ReadDataAdvanced.java

/*
 *------------------------------------------------------------------------------
 *  Copyright (C) 2006-2016 University of Dundee & Open Microscopy Environment.
 *  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 training;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.Set;

import omero.api.IContainerPrx;
import omero.api.IQueryPrx;
import omero.gateway.Gateway;
import omero.gateway.LoginCredentials;
import omero.gateway.SecurityContext;
import omero.gateway.facility.DataManagerFacility;
import omero.log.SimpleLogger;
import omero.model.Dataset;
import omero.model.IObject;
import omero.model.Project;
import omero.model.TagAnnotation;
import omero.sys.Filter;
import omero.sys.ParametersI;
import omero.gateway.model.DatasetData;
import omero.gateway.model.ExperimenterData;
import omero.gateway.model.ImageData;
import omero.gateway.model.ProjectData;
import omero.gateway.model.TagAnnotationData;

/**
 * More advanced code for how to load data from an OMERO server.
 *
 * @author Jean-Marie Burel     
 * <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
 * @since Beta4.3.2
 */
public class ReadDataAdvanced
{

    //The value used if the configuration file is not used. To edit*/
    /** The server address.*/
    private static String hostName = "serverName";

    /** The username.*/
    private static String userName = "userName";

    /** The password.*/
    private static String password = "password";
    //end edit

    /** The name of a Dataset.*/
    private String datasetName = "MyDataset";

    /** The name of a Tag.*/
    private String tagName = "MyTag";

    private Gateway gateway;

    private SecurityContext ctx;

    /**
     * Creates 3 Datasets with the name defined by {@link #datasetName}.
     */
    private void createDatasets()
            throws Exception
    {
        DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
        for (int i = 0; i < 3; i ++)
        {
            DatasetData d = new DatasetData();
            d.setName(datasetName);
            dm.saveAndReturnObject(ctx, d);
        }
    }

    /**
     * Creates 3 Tags with the namespace value defined by {@link #tagName}.
     */
    private void createTags()
            throws Exception
    {
        DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
        for (int i = 0; i < 3; i ++)
        {
            TagAnnotationData t = new TagAnnotationData(tagName);
            ((TagAnnotation)t.asIObject()).setNs(omero.rtypes.rstring(Setup.TRAINING_NS));
            t.setDescription(String.format("%s %s", tagName, i));
            dm.saveAndReturnObject(ctx, t);
        }
    }


    /**
     * Retrieve the Datasets that match the name value.
     */
    private void loadDatasetsByName()
            throws Exception
    {
        final boolean caseSensitive = true;
        final Filter filter = new Filter();
        // Return the first 10 hits or less.
        filter.limit = omero.rtypes.rint(10);
        filter.offset = omero.rtypes.rint(0);
        IQueryPrx proxy = gateway.getQueryService(ctx);
        List<IObject> datasets = (List<IObject>)
                proxy.findAllByString("Dataset", "name", datasetName, caseSensitive,
                        filter);
        System.out.println("\nList Datasets:");
        for (IObject obj : datasets)
        {
            Dataset d = (Dataset) obj;
            System.out.println("ID: " + d.getId().getValue() + " Name: " +
                    d.getName().getValue());
        }
    }

    /**
     * Retrieve the Tags that match the namespace value.
     */
    private void loadTagsByNS()
            throws Exception
    {
        final boolean caseSensitive = true;
        final Filter filter = new Filter();
        // Return the first 10 hits or less.
        filter.limit = omero.rtypes.rint(10);
        filter.offset = omero.rtypes.rint(0);
        IQueryPrx proxy = gateway.getQueryService(ctx);
        List<IObject> tags = (List<IObject>)
                proxy.findAllByString("TagAnnotation", "ns",
                        Setup.TRAINING_NS, caseSensitive, filter);
        System.out.println("\nList Tags:");
        for (IObject obj : tags)
        {
            TagAnnotation t = (TagAnnotation) obj;
            System.out.println("ID: " + t.getId().getValue() + " NS: " +
                    t.getNs().getValue());
        }
    }

    /** 
     * Retrieve the projects and the orphaned datasets i.e. datasets not in
     * a project.
     *
     * If a project contains datasets, the datasets will automatically be loaded.
     */
    private void loadProjectsAndOrphanedDatasets()
            throws Exception
    {
        IContainerPrx proxy = gateway.getPojosService(ctx);
        ParametersI param = new ParametersI();
        long userId = gateway.getLoggedInUser().getId();
        param.exp(omero.rtypes.rlong(userId));
        //Load the orphaned datasets.
        param.orphan();
        //Do not load the images.
        param.noLeaves(); //indicate to load the images
        //param.noLeaves(); //no images loaded, this is the default value.
        List<IObject> results = proxy.loadContainerHierarchy(
                Project.class.getName(), new ArrayList<Long>(), param);
        //You can directly interact with the IObject or the Pojos object.
        //Follow interaction with the Pojos.
        Iterator<IObject> i = results.iterator();
        ProjectData project;
        DatasetData dataset;
        IObject o;
        long datasetId = -1;
        while (i.hasNext()) {
            o = i.next();
            if (o instanceof Project) {
                project = new ProjectData((Project) o);
                System.err.println("Project:"+project.getId()+" "+
                        project.getName());
            } else if (o instanceof Dataset) {
                dataset = new DatasetData((Dataset) o);
                System.err.println("Dataset:"+dataset.getId()+" "+
                        dataset.getName());
                if (datasetId < 0) datasetId = dataset.getId();
                //Image not loaded.
            }
        }

        //Now load the image for the first orphaned dataset
        if (datasetId < 0) return;
        param = new ParametersI();
        param.exp(omero.rtypes.rlong(userId));
        param.leaves();
        results = proxy.loadContainerHierarchy(
                Dataset.class.getName(), Arrays.asList(datasetId), param);
        i = results.iterator();
        Iterator j;
        while (i.hasNext()) {
            dataset = new DatasetData((Dataset) i.next());
            Set images = dataset.getImages();
            j = images.iterator();
            System.err.println("Size:"+images.size());
            while (j.hasNext()) {
                ImageData image = (ImageData) j.next();
                System.err.println("Image:"+image.getId()+" "+image.getName());
            }
        }
    }

    /**
     * Connects and invokes the various methods.
     *
     * @param args The login credentials.
     */
    ReadDataAdvanced(String[] args)
    {
        LoginCredentials cred = new LoginCredentials(args);
        gateway = new Gateway(new SimpleLogger());
        try {
            // First connect.
            ExperimenterData user = gateway.connect(cred);
            ctx = new SecurityContext(user.getGroupId());
            createDatasets();
            createTags();
            loadDatasetsByName();
            loadTagsByNS();
            loadProjectsAndOrphanedDatasets();
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            try {
                gateway.disconnect(); // Be sure to disconnect
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }

    /**
     * Runs the script without configuration options.
     * 
     * @param args The login credentials.
     */
    public static void main(String[] args)
    {
        if (args == null || args.length == 0)
            args = new String[] { "--omero.host=" + hostName,
                "--omero.user=" + userName, "--omero.pass=" + password };

        new ReadDataAdvanced(args);
        System.exit(0);
    }

}