edu.harvard.med.screensaver.db.CellsDAOImpl.java Source code

Introduction

Here is the source code for edu.harvard.med.screensaver.db.CellsDAOImpl.java

Source

// $HeadURL: http://seanderickson1@forge.abcd.harvard.edu/svn/screensaver/branches/serickson/3200/core/src/main/java/edu/harvard/med/screensaver/db/LibrariesDAOImpl.java $
// $Id: LibrariesDAOImpl.java 6951 2012-01-13 19:13:34Z atolopko $
//
// Copyright  2006, 2010, 2011, 2012 by the President and Fellows of Harvard College.
//
// Screensaver is an open-source project developed by the ICCB-L and NSRB labs
// at Harvard Medical School. This software is distributed under the terms of
// the GNU General Public License.

package edu.harvard.med.screensaver.db;

import java.util.List;
import java.util.Set;
import java.util.SortedSet;

import org.apache.log4j.Logger;
import org.hibernate.Session;

import com.google.common.base.Function;
import com.google.common.base.Joiner;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;

import edu.harvard.med.screensaver.model.cells.Cell;
import edu.harvard.med.screensaver.model.cells.ExperimentalCellInformation;
import edu.harvard.med.screensaver.model.libraries.Reagent;
import edu.harvard.med.screensaver.model.libraries.SmallMoleculeReagent;
import edu.harvard.med.screensaver.model.libraries.Well;
import edu.harvard.med.screensaver.model.libraries.WellKey;
import edu.harvard.med.screensaver.model.screens.Screen;

public class CellsDAOImpl extends AbstractDAO implements CellsDAO {
    private static Logger log = Logger.getLogger(CellsDAOImpl.class);

    private GenericEntityDAO _dao;

    private LibrariesDAO _librariesDao;

    /**
     * @motivation for CGLIB dynamic proxy creation
     */
    public CellsDAOImpl() {
    }

    public CellsDAOImpl(GenericEntityDAO dao, LibrariesDAO librariesDao) {
        _dao = dao;
        _librariesDao = librariesDao;
    }

    @SuppressWarnings("unchecked")
    public Cell findCellFromCLOId(String cloId) {
        return _dao.findEntityByProperty(Cell.class, "cloid", cloId);
    }

    public Set<ExperimentalCellInformation> findCellInformation(Screen screen) {
        return null;
    }

    @Override
    public SortedSet<ExperimentalCellInformation> findCellExperimentsFromCLOIds(String[] cloIds) {

        Set<Cell> cells = findCellsByCloIds(cloIds);

        SortedSet<ExperimentalCellInformation> icis = Sets.newTreeSet();

        for (Cell cell : cells) {
            icis.addAll(_dao.findEntitiesByProperty(ExperimentalCellInformation.class, "cell", cell));
        }
        log.debug("found: " + icis.size() + " icis for this list of cells");
        return icis;
    }

    @Override
    public Set<Cell> findCellsByCloIds(String[] cloIds) {
        Set<Cell> cells = Sets.newHashSet();
        for (String s : cloIds) {
            Cell temp = _dao.findEntityByProperty(Cell.class, "cloId", s);
            if (temp == null) {
                log.info("no cell found for clo_id: " + s);
                continue;
            }
            cells.add(temp);
        }
        log.debug("found: " + cells.size() + " cells for " + Joiner.on(",").join(cloIds) + ": " + cells);
        return cells;
    }

    @Override
    public Set<Cell> findCellsByHMSID(String[] ids) {
        Set<Cell> cells = Sets.newHashSet();
        for (String s : ids) {
            Cell temp = _dao.findEntityByProperty(Cell.class, "facilityId", s);
            if (temp == null) {
                log.info("no cell found for facility: " + s);
                continue;
            }
            cells.add(temp);
        }
        log.debug("found: " + cells.size() + " cells for " + Joiner.on(",").join(ids) + ": " + cells);
        return cells;
    }

    @Override
    public Set<String> findCanonicalCompoundsScreenedByWellId(final Cell cell) {

        List<Well> wells = _dao.runQuery(new edu.harvard.med.screensaver.db.Query<Well>() {
            public List<Well> execute(Session session) {
                //          String hql = "select w from ResultValue rv join rv.well w " +
                //                "join rv.dataColumn dc join dc.screenResult sc join sc.screen s join s.experimentalCellInformationSet eci join eci.cell c where c= ? ";
                //          String hql = "select w from SmallMoleculeReagent r left join fetch r.well w left join fetch r.compoundNames cn, ResultValue rv " +
                //                "join rv.dataColumn dc join dc.screenResult sc join sc.screen s join s.experimentalCellInformationSet eci join eci.cell c where w.latestReleasedReagent=r and rv.well = w and c= ? ";
                String hql = "select w from ResultValue rv join rv.well w "
                        + "join rv.dataColumn dc join dc.screenResult sc join sc.screen s join s.experimentalCellInformationSet eci join eci.cell c where c.facilityId= ? ";

                org.hibernate.Query q = session.createQuery(hql);
                q.setParameter(0, cell.getFacilityId());
                return q.list();
            }
        });

        if (wells == null || wells.isEmpty())
            return null;

        Set<String> wellIds = Sets.newHashSet(Lists.transform(wells, new Function<Well, String>() {
            @Override
            public String apply(Well from) {
                return from.getWellId();
            }
        }));

        return _librariesDao.findCanonicalReagentWellIds(Sets.newHashSet(wellIds));
    }

}