ispyb.server.mx.services.sample.Protein3ServiceBean.java Source code

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Here is the source code for ispyb.server.mx.services.sample.Protein3ServiceBean.java

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/*************************************************************************************************
 * This file is part of ISPyB.
 * 
 * ISPyB is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * ISPyB 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 Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with ISPyB.  If not, see <http://www.gnu.org/licenses/>.
 * 
 * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos
 ****************************************************************************************************/
package ispyb.server.mx.services.sample;

import ispyb.server.mx.services.ws.rest.WsServiceBean;
import ispyb.server.mx.vos.sample.Protein3VO;

import java.util.List;
import java.util.Map;

import javax.annotation.Resource;
import javax.ejb.SessionContext;
import javax.ejb.Stateless;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.Query;

import org.apache.log4j.Logger;
import org.hibernate.Criteria;
import org.hibernate.FetchMode;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.criterion.Order;
import org.hibernate.criterion.Restrictions;
import org.hibernate.transform.AliasToEntityMapResultTransformer;

/**
 * <p>
 * This session bean handles ISPyB Protein3.
 * </p>
 */
@Stateless
public class Protein3ServiceBean extends WsServiceBean implements Protein3Service, Protein3ServiceLocal {

    private final static Logger LOG = Logger.getLogger(Protein3ServiceBean.class);

    // Generic HQL request to find instances of Protein3 by pk
    // TODO choose between left/inner join
    private static final String FIND_BY_PK(boolean fetchCrystals) {
        return "from Protein3VO vo " + (fetchCrystals ? " left join fetch vo.crystalVOs " : "")
                + " where vo.proteinId = :pk";
    }

    // Generic HQL request to find all instances of Protein3
    // TODO choose between left/inner join
    private static final String FIND_ALL(boolean fetchLink1) {
        return "from Protein3VO vo " + (fetchLink1 ? "left join fetch vo.crystalVOs " : "");
    }

    private final static String UPDATE_PROPOSALID_STATEMENT = " update Protein  set proposalId = :newProposalId "
            + " WHERE proposalId = :oldProposalId"; // 2 old value to be replaced

    @PersistenceContext(unitName = "ispyb_db")
    private EntityManager entityManager;

    @Resource
    private SessionContext context;

    public Protein3ServiceBean() {
    };

    /**
     * Create new Protein3.
     * 
     * @param vo
     *            the entity to persist.
     * @return the persisted entity.
     */
    public Protein3VO create(final Protein3VO vo) throws Exception {

        checkCreateChangeRemoveAccess();
        // TODO Edit this business code
        this.checkAndCompleteData(vo, true);
        this.entityManager.persist(vo);
        return vo;
    }

    /**
     * Update the Protein3 data.
     * 
     * @param vo
     *            the entity data to update.
     * @return the updated entity.
     */
    public Protein3VO update(final Protein3VO vo) throws Exception {

        checkCreateChangeRemoveAccess();
        // TODO Edit this business code
        this.checkAndCompleteData(vo, false);
        return entityManager.merge(vo);
    }

    /**
     * Remove the Protein3 from its pk
     * 
     * @param vo
     *            the entity to remove.
     */
    public void deleteByPk(final Integer pk) throws Exception {

        checkCreateChangeRemoveAccess();
        Protein3VO vo = findByPk(pk, false);
        // TODO Edit this business code
        delete(vo);
    }

    /**
     * Remove the Protein3
     * 
     * @param vo
     *            the entity to remove.
     */
    public void delete(final Protein3VO vo) throws Exception {

        checkCreateChangeRemoveAccess();
        // TODO Edit this business code
        entityManager.remove(vo);
    }

    /**
     * Finds a Scientist entity by its primary key and set linked value objects if necessary
     * 
     * @param pk
     *            the primary key
     * @param withLink1
     * @param withLink2
     * @return the Protein3 value object
     */
    public Protein3VO findByPk(final Integer pk, final boolean withLink1) throws Exception {

        checkCreateChangeRemoveAccess();
        // TODO Edit this business code
        try {
            Query query = entityManager.createQuery(FIND_BY_PK(withLink1)).setParameter("pk", pk);
            return (Protein3VO) query.getSingleResult();
        } catch (NoResultException e) {
            return null;
        }
    }

    // TODO remove following method if not adequate
    /**
     * Find all Protein3s and set linked value objects if necessary
     * 
     * @param withLink1
     * @param withLink2
     */
    @SuppressWarnings("unchecked")
    public List<Protein3VO> findAll(final boolean withLink1) throws Exception {

        List<Protein3VO> foundEntities = entityManager.createQuery(FIND_ALL(withLink1)).getResultList();
        return foundEntities;
    }

    @SuppressWarnings("unchecked")
    public List<Protein3VO> findByAcronymAndProposalId(final Integer proposalId, final String acronym,
            final boolean withCrystal, final boolean sortByAcronym) throws Exception {

        Session session = (Session) this.entityManager.getDelegate();

        Criteria crit = session.createCriteria(Protein3VO.class);
        Criteria subCrit = crit.createCriteria("proposalVO");

        crit.setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY); // DISTINCT RESULTS !

        if (proposalId != null) {
            subCrit.add(Restrictions.eq("proposalId", proposalId));
        }

        if (acronym != null && !acronym.isEmpty()) {
            crit.add(Restrictions.like("acronym", acronym.toUpperCase()));
        }

        if (withCrystal) {
            crit.setFetchMode("crystalVOs", FetchMode.JOIN);
        }
        if (sortByAcronym) {
            crit.addOrder(Order.asc("acronym"));
        } else
            crit.addOrder(Order.desc("proteinId"));

        List<Protein3VO> foundEntities = crit.list();
        return foundEntities;
    }

    public List<Protein3VO> findByAcronymAndProposalId(final Integer proposalId, final String acronym)
            throws Exception {
        return findByAcronymAndProposalId(proposalId, acronym, false, false);
    }

    public Protein3VO loadEager(Protein3VO vo) throws Exception {
        Protein3VO newVO = this.findByPk(vo.getProteinId(), true);
        return newVO;
    }

    private String getViewTableQuery() {
        return this.getQueryFromResourceFile("/queries/ProteinServiceBean/getViewTableQuery.sql");
    }

    /**
     * Check if user has access rights to create, change and remove Protein3 entities. If not set rollback only and
     * throw AccessDeniedException
     * 
     * @throws AccessDeniedException
     */
    private void checkCreateChangeRemoveAccess() throws Exception {

        // AuthorizationServiceLocal autService = (AuthorizationServiceLocal)
        // ServiceLocator.getInstance().getService(AuthorizationServiceLocalHome.class); // TODO change method
        // to the one checking the needed access rights
        // autService.checkUserRightToChangeAdminData();
    }

    /**
     * update the proposalId, returns the nb of rows updated
     * 
     * @param newProposalId
     * @param oldProposalId
     * @return
     * @throws Exception
     */
    public Integer updateProposalId(final Integer newProposalId, final Integer oldProposalId) throws Exception {

        int nbUpdated = 0;
        Query query = entityManager.createNativeQuery(UPDATE_PROPOSALID_STATEMENT)
                .setParameter("newProposalId", newProposalId).setParameter("oldProposalId", oldProposalId);
        nbUpdated = query.executeUpdate();

        return new Integer(nbUpdated);
    }

    @Override
    public List<Protein3VO> findByProposalId(Integer proposalId) throws Exception {
        return this.findByAcronymAndProposalId(proposalId, null, false, false);
    }

    public List<Protein3VO> findByProposalId(final Integer proposalId, final boolean withCrystal,
            boolean sortByAcronym) throws Exception {
        return this.findByAcronymAndProposalId(proposalId, null, withCrystal, sortByAcronym);
    }

    /* Private methods ------------------------------------------------------ */

    /**
     * Checks the data for integrity. E.g. if references and categories exist.
     * 
     * @param vo
     *            the data to check
     * @param create
     *            should be true if the value object is just being created in the DB, this avoids some checks like
     *            testing the primary key
     * @exception VOValidateException
     *                if data is not correct
     */
    private void checkAndCompleteData(Protein3VO vo, boolean create) throws Exception {

        if (create) {
            if (vo.getProteinId() != null) {
                throw new IllegalArgumentException(
                        "Primary key is already set! This must be done automatically. Please, set it to null!");
            }
        } else {
            if (vo.getProteinId() == null) {
                throw new IllegalArgumentException("Primary key is not set for update!");
            }
        }
        // check value object
        vo.checkValues(create);
        // TODO check primary keys for existence in DB
    }

    @Override
    public List<Map<String, Object>> getStatsByProposal(int proposalId) {
        String mySQLQuery = getViewTableQuery() + " where proposalId = :proposalId";
        Session session = (Session) this.entityManager.getDelegate();
        SQLQuery query = session.createSQLQuery(mySQLQuery);
        query.setParameter("proposalId", proposalId);
        query.setResultTransformer(AliasToEntityMapResultTransformer.INSTANCE);
        return executeSQLQuery(query);
    }

}