module.script.epimed_ontology.AddEpimedGroupToSamples.java Source code

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Here is the source code for module.script.epimed_ontology.AddEpimedGroupToSamples.java

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/**
 * 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.script.epimed_ontology;

import java.util.ArrayList;
import java.util.List;

import org.bson.Document;
import org.hibernate.Session;
import org.hibernate.SessionFactory;

import com.mongodb.MongoClient;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Filters;

import config.HibernateUtil;
import config.MongoUtil;
import dao.ClTopologyDao;
import model.entity.ClEpimedGroup;
import model.entity.ClTopology;

public class AddEpimedGroupToSamples {

    public AddEpimedGroupToSamples() {

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

        // ===== Session Mongo =====

        MongoClient mongoClient = MongoUtil.buildMongoClient();
        MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
        MongoCollection<Document> collectionSample = db.getCollection("sample");

        List<Document> samples = collectionSample.find().into(new ArrayList<Document>());

        for (int i = 0; i < samples.size(); i++) {
            Document sample = samples.get(i);
            Document expgroup = sample.get("exp_group", Document.class);

            String idTopology = expgroup.getString("id_topology");

            if (idTopology != null && !idTopology.isEmpty()) {

                ClTopology topology = topologyDao.find(idTopology);
                ClEpimedGroup grp1 = topology.getClEpimedGroup();
                ClEpimedGroup grp2 = grp1.getParent();
                ClEpimedGroup grp3 = grp2.getParent();
                expgroup.append("tissue_group_level1", grp1.getName());
                expgroup.append("tissue_group_level2", grp2.getName());
                expgroup.append("tissue_group_level3", grp3.getName());

                System.out.println((i + 1) + "/" + samples.size() + " " + expgroup);

                sample.append("exp_group", expgroup);
                collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")),
                        new Document("$set", sample));
            }

        }

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

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

        mongoClient.close();
    }

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

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

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

}