es.uvigo.ei.sing.gc.view.models.committee.geneset.SelectGenesSubtask.java Source code

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Here is the source code for es.uvigo.ei.sing.gc.view.models.committee.geneset.SelectGenesSubtask.java

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/*
   This file is part of GeneCommittee.
    
   GeneCommittee 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 3 of the License, or
   (at your option) any later version.
    
   GeneCommittee 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 GeneCommittee.  If not, see <http://www.gnu.org/licenses/>.
*/
package es.uvigo.ei.sing.gc.view.models.committee.geneset;

import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.hibernate.Session;

import es.uvigo.ei.sing.datatypes.data.Variable;
import es.uvigo.ei.sing.datatypes.featureselection.FeatureSelectionResults;
import es.uvigo.ei.sing.datatypes.featureselection.FeatureSelector;
import es.uvigo.ei.sing.gc.execution.AbortException;
import es.uvigo.ei.sing.gc.execution.Subtask;
import es.uvigo.ei.sing.gc.execution.Task;
import es.uvigo.ei.sing.gc.model.entities.Committee;
import es.uvigo.ei.sing.gc.model.entities.RankedGene;
import es.uvigo.ei.sing.gc.utils.HibernateUtil;

final class SelectGenesSubtask implements Subtask<Set<RankedGene>> {
    private final FeatureSelector fs;
    private final Integer committeeId;
    private Task<Set<RankedGene>> task;
    private boolean aborted;

    public SelectGenesSubtask(FeatureSelector fs, int committeeId) {
        this.fs = fs;
        this.committeeId = committeeId;
    }

    @Override
    public Set<RankedGene> call() throws Exception {
        try {
            if (this.aborted)
                throw new AbortException();

            final FeatureSelectionResults fsResults = fs.obtainFeatureSelection();
            final List<Variable> selectedVariables = fsResults.getSelectedVariables();
            final List<Double> ranking = fsResults.getRanking();

            final Session session = HibernateUtil.getSessionFactory().openSession();
            session.beginTransaction();
            final Set<RankedGene> genes = new HashSet<RankedGene>();

            int i = 0;
            for (Variable selectedVariable : selectedVariables) {
                if (this.aborted)
                    throw new AbortException();
                final RankedGene gene = new RankedGene(i + 1, selectedVariable.getName(), ranking.get(i++));
                session.persist(gene);
                session.flush();
                genes.add(gene);
            }

            if (this.aborted)
                throw new AbortException();

            final Committee committee = (Committee) session.get(Committee.class, committeeId);

            committee.getRankedGenes().clear();
            committee.getRankedGenes().addAll(genes);
            session.update(committee);

            session.getTransaction().commit();
            session.close();
            return committee.getRankedGenes();
        } catch (Exception e) {
            e.printStackTrace();
            throw e;
        }
    }

    @Override
    public void abort() {
        this.aborted = true;
    }

    @Override
    public Task<Set<RankedGene>> getTask() {
        return this.task;
    }

    @Override
    public void setTask(Task<Set<RankedGene>> task) {
        this.task = task;
    }
}