module.ExportTissueOntology.java Source code

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Here is the source code for module.ExportTissueOntology.java

Source

/**
 * EpiMed - Information system for bioinformatics developments in the field of epigenetics
 * 
 * This software is a computer program which performs the data management 
 * for EpiMed platform of the Institute for Advances Biosciences (IAB)
 *
 * Copyright University of Grenoble Alps (UGA)
 * GNU GENERAL PUBLIC LICENSE
 * Please check LICENSE file
 *
 * Author: Ekaterina Bourova-Flin 
 *
 */
package module;

import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;

import org.hibernate.Session;
import org.hibernate.SessionFactory;

import config.HibernateUtil;
import dao.ClTopologyDao;
import model.entity.ClTopology;
import service.FileService;

public class ExportTissueOntology extends BaseModule {

    private FileService fileService = new FileService();
    private SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy.MM.dd");

    public ExportTissueOntology() {

        // === Output matrix ===
        List<Object> data = new ArrayList<Object>();
        List<String> header = new ArrayList<String>();
        header.add("id_topology");
        header.add("topology");
        header.add("id_topology_group");
        header.add("topology_group");

        // ===== Session PostgreSQL =====
        SessionFactory sessionFactory = HibernateUtil
                .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
        Session session = sessionFactory.openSession();

        // ===== Begin transaction =====
        session.beginTransaction();

        ClTopologyDao topologyDao = new ClTopologyDao(session);
        List<ClTopology> listTopologies = topologyDao.findAll();

        for (ClTopology t : listTopologies) {
            System.out.println(t);

            Object[] dataline = new Object[header.size()];

            int j = 0;
            dataline[j] = t.getIdTopology();
            dataline[++j] = t.getName();
            dataline[++j] = t.getClTopologyGroup().getIdGroup();
            dataline[++j] = t.getClTopologyGroup().getName();

            data.add(dataline);

            System.out.println(Arrays.toString(dataline));

        }

        // === Output  file ===

        String fileName = this.getOutputDirectory() + this.getDirSeparator() + "EpiMed_tissue_ontology" + "_"
                + dateFormat.format(new Date()) + ".xlsx";
        fileService.writeExcelFile(fileName, header, data);
        System.out.println(fileName);

        // === Commit transaction ===
        // session.getTransaction().commit();
        session.getTransaction().rollback();

        if (session.isOpen()) {
            session.close();
        }
        sessionFactory.close();

    }

    /** =============================================================== */

    public static void main(String[] args) {
        new ExportTissueOntology();
    }

    /** ============================================================== */

}