edu.berkeley.compbio.ncbitaxonomy.jpadao.NcbiTaxonomyNodeDaoImpl.java Source code

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Here is the source code for edu.berkeley.compbio.ncbitaxonomy.jpadao.NcbiTaxonomyNodeDaoImpl.java

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/*
 * Copyright (c) 2008-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.ncbitaxonomy.jpadao;

import com.davidsoergel.springjpautils.GenericDaoImpl;
import edu.berkeley.compbio.ncbitaxonomy.dao.NcbiTaxonomyNodeDao;
import edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode;
import org.jetbrains.annotations.NotNull;
import org.springframework.stereotype.Repository;

import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import java.util.List;

/**
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */

@Repository
public class NcbiTaxonomyNodeDaoImpl extends GenericDaoImpl<NcbiTaxonomyNode> implements NcbiTaxonomyNodeDao {
    // ------------------------------ FIELDS ------------------------------

    @PersistenceContext
    private EntityManager entityManager;

    // --------------------- GETTER / SETTER METHODS ---------------------

    /**
     * {@inheritDoc}
     */
    @Override
    public EntityManager getEntityManager() {
        return entityManager;
    }

    /*   @PersistenceContext
       public void setEntityManager(EntityManager entityManager)
          {
          this.entityManager = entityManager;
          }
    */
    // ------------------------ INTERFACE METHODS ------------------------

    // --------------------- Interface GenericDao ---------------------

    //@Transactional(propagation = Propagation.SUPPORTS)

    /**
     * {@inheritDoc}
     */
    @NotNull
    //@Transactional
    public NcbiTaxonomyNode findById(Integer id) {
        NcbiTaxonomyNode node = entityManager.find(NcbiTaxonomyNode.class, id);
        if (node == null) {
            throw new NoResultException("Could not find taxon: " + id);
        }
        // eagerly load the path
        //node.getAncestorPath();
        return node;
    }

    /**
     * Need this to do recursive calls without running out of memory, by starting a new transaction for each query.  Slow,
     * but works.
     *
     * @return
     */
    /*   public List<Integer> findChildIds(Integer id)
          {
          NcbiTaxonomyNode node = entityManager.find(NcbiTaxonomyNode.class, id);
          if (node == null)
     {
     throw new NoResultException("Could not find taxon: " + id);
     }
        
          List<Integer> result = new ArrayList<Integer>();
          for (NcbiTaxonomyNode child : node.getChildren())
     {
     result.add(child.getPayload());
     }
          return result;
          }
    */
    public List<Integer> findChildIds(Integer id) {
        List<Integer> result = (List<Integer>) (entityManager.createNamedQuery("NcbiTaxonomyNode.findChildIds")
                .setParameter("id", id).getResultList());

        // stupid hack because the root is its own child
        result.remove(new Integer(1));
        return result;
    }

    /**
     * {@inheritDoc}
     */
    /*public List<PhylogenyNode<Integer>> getAncestorPath(NcbiTaxonomyNode n)
       {
       List<PhylogenyNode<Integer>> result = new LinkedList<PhylogenyNode<Integer>>();
       NcbiTaxonomyNode trav = n;
        
       while (trav != null)
     {
     result.add(0, trav);
     trav = trav.getParent();
     }
        
       return result;
       }*/

    // --------------------- Interface NcbiTaxonomyNodeDao ---------------------

    // same as findById

    /*   @Transactional(propagation = Propagation.SUPPORTS, noRollbackFor = javax.persistence.NoResultException.class)
    public NcbiTaxonomyNode findByTaxId(Integer taxid)
       {
       return (NcbiTaxonomyNode) (entityManager.createNamedQuery("NcbiTaxonomyNode.findByTaxId")
        .setParameter("taxid", taxid).getSingleResult());
       }*/
    //   @Transactional(propagation = Propagation.REQUIRED, noRollbackFor = javax.persistence.NoResultException.class)
    public List<NcbiTaxonomyNode> findByRank(String rankName) {
        return (List<NcbiTaxonomyNode>) (entityManager.createNamedQuery("NcbiTaxonomyNode.findByRank")
                .setParameter("rank", rankName).getResultList());
    }

    //   @Transactional(propagation = Propagation.REQUIRED, noRollbackFor = javax.persistence.NoResultException.class)
    public List<Integer> findIdsByRank(String rankName) {
        return (List<Integer>) (entityManager.createNamedQuery("NcbiTaxonomyNode.findIdsByRank")
                .setParameter("rank", rankName).getResultList());
    }

    public List<Integer> findAllIds() {
        return (List<Integer>) (entityManager.createNamedQuery("NcbiTaxonomyNode.findAllIds").getResultList());
    }
}