMimetype();
				if (value != null) script.setMIMEType(value.getValue());
				script.setOfficial(false);
				scripts.add(script);
			}
		} catch (Exception e) {
			handleException(e, "Cannot load the scripts. ");
		}
		return scripts;
	}

	/**
	 * Returns all the official scripts with a UI.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ScriptObject> loadRunnableScriptsWithUI(SecurityContext ctx)
		throws DSOutOfServiceException, DSAccessException
	{
		List<ScriptObject> scripts = new ArrayList<ScriptObject>();
		try {
		    IScriptPrx svc = getScriptService(ctx);
			List<OriginalFile> storedScripts = svc.getScripts();

			if (CollectionUtils.isEmpty(storedScripts))
				return scripts;
			Iterator<OriginalFile> j = storedScripts.iterator();
			ScriptObject script;
			OriginalFile of;
			RString value;
			String v = null;
			while (j.hasNext()) {
				of = j.next();
				value = of.getName();
				v = of.getPath().getValue()+ value.getValue();
				if (SCRIPTS_UI_AVAILABLE.contains(v)) {
					script = new ScriptObject(of.getId().getValue(),
							of.getPath().getValue(), of.getName().getValue());
					value = of.getMimetype();
					if (value != null) script.setMIMEType(value.getValue());
					scripts.add(script);
				}
			}
		} catch (Exception e) {
			handleException(e, "Cannot load the scripts with UI. ");
		}
		return scripts;
	}

	/**
	 * Loads and returns the script w/ parameters corresponding to the passed
	 * identifier.
	 *
	 * @param ctx The security context.
	 * @param scriptID The id of the script.
	 * @return See above.
	 * @throws ProcessException  If the script could not be loaded.
	 */
	ScriptObject loadScript(SecurityContext ctx, long scriptID)
		throws ProcessException
	{
		ScriptObject script = null;
		try {
			IScriptPrx svc = getScriptService(ctx);
			script = new ScriptObject(scriptID, "", "");
			script.setJobParams(svc.getParams(scriptID));
		} catch (Exception e) {
			handleConnectionException(e);
			throw new ProcessException("Cannot load the script: "+scriptID, e);
		}
		return script;
	}

	/**
	 * Returns all the scripts currently stored into the system.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Map<Long, String> getScriptsAsString(SecurityContext ctx)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IScriptPrx svc = getScriptService(ctx);
			List<OriginalFile> scripts = svc.getScripts();
			Map<Long, String> m = new HashMap<Long, String>();
			if (scripts != null) {
				Iterator<OriginalFile> i = scripts.iterator();
				OriginalFile of;
				String name = null;
				RString v;
				while (i.hasNext()) {
					of = i.next();
					v = of.getName();
					if (v != null) name = v.getValue();
					if (name != null) m.put(of.getId().getValue(), name);
				}
			}
			return m;
		} catch (Exception e) {
			handleException(e, "Cannot load the scripts. ");
		}
		return new HashMap<Long, String>();
	}

	/**
	 * Returns all the scripts currently stored into the system.
	 *
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<OriginalFile> getScripts(SecurityContext ctx)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    IScriptPrx svc = getScriptService(ctx);
			return svc.getScripts();
		} catch (Exception e) {
			handleException(e, "Cannot load the scripts. ");
		}
		return new ArrayList<OriginalFile>();
	}



	/**
	 * Creates a split view figure.
	 * Returns the id of the annotation hosting the figure.
	 *
	 * @param ctx The security context.
	 * @param objectIDs The id of the objects composing the figure.
	 * @param type The type of objects.
	 * @param param The parameters to use.
	 * @param userID The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 * @throws ProcessException If an error occurred while running the script.
	 */
	ScriptCallback createFigure(SecurityContext ctx, List<Long> objectIDs,
			Class type, FigureParam param, long userID)
		throws ProcessException, DSOutOfServiceException, DSAccessException
	{
		long id = getScriptID(ctx, param.getScriptName(),
				"Cannot start "+param.getScriptName());
		if (id <= 0) return null;
		int scriptIndex = param.getIndex();
		List<RType> ids = new ArrayList<RType>(objectIDs.size());
		Iterator<Long> i = objectIDs.iterator();
		while (i.hasNext())
			ids.add(omero.rtypes.rlong(i.next()));

		Map<String, RType>  map = new HashMap<String, RType>();
		RString dataType;
		dataType = omero.rtypes.rstring("Image");
		if (DatasetData.class.equals(type)) {
			dataType = omero.rtypes.rstring("Dataset");
		}
		map.put("Data_Type", dataType);
		switch (scriptIndex) {
			case FigureParam.THUMBNAILS:
				DataObject d = (DataObject) param.getAnchor();
				long parentID = -1;
				if (d instanceof DatasetData ||
						d instanceof ProjectData) parentID = d.getId();

				//map.put("Data_Type", dataType);
				map.put("IDs", omero.rtypes.rlist(ids));
				List<Long> tags = param.getTags();
				if (tags != null && tags.size() > 0) {
					ids = new ArrayList<RType>(tags.size());
					i = tags.iterator();
					while (i.hasNext())
						ids.add(omero.rtypes.rlong(i.next()));
					map.put("Tag_IDs", omero.rtypes.rlist(ids));
				}

				if (parentID > 0)
					map.put("Parent_ID", omero.rtypes.rlong(parentID));
				map.put("Show_Untagged_Images",
						omero.rtypes.rbool(param.isIncludeUntagged()));

				map.put("Thumbnail_Size", omero.rtypes.rint(param.getWidth()));
				map.put("Max_Columns", omero.rtypes.rint(
						param.getMaxPerColumn()));
				map.put("Format",
						omero.rtypes.rstring(param.getFormatAsString()));
				map.put("Figure_Name",
						omero.rtypes.rstring(param.getName()));
				return runScript(ctx, id, map);
			case FigureParam.MOVIE:
				map.put("Max_Columns",
						omero.rtypes.rint(param.getMaxPerColumn()));
		}
		//merge channels
		Iterator j;
		Map<String, RType> merge = new LinkedHashMap<String, RType>();
		Entry entry;
		Map<Integer, Integer> mergeChannels = param.getMergeChannels();
		if (mergeChannels != null) {
			j = mergeChannels.entrySet().iterator();
			while (j.hasNext()) {
				entry = (Entry) j.next();
				merge.put(""+(Integer) entry.getKey(),
						omero.rtypes.rlong((Integer) entry.getValue()));
			}
		}

		//split
		Map<String, RType> split = new LinkedHashMap<String, RType>();

		Map<Integer, String> splitChannels = param.getSplitChannels();
		if (splitChannels != null) {
			j = splitChannels.entrySet().iterator();
			while (j.hasNext()) {
				entry = (Entry) j.next();
				split.put(""+(Integer) entry.getKey(),
						omero.rtypes.rstring((String) entry.getValue()));
			}
		}
		List<Integer> splitActive = param.getSplitActive();
		if (splitActive != null && splitActive.size() > 0) {
			List<RType> sa = new ArrayList<RType>(splitActive.size());
			Iterator<Integer> k = splitActive.iterator();
			while (k.hasNext()) {
				sa.add(omero.rtypes.rint(k.next()));
			}
			map.put("Split_Indexes", omero.rtypes.rlist(sa));
		}
		map.put("Merged_Names", omero.rtypes.rbool(
				param.getMergedLabel()));
		map.put("IDs", omero.rtypes.rlist(ids));
		if (param.getStartZ() >= 0)
			map.put("Z_Start", omero.rtypes.rint(param.getStartZ()));
		if (param.getEndZ() >= 0)
			map.put("Z_End", omero.rtypes.rint(param.getEndZ()));
		if (split.size() > 0)
			map.put("Channel_Names", omero.rtypes.rmap(split));
		if (merge.size() > 0)
			map.put("Merged_Colours", omero.rtypes.rmap(merge));
		if (scriptIndex == FigureParam.MOVIE) {
			List<Integer> times = param.getTimepoints();
			List<RType> ts = new ArrayList<RType>(objectIDs.size());
			Iterator<Integer> k = times.iterator();
			while (k.hasNext())
				ts.add(omero.rtypes.rint(k.next()));
			map.put("T_Indexes", omero.rtypes.rlist(ts));
			map.put("Time_Units",
					omero.rtypes.rstring(param.getTimeAsString()));
		} else
			map.put("Split_Panels_Grey",
					omero.rtypes.rbool(param.isSplitGrey()));
		if (param.getScaleBar() > 0)
			map.put("Scalebar", omero.rtypes.rint(param.getScaleBar()));
		map.put("Overlay_Colour", omero.rtypes.rstring(param.getColor()));
		map.put("Width", omero.rtypes.rint(param.getWidth()));
		map.put("Height", omero.rtypes.rint(param.getHeight()));
		map.put("Stepping", omero.rtypes.rint(param.getStepping()));
		map.put("Format", omero.rtypes.rstring(param.getFormatAsString()));
		map.put("Algorithm",
				omero.rtypes.rstring(param.getProjectionTypeAsString()));
		map.put("Figure_Name",
				omero.rtypes.rstring(param.getName()));
		map.put("Image_Labels",
				omero.rtypes.rstring(param.getLabelAsString()));
		if (scriptIndex == FigureParam.SPLIT_VIEW_ROI) {
			map.put("ROI_Zoom", omero.rtypes.rfloat((float)
					param.getMagnificationFactor()));
		}
		return runScript(ctx, id, map);
	}

    /**
	 * Imports the specified file. Returns the image.
	 *
	 * @param ctx The security context.
	 * @param object Information about the file to import.
	 * @param container The folder to import the image.
	 * @param ic The import container.
	 * @param status The component used to give feedback.
     * @param close Pass <code>true</code> to close the import,
     * 		<code>false</code> otherwise.
     * @param userName The user's name.
	 * @return See above.
	 * @throws ImportException If an error occurred while importing.
	 */
    Object importImageFile(SecurityContext ctx, ImportableObject object,
            IObject container, ImportContainer ic, StatusLabel status,
            boolean close, String userName)
        throws ImportException, DSAccessException, DSOutOfServiceException
	{
        status.setImportContainer(ic);
        ImportConfig config = new ImportConfig();
        //FIXME: unclear why we would need to set these values on
        // both the ImportConfig and the ImportContainer.
        if (container != null) {
        	 config.targetClass.set(container.getClass().getSimpleName());
             config.targetId.set(container.getId().getValue());
             ic.setTarget(container);
        }

        ic.setUserPixels(object.getPixelsSize());
        OMEROMetadataStoreClient omsc = null;
        OMEROWrapper reader = null;
		try {
			omsc = getImportStore(ctx, userName);
			reader = new OMEROWrapper(config);
			ImportLibrary library = new ImportLibrary(omsc, reader);
			library.addObserver(status);

			//TODO create the handler
			//TMP Code to be moved to the import
			final ImportProcessPrx proc = library.createImport(ic);
	        final HandlePrx handle;
	        final String[] srcFiles = ic.getUsedFiles();
	        final List<String> checksums = new ArrayList<String>();
	        final byte[] buf = new byte[omsc.getDefaultBlockSize()];
	        Map<Integer, String> failingChecksums = new HashMap<Integer, String>();
	        final TimeEstimator estimator = new ProportionalTimeEstimatorImpl(
	                    ic.getUsedFilesTotalSize());

	        if (status.isMarkedAsCancel()) return Boolean.valueOf(false);
	        library.notifyObservers(new ImportEvent.FILESET_UPLOAD_START(
	                null, 0, srcFiles.length, null, null, null));

	        for (int i = 0; i < srcFiles.length; i++) {
	            checksums.add(library. uploadFile(proc, srcFiles, i,
	                    checksumProviderFactory, estimator,
	                    buf));
	        }

	        try {
	            handle = proc.verifyUpload(checksums);
	        } catch (ChecksumValidationException cve) {
	            failingChecksums = cve.failingChecksums;
	            return new ImportException(cve);
	        } finally {
	            try {
	                proc.close();
	            } catch (Exception e) {
	                dsFactory.getLogger().error(this, "Cannot close import process.");
	            }
	            library.notifyObservers(new ImportEvent.FILESET_UPLOAD_END(
	                    null, 0, srcFiles.length, null, null, srcFiles,
	                    checksums, failingChecksums, null));
	        }
	        final ImportRequest req = (ImportRequest) handle.getRequest();
	        final Fileset fs = req.activity.getParent();
	        status.setFilesetData(new FilesetData(fs));
	        return library.createCallback(proc, handle, ic);
		} catch (Throwable e) {
			try {
				if (reader != null) reader.close();
			} catch (Exception ex) {}

			handleConnectionException(e);
			if (close) closeImport(ctx, userName);
            return new ImportException(e);
		} finally {
			try {
				if (reader != null) reader.close();
			} catch (Exception ex) {}
			if (omsc != null && close)
				closeImport(ctx, userName);
		}
	}

	/**
	 * Returns the import candidates.
	 *
	 * @param ctx The security context.
	 * @param object Host information about the file to import.
	 * @param file The file to import.
	 * @param archived Pass <code>true</code> to archived the files,
	 *                 <code>false</code> otherwise.
	 * @param depth The depth used to set the name. This will be taken into
	 *              account if the file is a directory.
	 * @return See above.
	 * @throws ImportException If an error occurred while importing.
	 */
	ImportCandidates getImportCandidates(SecurityContext ctx,
			ImportableObject object, File file, StatusLabel status)
		throws ImportException
	{
		OMEROWrapper reader = null;
		try {
			ImportConfig config = new ImportConfig();
			reader = new OMEROWrapper(config);
			String[] paths = new String[1];
			paths[0] = file.getAbsolutePath();
			ImportCandidates icans = new ImportCandidates(reader, paths, status);
			
			if(object.isOverrideName()) {
			    String name = UIUtilities.getDisplayedFileName(file.getAbsolutePath(), object.getDepthForName());
			    for(ImportContainer ic : icans.getContainers()) {
			        ic.setUserSpecifiedName(name);
			    }
			}
			
			return icans;
		} catch (Throwable e) {
			throw new ImportException(e);
		} finally {
			if (reader != null) {
				try {
					reader.close();
				} catch (Exception ex) {}
			}
		}
	}

	/**
	 * Removes the rendering service corresponding to the pixels set ID.
	 *
	 * @param ctx The security context.
	 * @param pixelsID The pixels set Id to handle.
	 */
	void removeREService(SecurityContext ctx, long pixelsID)
	{
		gw.shutdownRenderingEngine(ctx, pixelsID);
	}

	/**
	 * Loads the folder identified by its absolute path.
	 *
	 * @param absolutePath The absolute path.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	DataObject loadFolder(String absolutePath)
		throws DSOutOfServiceException, DSAccessException
	{
		try {

		} catch (Exception e) {
			handleException(e, "Cannot find the folder with path: "
					+absolutePath);
		}
		return null;
	}

	/**
	 * Loads the instrument and its components.
	 *
	 * @param ctx The security context.
	 * @param id The id of the instrument.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Object loadInstrument(SecurityContext ctx, long id)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			Instrument instrument = service.loadInstrument(id);
			if (instrument == null) return null;
			return new InstrumentData(instrument);

		} catch (Exception e) {
			handleException(e, "Cannot load the instrument: "+id);
		}
		return null;
	}

	/**
	 * Loads the table associated to a given node.
	 *
	 * @param ctx The security context.
	 * @param parameters The parameters used to retrieve the table.
	 * @param userID The user's identifier.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<TableResult> loadTabularData(SecurityContext ctx,
			TableParameters parameters, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
		TablePrx tablePrx = null;
		long id = -1;
		List<TableResult> results = new ArrayList<TableResult>();
		try {
		    SharedResourcesPrx svc = getSharedResources(ctx);
			long[] rows;
			TableResult result;
			List<Long> ids;
			if (parameters.getNodeType() != null) {
				//TMP solution
				List<Long> objects = new ArrayList<Long>(1);
				objects.add(parameters.getNodeID());
				Map map = loadAnnotations(ctx, parameters.getNodeType(),
						objects, null, null, new Parameters());
				Collection list = (Collection) map.get(parameters.getNodeID());
				Iterator j = list.iterator();
				FileAnnotationData fa;
				ids = new ArrayList<Long>();
				Object k;
				while (j.hasNext()) {
					k = j.next();
					if (k instanceof FileAnnotationData) {
						fa = (FileAnnotationData) k;
						if (FileAnnotationData.BULK_ANNOTATIONS_NS.equals(
								fa.getNameSpace()))
							ids.add(fa.getFileID());
					}
				}
			} else ids = parameters.getOriginalFileIDs();
			if (ids != null && ids.size() > 0) {
				Iterator<Long> i = ids.iterator();
				while (i.hasNext()) {
					id = i.next();
					tablePrx = svc.openTable(new OriginalFileI(id, false));
					if (tablePrx != null) {
						rows = new long[(int) tablePrx.getNumberOfRows()];
						for (int j = 0; j < rows.length; j++)
							rows[j] = j;
						result = createTableResult(tablePrx, rows);
						if (result != null)
							results.add(result);
					}
				}
			}
		} catch (Exception e) {
			handleException(e, "Cannot load the table: "+id);
		}
		return results;
	}

	/**
	 * Loads the ROI related to the specified image.
	 *
	 * @param ctx The security context.
	 * @param imageID 	The image's ID.
	 * @param userID	The user's ID.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ROIResult> loadROI(SecurityContext ctx, long imageID,
			List<Long> measurements, long userID)
		throws DSOutOfServiceException, DSAccessException
	{
        try {
            ROIFacility roifac = gw.getFacility(ROIFacility.class);
            return roifac.loadROIs(ctx, imageID, measurements, userID);
        } catch (ExecutionException e1) {
            handleException(e1, "Cannot load the ROI for image: "+imageID);
        }
	    return Collections.EMPTY_LIST;
	}

	/**
	 * Save the ROI for the image to the server.
	 *
	 * @param ctx The security context.
	 * @param imageID 	The image's ID.
	 * @param userID	The user's ID.
	 * @param roiList	The list of ROI to save.
	 * @return updated list of ROIData objects.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection<ROIData> saveROI(SecurityContext ctx, long imageID, long userID,
			List<ROIData> roiList)
		throws DSOutOfServiceException, DSAccessException
	{
		try {
		    ROIFacility roifac = gw.getFacility(ROIFacility.class);
		    return roifac.saveROIs(ctx, imageID, userID, roiList);
		} catch (Exception e) {
			handleException(e, "Cannot Save the ROI for image: "+imageID);
		}
		return Collections.EMPTY_LIST;
	}

	/**
	 * Loads the <code>FileAnnotationData</code>s for the passed image.
	 *
	 * @param ctx The security context.
	 * @param imageID 	The image's id.
	 * @param userID	The id of the user.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Collection loadROIMeasurements(SecurityContext ctx, long imageID,
			long userID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IRoiPrx svc = gw.getROIService(ctx);
			RoiOptions options = new RoiOptions();
			options.userId = omero.rtypes.rlong(userID);
			Collection files = PojoMapper.asDataObjects(
					svc.getRoiMeasurements(imageID, options));
			List results = new ArrayList();
			if (files != null) {
				Iterator i = files.iterator();
				FileAnnotationData fa;
				long tableID;
				TableResult table;
				while (i.hasNext()) {
					fa = (FileAnnotationData) i.next();
					if (OVERLAYS.equals(fa.getDescription())) {
						//load the table
						tableID = fa.getId();
						table = createOverlay(imageID, svc.getTable(tableID));
						if (table != null) {
							table.setTableID(tableID);
							results.add(table);
						}
					} else
						results.add(fa);
				}
			}
			return results;

		} catch (Exception e) {
			handleException(e, "Cannot load the ROI measurements for image: "+
					imageID);
		}
		return new ArrayList<Object>();
	}

	/**
	 * Returns the file
	 *
	 * @param index Either OME-XML or OME-TIFF.
	 * @param file		The file to write the bytes.
	 * @param imageID	The id of the image.
	 * @param ctx The security context.
	 * @param file The file to write the bytes.
	 * @param imageID The id of the image.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	void exportImageAsOMEObject(SecurityContext ctx, int index, File f,
			long imageID)
		throws DSAccessException, DSOutOfServiceException
	{
		FileOutputStream stream = null;
		DSAccessException exception = null;
		
		try {
		    ExporterPrx store = gw.getExporterService(ctx);
			stream = new FileOutputStream(f);
			try {
				store.addImage(imageID);
				try {
					long size = 0;
					if (index == OmeroImageService.EXPORT_AS_OME_XML)
						size = store.generateXml();
					else size = store.generateTiff();
					long offset = 0;
					try {
						for (offset = 0; (offset+INC) < size;) {
							stream.write(store.read(offset, INC));
							offset += INC;
						}
					} finally {
						stream.write(store.read(offset, (int) (size-offset)));
						stream.close();
					}
				} catch (Exception e) {
					if (stream != null) stream.close();
					if (f != null) f.delete();
					exception = new DSAccessException(
							"Cannot export the image as an OME-formats ", e);
					handleConnectionException(e);
				}
			} finally {
			    gw.closeService(ctx, store);
				if (exception != null)
				    throw exception;
			}
		} catch (Throwable t) {
			if (f != null) f.delete();
			throw new DSAccessException(
					"Cannot export the image as an OME-TIFF", t);
		}
	}

	/**
	 * Runs the script.
	 *
	 * @param ctx The security context.
	 * @param script The script to run.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 * @throws ProcessException If an error occurred while running the script.
	 */
	ScriptCallback runScript(SecurityContext ctx, ScriptObject script)
		throws ProcessException, DSOutOfServiceException, DSAccessException
	{
		long id = -1;
		try {
			id = script.getScriptID();
			if (id < 0) return null;
		} catch (Exception e) {
			handleException(e, "Cannot run the script.");
		}
		return runScript(ctx, id, script.getValueToPass());
	}

	/**
	 * Runs the script.
	 *
	 * @param ctx The security context.
	 * @param script The script to run.
	 * @param official Pass <code>true</code> to indicate that the script will
	 * 				   be uploaded as an official script, <code>false</code>
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 * @throws ValidationException      If the script validation failed
	 */
	Object uploadScript(SecurityContext ctx, ScriptObject script,
			boolean official)
		throws DSOutOfServiceException, DSAccessException, ValidationException
	{
		FileInputStream stream = null;
		try {
		    IScriptPrx svc = getScriptService(ctx);
			StringBuffer buf = new StringBuffer("");
			try {
				File file = new File(script.getPath());
				stream = new FileInputStream(file);
				int c;
				while ((c = stream.read()) != -1)
					buf.append((char) c);
				try {
					if (stream != null) stream.close();
				} catch (Exception e) {}
			} catch (Exception e) {
				try {
					stream.close();
				} catch (Exception ex) {
					//n
				}
				handleException(e,
						"Cannot upload the script: "+script.getName()+".");
				return -1;
			}
			String path = script.getFolder();
			List<OriginalFile> scripts = getScripts(ctx);
			if (scripts.size() > 0) {
				Iterator<OriginalFile> i = scripts.iterator();
				OriginalFile of;
				StringBuffer buffer = new StringBuffer();
				RString v;
				while (i.hasNext()) {
					of = i.next();
					v = of.getPath();
					if (v != null) buffer.append(v.getValue());
					v = of.getName();
					if (v != null) buffer.append(v.getValue());
					//check if the script already exists.
					if (buffer.toString().equals(path)) {
						svc.editScript(of, buf.toString());
						return of.getId().getValue();
					}
				}
			}
			if (official)
				return svc.uploadOfficialScript(path, buf.toString());
			return svc.uploadScript(path, buf.toString());
		} catch (Exception e) {
		    if (e instanceof ValidationException) 
		        throw (ValidationException)e;
		    else
		        handleException(e,
					"Cannot upload the script: "+script.getName()+".");
		}
		try {
			if (stream != null) stream.close();
		} catch (Exception e) {
		}
		return -1;
	}

	//Admin

	/**
	 * Creates the experimenters.
	 *
	 * @param ctx The security context.
	 * @param object The object hosting information about the experimenters
	 * to create.
	 * @param roles The system roles.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ExperimenterData> createExperimenters(SecurityContext ctx,
			AdminObject object, Roles roles)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		List<ExperimenterData> results = new ArrayList<ExperimenterData>();
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			Map<ExperimenterData, UserCredentials>
				m = object.getExperimenters();
			Entry entry;
			Iterator i = m.entrySet().iterator();
			Experimenter exp;
			UserCredentials uc;
			String password;
			List<GroupData> groups = object.getGroups();
			ExperimenterGroup g = null;
			List<ExperimenterGroup> l = new ArrayList<ExperimenterGroup>();
			if (groups != null && groups.size() >= 1) {
				g = groups.get(0).asGroup();
				Iterator<GroupData> j = groups.iterator();
				while (j.hasNext())
					l.add(((GroupData) j.next()).asGroup());
			}
			long id;
			Experimenter value;
			boolean systemGroup = false;
			final ExperimenterGroup userGroup = new ExperimenterGroupI(
			        roles.userGroupId, false);
			ExperimenterGroup system = new ExperimenterGroupI(
                    roles.systemGroupId, false);
			while (i.hasNext()) {
				entry = (Entry) i.next();
				exp = (Experimenter) ModelMapper.createIObject(
						(DataObject) entry.getKey());
				uc = (UserCredentials) entry.getValue();
				value = lookupExperimenter(ctx, uc.getUserName());
				if (value == null) {
					if (uc.isAdministrator()) {
						l.add(userGroup);
						l.add(system);
					} else l.add(userGroup);
					if (g == null) {
						g = l.get(0);
						systemGroup = true;
					}
					exp.setOmeName(omero.rtypes.rstring(uc.getUserName()));
					exp.setLdap(omero.rtypes.rbool(false));
					password = uc.getPassword();
					if (password != null && password.length() > 0) {
						id = svc.createExperimenterWithPassword(exp,
								omero.rtypes.rstring(password), g, l);
					} else
						id = svc.createExperimenter(exp, g, l);
					exp = svc.getExperimenter(id);
					if (uc.isOwner() && !systemGroup)
						svc.setGroupOwner(g, exp);
					results.add((ExperimenterData)
							PojoMapper.asDataObject(exp));
				}
			}
		} catch (Exception e) {
			handleException(e, "Cannot create the experimenters.");
		}
		return results;
	}

	/**
	 * Creates the experimenters.
	 *
	 * @param ctx The security context.
	 * @param object The object hosting information about the experimenters
	 * to create.
	 * @param roles The security roles.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	GroupData createGroup(SecurityContext ctx, AdminObject object, Roles roles)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			Map<ExperimenterData, UserCredentials>
				m = object.getExperimenters();
			Entry entry;
			Iterator i = m.entrySet().iterator();
			Experimenter exp;
			UserCredentials uc;
			String password;
			GroupData groupData = (GroupData) object.getGroup();
			ExperimenterGroup g = lookupGroup(ctx, groupData.getName());

			if (g != null) return null;

			g = new ExperimenterGroupI();
			g.setName(omero.rtypes.rstring(groupData.getName()));
			g.setLdap(omero.rtypes.rbool(false));
			g.setDescription(omero.rtypes.rstring(groupData.getDescription()));
			g.getDetails().setPermissions(createPermissions(
					object.getPermissions()));
			long groupID = svc.createGroup(g);
			g = svc.getGroup(groupID);
			List<ExperimenterGroup> list = new ArrayList<ExperimenterGroup>();
			list.add(g);

			List<ExperimenterGroup> l = new ArrayList<ExperimenterGroup>();
			long id;
			Experimenter value;
			GroupData defaultGroup = null;
			ExperimenterData expData;
			final ExperimenterGroup userGroup =
			        new ExperimenterGroupI(roles.userGroupId, false);
			final ExperimenterGroup systemGroup = new ExperimenterGroupI(
			        roles.systemGroupId, false);
			while (i.hasNext()) {
				entry = (Entry) i.next();
				uc = (UserCredentials) entry.getValue();
				//Check if the experimenter already exist
				value = lookupExperimenter(ctx, uc.getUserName());
				if (value != null) {
					exp = value;
					expData = new ExperimenterData(exp);
					defaultGroup = expData.getDefaultGroup();
					if (dsFactory.getAdmin().isSecuritySystemGroup(
					        defaultGroup.getId()))
						defaultGroup = null;
				} else {
					exp = (Experimenter) ModelMapper.createIObject(
							(ExperimenterData) entry.getKey());
					if (uc.isAdministrator()) {
						l.add(userGroup);
						l.add(systemGroup);
					} else l.add(userGroup);
					exp.setOmeName(omero.rtypes.rstring(uc.getUserName()));
					exp.setLdap(omero.rtypes.rbool(false));
					password = uc.getPassword();
					if (password != null && password.length() > 0) {
						id = svc.createExperimenterWithPassword(exp,
								omero.rtypes.rstring(password), g, l);
					} else
						id = svc.createExperimenter(exp, g, l);
					exp = svc.getExperimenter(id);
				}

				svc.setGroupOwner(g, exp);
				if (defaultGroup == null) {
					svc.setDefaultGroup(exp, g);
				}
			}
			return (GroupData) PojoMapper.asDataObject(g);
		} catch (Exception e) {
			handleException(e, "Cannot create group and owner.");
		}
		return null;
	}

	/**
	 * Counts the number of experimenters within the specified groups.
	 * Returns a map whose keys are the group identifiers and the values the
	 * number of experimenters in the group.
	 *
	 * @param ctx The security context.
	 * @param ids The group identifiers.
	 * @return See above
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Map<Long, Long> countExperimenters(SecurityContext ctx, List<Long> groupIds)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		Map<Long, Long> r = new HashMap<Long, Long>();
		try {
		    IQueryPrx svc = gw.getQueryService(ctx);
			ParametersI p = new ParametersI();
			p.addLongs("gids", groupIds);
	        List list = (List) svc.findAllByQuery("select m " +
	                "from GroupExperimenterMap as m"
	                + " left outer join fetch m.parent"
	                +" where m.parent.id in (:gids)", p);
	        Iterator i = list.iterator();
	        GroupExperimenterMap g;
	        long id;
	        Long count;
	        ExperimenterGroup group;
	        while (i.hasNext()) {
	            g = (GroupExperimenterMap) i.next();
	            group = g.getParent();
	            id = group.getId().getValue();
	            groupIds.remove(id);
	            count = r.get(id);
	            if (count == null) count = 0L;
	            count++;
	            r.put(id, count);
	        }
	        if (groupIds.size() > 0) {
	            i = groupIds.iterator();
	            while (i.hasNext()) {
	                r.put((Long) i.next(), 0L);
	            }
	        }
	    } catch (Throwable t) {
	        handleException(t, "Cannot count the experimenters.");
	    }
	    return r;
	}

	/**
	 * Returns the collection of groups the user is a member of.
	 *
	 * @param experimenterID The experimenter's identifier.
	 * @return See above.
	 *  @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<GroupData> getGroups(SecurityContext ctx, long experimenterID)
		throws DSOutOfServiceException, DSAccessException
	{
		List<GroupData> pojos = new ArrayList<GroupData>();
		if (experimenterID < 0) return pojos;
		
		try {
		    IQueryPrx svc = gw.getQueryService(ctx);
			List<ExperimenterGroup> groups = null;
			ParametersI p = new ParametersI();
			p.addId(experimenterID);
			groups = (List) svc.findAllByQuery("select distinct g " +
					"from ExperimenterGroup g "
	                + "left outer join fetch g.groupExperimenterMap m "
	                + "left outer join fetch m.child u " +
	                		" where u.id = :id", p);
			ExperimenterGroup group;
			//GroupData pojoGroup;
			Iterator<ExperimenterGroup> i = groups.iterator();
			while (i.hasNext()) {
				group = i.next();
				if (!dsFactory.getAdmin().isSecuritySystemGroup(
				        group.getId().getValue()))
					pojos.add((GroupData) PojoMapper.asDataObject(group));
			}
		} catch (Exception e) {
			handleConnectionException(e);
		}

		return pojos;
	}

	/**
	 * Loads the groups the experimenters.
	 *
	 * @param ctx The security context.
	 * @param id The group identifier or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<GroupData> loadGroups(SecurityContext ctx, long id)
		throws DSOutOfServiceException, DSAccessException
	{
		List<GroupData> pojos = new ArrayList<GroupData>();
		
		try {
	        IQueryPrx svc = gw.getQueryService(ctx);
			List<ExperimenterGroup> groups = null;
			if (id < 0) {
				groups = (List)
				svc.findAllByQuery("select distinct g from ExperimenterGroup g "
		                , null);
			} else {
				ParametersI p = new ParametersI();
				p.addId(id);
				groups = (List) svc.findAllByQuery("select distinct g " +
						"from ExperimenterGroup g "
		                + "left outer join fetch g.groupExperimenterMap m "
		                + "left outer join fetch m.child u "
		                + "left outer join fetch u.groupExperimenterMap m2 "
		                + "left outer join fetch m2.parent" +
		                		" where g.id = :id", p);
			}
			pojos.addAll(PojoMapper.asDataObjects(groups));
			return pojos;
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the available groups ");
		}
		return pojos;
	}

	/**
	 * Loads the groups the experimenters.
	 *
	 * @param ctx The security context.
	 * @param id The group identifier or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<GroupData> loadGroupsForExperimenter(SecurityContext ctx, long id)
		throws DSOutOfServiceException, DSAccessException
	{
		List<GroupData> pojos = new ArrayList<GroupData>();
		
		try {
		    IQueryPrx svc = gw.getQueryService(ctx);
			List<ExperimenterGroup> groups = null;
			ParametersI p = new ParametersI();
			p.addId(id);
			groups = (List) svc.findAllByQuery("select distinct g " +
					"from ExperimenterGroup g "
	                + "left outer join fetch g.groupExperimenterMap m "
	                + "left outer join fetch m.child u "
	                + " where u.id = :id", p);
			pojos.addAll(PojoMapper.asDataObjects(groups));
			return pojos;
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the available groups ");
		}
		return pojos;
	}

	/**
	 * Loads the experimenters contained in the specified group or all
	 * experimenters if the value passed is <code>-1</code>.
	 *
	 * @param ctx The security context.
	 * @param id The group identifier or <code>-1</code>.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ExperimenterData> loadExperimenters(SecurityContext ctx, long groupID)
		throws DSOutOfServiceException, DSAccessException
	{
		List<ExperimenterData> pojos = new ArrayList<ExperimenterData>();
		
		try {
		    IAdminPrx service = gw.getAdminService(ctx);
			List<Experimenter> l = service.lookupExperimenters();
			pojos.addAll(PojoMapper.asDataObjects(l));
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the existing groups.");
		}
		return pojos;
	}

	/**
	 * Deletes the specified experimenters. Returns the experimenters
	 * that could not be deleted.
	 *
	 * @param ctx The security context.
	 * @param experimenters The experimenters to delete.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ExperimenterData> deleteExperimenters(SecurityContext ctx,
			List<ExperimenterData> experimenters)
		throws DSOutOfServiceException, DSAccessException
	{
		List<ExperimenterData> r = new ArrayList<ExperimenterData>();
		
		IAdminPrx svc;
		Iterator<ExperimenterData> i = experimenters.iterator();
		ExperimenterData exp;
		while (i.hasNext()) {
			exp = i.next();
			try {
			    svc = gw.getAdminService(ctx);
				svc.deleteExperimenter(exp.asExperimenter());
			} catch (Exception e) {
				handleConnectionException(e);
				r.add(exp);
			}
		}
		return r;
	}

	/**
	 * Copies the experimenter to the specified group.
	 * Returns the experimenters that could not be copied.
	 *
	 * @param ctx The security context.
	 * @param group The group to add the experimenters to.
	 * @param experimenters The experimenters to add.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ExperimenterData> copyExperimenters(SecurityContext ctx,
			GroupData group, Collection experimenters)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		IAdminPrx svc;
		List<ExperimenterData> r = new ArrayList<ExperimenterData>();
		Iterator<ExperimenterData> i = experimenters.iterator();
		ExperimenterData exp;
		List<ExperimenterGroup> groups = new ArrayList<ExperimenterGroup>();
		groups.add(group.asGroup());
		while (i.hasNext()) {
			exp = i.next();
			try {
			    svc = gw.getAdminService(ctx);
				svc.addGroups(exp.asExperimenter(), groups);
			} catch (Exception e) {
				handleConnectionException(e);
				r.add(exp);
			}
		}
		return r;
	}

	/**
	 * Removes the experimenters from the specified group.
	 * Returns the experimenters that could not be removed.
	 *
	 * @param ctx The security context.
	 * @param group The group to add the experimenters to.
	 * @param experimenters The experimenters to add.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<ExperimenterData> removeExperimenters(SecurityContext ctx,
			GroupData group, Collection experimenters)
		throws DSOutOfServiceException, DSAccessException
	{
		List<ExperimenterData> r = new ArrayList<ExperimenterData>();
		
		IAdminPrx svc;
		Iterator<ExperimenterData> i = experimenters.iterator();
		ExperimenterData exp;
		List<ExperimenterGroup> groups = new ArrayList<ExperimenterGroup>();
		groups.add(group.asGroup());
		while (i.hasNext()) {
			exp = i.next();
			try {
			    svc = gw.getAdminService(ctx);
				svc.removeGroups(exp.asExperimenter(), groups);
			} catch (Exception e) {
				handleConnectionException(e);
				r.add(exp);
			}
		}
		return r;
	}

	/**
	 * Deletes the specified groups. Returns the groups that could not be
	 * deleted.
	 *
	 * @param ctx The security context.
	 * @param groups The groups to delete.
	 * @return See above.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	List<GroupData> deleteGroups(SecurityContext ctx, List<GroupData> groups)
		throws DSOutOfServiceException, DSAccessException
	{
		List<GroupData> r = new ArrayList<GroupData>();
		
		IAdminPrx svc = null;
		Iterator<GroupData> i = groups.iterator();
		GroupData g;
		while (i.hasNext()) {
			g = i.next();
			try {
			    svc = gw.getAdminService(ctx);
				svc.deleteGroup(g.asGroup());
			} catch (Exception e) {
				handleConnectionException(e);
				r.add(g);
			}
		}
		return r;
	}

	/**
	 * Resets the password of the specified user.
	 *
	 * @param ctx The security context.
	 * @param userName 	The login name.
	 * @param userID 	The id of the user.
	 * @param password 	The password to set.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	void resetPassword(SecurityContext ctx, String userName, long userID,
			String password)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx, true);
			svc.changeUserPassword(userName, omero.rtypes.rstring(password));
		} catch (Throwable t) {
			handleException(t, "Cannot modify the password for:"+userName);
		}
	}

	/**
	 * Resets the login name of the specified user.
	 * Returns <code>true</code> if the user name could be reset,
	 * <code>false</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param userName The login name.
	 * @param experimenter The experimenter to handle.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	boolean resetUserName(SecurityContext ctx, String userName,
			ExperimenterData experimenter)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx service = gw.getAdminService(ctx);
			//First check that no user with the name already exists
			Experimenter value = lookupExperimenter(ctx, userName);
			if (value == null) {
				Experimenter exp = experimenter.asExperimenter();
				exp.setOmeName(omero.rtypes.rstring(userName));
				service.updateExperimenter(exp);
				return true;
			}
		} catch (Throwable t) {
			handleException(t, "Cannot modify the loginName for:"+
					experimenter.getId());
		}
		return false;
	}

	/**
	 * Invokes when the user has forgotten his/her password.
	 *
	 * @param ctx The security context.
	 * @param userName The login name.
	 * @param email The e-mail if set.
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	void reportForgottenPassword(SecurityContext ctx, String userName,
			String email)
		throws DSOutOfServiceException, DSAccessException
	{
		//root need to login and send an e-mail.

	}

	/**
	 * Returns the group corresponding to the passed name or <code>null</code>.
	 *
	 * @param ctx The security context.
	 * @param name The name of the group.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	ExperimenterGroup lookupGroup(SecurityContext ctx, String name)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			return svc.lookupGroup(name);
		} catch (Exception e) {
			if (e instanceof ApiUsageException)
				return null;
			handleException(e, "Cannot load the group.");
		}
		return null;
	}

	/**
	 * Returns the experimenter corresponding to the passed name or
	 * <code>null</code>.
	 *
	 * @param ctx The security context.
	 * @param name The name of the experimenter.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Experimenter lookupExperimenter(SecurityContext ctx, String name)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			return svc.lookupExperimenter(name);
		} catch (Exception e) {
			if (e instanceof ApiUsageException)
				return null;
			handleException(e, "Cannot load the required group.");
		}
		return null;
	}

	/**
	 * Reads the file hosting the user photo.
	 *
	 * @param ctx The security context.
	 * @param fileID The id of the file.
	 * @param size   The size of the file.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	byte[] getUserPhoto(SecurityContext ctx, long fileID, long size)
		throws DSOutOfServiceException, DSAccessException
	{
		return retrieveUserPhoto(ctx, fileID, size);
	}

	/**
	 * Reads the file hosting the user photo.
	 *
	 * @param ctx The security context.
	 * @param fileID The id of the file.
	 * @param size   The size of the file.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	private byte[] retrieveUserPhoto(SecurityContext ctx,
			long fileID, long size)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		RawFileStorePrx store = null;
		try {
		    store = gw.getRawFileService(ctx);
			store.setFileId(fileID);
			return store.read(0, (int) size);
		} catch (Exception e) {
			handleConnectionException(e);
			throw new DSAccessException("Cannot read the file" +fileID, e);
		} finally {
		    if (store != null) gw.closeService(ctx, store);
		}
	}

	/**
	 * Uploads the photo hosting the user photo.
	 *
	 * @param ctx The security context.
	 * @param fileID The id of the file.
	 * @param size   The size of the file.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	long uploadExperimenterPhoto(SecurityContext ctx, File file, String format,
			long experimenterID)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		IAdminPrx svc = gw.getAdminService(ctx);
		FileInputStream stream = null;
		try {
			stream = new FileInputStream(file);
			long length = file.length();
			//Make sure the file is not too big.
			byte[] bytes = new byte[(int) length];
			int offset = 0; int r = 0;
			while (offset < bytes.length &&
					(r = stream.read(bytes, offset, bytes.length-offset)) >= 0)
				offset += r;
			if (offset < bytes.length)
				throw new IOException("Could not completely read file "+
						file.getName());
			
			return svc.uploadMyUserPhoto(file.getName(), format, bytes);
		} catch (Exception e) {
			handleException(e, "Cannot upload the photo.");
		} finally {
		    try {
		        if (stream != null) stream.close();
            } catch (Exception e2) {
                dsFactory.getLogger().debug(this, "Cannot close stream.");
            }
		}
		return -1;
	}

	/**
	 * Returns the back-off time if it requires a pyramid to be built,
	 * <code>null</code> otherwise.
	 *
	 * @param ctx The security context.
	 * @param pixelsId The identifier of the pixels set to handle.
	 * @return See above
	 * @throws DSOutOfServiceException  If the connection is broken, or logged
	 *                                  in.
	 * @throws DSAccessException        If an error occurred while trying to
	 *                                  retrieve data from OMEDS service.
	 */
	Boolean isLargeImage(SecurityContext ctx, long pixelsId)
		throws DSOutOfServiceException, DSAccessException
	{
       
        RawPixelsStorePrx store = null;
	    try {
	        store = gw.getPixelsStore(ctx);
			store.setPixelsId(pixelsId, true);
			return store.requiresPixelsPyramid();
		} catch (Exception e) {
			handleException(e, "Cannot start the Raw pixels store.");
		} finally {
		    if (store != null) gw.closeService(ctx, store);
		}
		return null;
	}

	/**
	 * Closes the services initialized by the importer.
	 *
	 * @param ctx The security context.
	 * @param userName The user's name.
	 */
	void closeImport(SecurityContext ctx, String userName)
	{
	    gw.closeImport(ctx, userName);
	}

	/**
	 * Adds the experimenters to the specified group.
	 *
	 * @param ctx The security context.
	 * @param group The group to add the experimenters to.
	 * @param experimenters The experimenters to add.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	void addExperimenters(SecurityContext ctx, GroupData group,
			List<ExperimenterData> experimenters)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		Iterator<ExperimenterData> i = experimenters.iterator();
		try {
		    IAdminPrx svc = gw.getAdminService(ctx);
			List<ExperimenterGroup> groups = new ArrayList<ExperimenterGroup>();
			groups.add(group.asGroup());
			while (i.hasNext()) {
				svc.addGroups(i.next().asExperimenter(), groups);
			}
		} catch (Exception e) {
			handleException(e, "Cannot add the experimenters.");
		}
	}

	/**
	 * Checks that the specified context and the object match, if they don't
	 * creates and returns a matching context.
	 *
	 * @param ctx The context to handle.
	 * @param ho The context to handle.
	 * @return See above.
	 */
	SecurityContext checkContext(SecurityContext ctx, DataObject ho)
	{
		if (ctx == null && ho.getId() >= 0)
			return new SecurityContext(ho.getGroupId());
		if (ho.getId() < 0) return ctx;
		if (ho.getGroupId() == ctx.getGroupID()) return ctx;
		return new SecurityContext(ho.getGroupId());
	}

	/**
	 * Checks if there is alreay a {@link Save} object for the same
	 * {@link IObject} in <code>saves</code> list. 
	 * @param save The Save to look for
	 * @param saves The collection of Saves to look in
	 * @return <code>true</code> if it's already in the list, <code>
	 *     false</code> otherwise.
	 */
	private boolean contains(Save save, List<Save> saves) {
	    for(Save save2 : saves) {
	        if(save2.obj == save.obj)
	            return true;
	    }
	    return false;
	}
	
	/**
	 * Moves data between groups.
	 *
	 * @param ctx The security context of the source group.
	 * @param target The security context of the destination group.
	 * @param map The object to move and where to move them
	 * @param options The options.
	 * @return See above
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	RequestCallback transfer(SecurityContext ctx, SecurityContext target,
			Map<DataObject, List<IObject>> map, Map<String, String> options)
		throws DSOutOfServiceException, DSAccessException
	{
	    // map ~ Map<'Object to move', 'Destinations to move the object to'>
		try {
			Entry<DataObject, List<IObject>> entry;
			Iterator<Entry<DataObject, List<IObject>>>
			i = map.entrySet().iterator();
			DataObject data;
			List<IObject> l;
			List<Request> commands = new ArrayList<Request>();
			List<Save> saves = new ArrayList<Save>();
			Save save;
			Map<String, List<Long>> objects = new HashMap<String, List<Long>>();
			while (i.hasNext()) {
				entry = i.next();
				data = entry.getKey();
				l = entry.getValue();
				String key = PojoMapper.getGraphType(data.getClass());
				List<Long> values = objects.get(key);
				if(values==null) {
				    values = new ArrayList<Long>();
				    objects.put(key, values);
				}
				values.add(data.getId());
				
				for (IObject obj : l) {
                  save = new Save();
                  save.obj = obj;
                    if (!contains(save, saves))
                        saves.add(save);
              }
			}
			
			commands.add(Requests.chgrp(objects, target.getGroupID()));
			commands.addAll(saves);
			
			return new RequestCallback(gw.submit(ctx, commands, target));
		} catch (Throwable e) {
			handleException(e, "Cannot transfer the data.");
		}
		return null;
	}

	/**
	 * Returns <code>true</code> if the object can be deleted,
	 * <code>false</code> otherwise.
	 *
	 * @param ho The object to handle.
	 * @return See above.
	 */
	boolean canDelete(IObject ho)
	{
		if (ho == null) return false;
		return ho.getDetails().getPermissions().canDelete();
	}

	/**
	 * Retrieves the dimensions in microns of the specified pixels set.
	 *
	 * @param ctx The security context.
	 * @param pixelsID  The pixels set ID.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	List<IObject> getPixels(SecurityContext ctx, List<DataObject> objects)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
	        IContainerPrx container = gw.getPojosService(ctx);
	        IQueryPrx query = gw.getQueryService(ctx);
			DataObject ho = objects.get(0);
			List<Long> ids = new ArrayList<Long>();
			Iterator<DataObject> i = objects.iterator();
			while (i.hasNext()) {
				ids.add(i.next().getId());
			}
			if (ho instanceof DatasetData) {
				Iterator<Image> j;
				List<Image> images = container.getImages(
						PojoMapper.getModelType(ho.getClass()).getName(), ids, new Parameters());
				j = images.iterator();
				ids.clear();
				while (j.hasNext()) {
					ids.add(j.next().getId().getValue());
				}
			} else if (ho instanceof PlateData) {
				Set<WellData> wells = loadPlateWells(ctx, ids);
				ids.clear();
				Iterator<WellData> k = wells.iterator();
				WellData well;
				Iterator<WellSampleData> j;
				while (k.hasNext()) {
					well = (WellData) k.next();
					j = well.getWellSamples().iterator();
					while (j.hasNext()) {
						ids.add(j.next().getImage().getId());
						break;//tmp solution
					}
				}
			}
			if (ids.size() == 0) return null;
			//Now load the pixels.
			StringBuffer buffer = new StringBuffer();
			buffer.append("select p from Pixels as p ");
			buffer.append("left outer join fetch p.pixelsType as pt ");
			buffer.append("left outer join fetch p.channels as c ");
			buffer.append("left outer join fetch c.logicalChannel as lc ");
			buffer.append("left outer join fetch c.statsInfo ");
			buffer.append("left outer join fetch lc.photometricInterpretation ");
			buffer.append("left outer join fetch lc.illumination ");
			buffer.append("left outer join fetch lc.mode ");
			buffer.append("left outer join fetch lc.contrastMethod ");
			buffer.append("join fetch p.image as i ");
			buffer.append("where i.id in (:ids)");
			ParametersI param = new ParametersI();
			List<RType> l = new ArrayList<RType>(ids.size());
			Iterator<Long> j = ids.iterator();
			while (j.hasNext())
				l.add(omero.rtypes.rlong(j.next()));
			param.add("ids", omero.rtypes.rlist(l));

           return query.findAllByQuery(buffer.toString(), param);
		} catch (Throwable t) {
			handleException(t, "Cannot retrieve the pixels sets");
		}
		return null;
	}

	void removeGroup(SecurityContext ctx) {
	    if (ctx == null)
	        return;
	    gw.closeConnector(ctx);
	}

	/**
	 * Loads the file set corresponding to the specified image.
	 *
	 * @param ctx The security context.
	 * @param imageIds The collection of images id.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Set<DataObject> getFileSet(SecurityContext ctx, Collection<Long> imageIds)
		throws DSOutOfServiceException, DSAccessException
	{
	   
		try {
		    IQueryPrx service = gw.getQueryService(ctx);
			List<RType> l = new ArrayList<RType>(imageIds.size());
			Iterator<Long> j = imageIds.iterator();
			while (j.hasNext())
				l.add(omero.rtypes.rlong(j.next()));
			ParametersI param = new ParametersI();
			param.add("imageIds", omero.rtypes.rlist(l));
			return PojoMapper.asDataObjects(service.findAllByQuery(
					createFileSetQuery(), param));
		} catch (Exception e) {
			handleException(e, "Cannot retrieve the file set");
		}
		return new HashSet<DataObject>();
	}

	/**
	 * Shuts down the connectors created while creating/importing data for
	 * other users.
	 *
	 * @param ctx
	 * @throws Exception Thrown if the connector cannot be closed.
	 */
	void shutDownDerivedConnector(SecurityContext ctx)
		throws Exception
	{
		gw.shutDownDerivedConnector(ctx);
	}

	/**
	 * Loads the annotations of the given type linked to the specified objects.
	 * Returns a map whose keys are the object's id and the values are a
	 * collection of annotation linked to that object.
	 *
	 * @param ctx The security context.
	 * @param rootType The type of object the annotations are linked to e.g.
	 * Image.
	 * @param rootIDs The collection of object's ids the annotations are linked
	 * to.
	 * @param nsInclude The annotation's name space to include if any.
	 * @param nsExlcude The annotation's name space to exclude if any.
	 * @param options Options to retrieve the data.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Map<Long, Collection<AnnotationData>>
	loadSpecifiedAnnotationsLinkedTo(SecurityContext ctx, Class<?> rootType,
			List<Long> rootIDs, Class<?> annotationType, List<String> nsInclude,
			List<String> nsExclude, Parameters options)
	throws DSOutOfServiceException, DSAccessException
	{
		String type = convertAnnotation(annotationType);
		
		try {
		    IMetadataPrx service = gw.getMetadataService(ctx);
			return PojoMapper.asDataObjects(
					service.loadSpecifiedAnnotationsLinkedTo(type, nsInclude,
							nsExclude, PojoMapper.getModelType(rootType).getName(),
							rootIDs, options));
		} catch (Throwable t) {
			handleException(t, "Cannot find annotation of "+annotationType+" " +
					"for "+rootType+".");
		}
		return new HashMap<Long, Collection<AnnotationData>>();
	}

	/**
	 * Executes the commands.
	 *
	 * @param commands The commands to execute.
	 * @param ctx The security context.
	 * @return See above.
	 * @throws ProcessException If an error occurred while running the script.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	RequestCallback submit(List<Request> commands, SecurityContext ctx)
		throws ProcessException, DSOutOfServiceException, DSAccessException
	{
		try {
			return new RequestCallback(gw.submit(ctx, commands, null));
		} catch (Throwable e) {
			handleException(e, "Cannot execute the command.");
			// Never reached
			throw new ProcessException("Cannot execute the command.", e);
		}
	}

	/**
	 * Given a list of IDs of a given type. Determines the filesets that will be
	 * split. Returns the a Map with fileset's ids as keys and the
	 * values if the map:
	 * Key = <code>True</code> value: List of image's ids that are contained.
	 * Key = <code>True</code> value: List of image's ids that are missing
	 * so the delete or change group cannot happen.
	 *
	 * @param ctx The security context, necessary to determine the service.
	 * @param rootType The top-most type which will be searched
	 *                  Mustn't be <code>null</code>.
	 * @param rootIDs A set of the IDs of objects.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
	Map<Long, Map<Boolean, List<Long>>> getImagesBySplitFilesets(
			SecurityContext ctx, Class<?> rootType, List<Long> rootIDs,
			Parameters options)
		throws DSOutOfServiceException, DSAccessException
	{
		
		try {
		    IContainerPrx service = gw.getPojosService(ctx);
			Map<String, List<Long>> m = new HashMap<String, List<Long>>();
			m.put(PojoMapper.getModelType(rootType).getName(),rootIDs);
			return service.getImagesBySplitFilesets(m, options);
		} catch (Throwable t) {
			handleException(t, "Cannot find split images.");
		}
		return null;
	}

	/**
	 * Returns the system groups and users
	 * 
	 * @param ctx The security context.
	 * @return See above.
	 * @throws DSOutOfServiceException If the connection is broken, or logged in
	 * @throws DSAccessException If an error occurred while trying to
	 * retrieve data from OMERO service.
	 */
    Roles getSystemRoles(SecurityContext ctx)
            throws DSOutOfServiceException, DSAccessException
    {
       
        IAdminPrx svc = gw.getAdminService(ctx);
        try {
            return svc.getSecurityRoles();
        } catch (Throwable t) {
            handleException(t, "Cannot load system users.");
        }
        return null;
     }

    /**
     * Loads the log files linked to the specified objects.
     *
     * @param ctx The security context.
     * @param rootType The type of object to handle.
     * @param rootIDs The collection of object's identifiers.
     * @return See above.
     * @throws DSOutOfServiceException If the connection is broken, or logged in
     * @throws DSAccessException If an error occurred while trying to 
     * retrieve data from OMERO service.
     */
    Map<Long, List<IObject>> loadLogFiles(SecurityContext ctx,
            Class<?> rootType, List<Long> rootIDs)
            throws DSOutOfServiceException, DSAccessException
    {
       
        try {
            IMetadataPrx service = gw.getMetadataService(ctx);
            return service.loadLogFiles(
                            PojoMapper.getModelType(rootType).getName(), rootIDs);
        } catch (Throwable t) {
            handleException(t, "Cannot load log files for " + rootType+".");
        }
        return new HashMap();
    }

    /**
     * Retrieves the rendering settings for the specified pixels set.
     *
     * @param ctx The security context.
     * @param rndID The rendering settings ID.
     * @return See above.
     * @throws DSOutOfServiceException If the connection is broken, or logged
     *                                 in.
     * @throws DSAccessException       If an error occurred while trying to
     *                                 retrieve data from OMEDS service.
     */
    RenderingDef getRenderingDef(SecurityContext ctx, long rndID)
        throws DSOutOfServiceException, DSAccessException
    {
       
        try {
            IPixelsPrx service = gw.getPixelsService(ctx);
            return service.loadRndSettings(rndID);
        } catch (Exception e) {
            handleException(e, "Cannot retrieve the rendering settings");
        }
        return null;
    }
}