module.script.pro12.TransferPro12.java Source code

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Here is the source code for module.script.pro12.TransferPro12.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.pro12;

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 module.BaseModule;

public class TransferPro12 extends BaseModule {

    @SuppressWarnings({ "unchecked" })
    public TransferPro12() {

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

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

        MongoClient mongoClient = MongoUtil.buildMongoClient();
        MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

        MongoCollection<Document> collection = db.getCollection("samples");

        String sql = "select id_sample from epimed_prod.om_sample join epimed_prod.om_sample_series using (id_sample) "
                + "join epimed_prod.om_series using (id_series) where id_series='PRO12'";

        List<String> list = session.createSQLQuery(sql).list();

        Document pro12 = new Document();
        pro12.append("series", "PRO12");

        for (String gsmNumber : list) {

            Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

            System.out.println("-----------------------------");
            System.out.println(gsmNumber + " " + doc);

            if (doc != null) {
                // Update Mongo document
                collection.updateOne(Filters.eq("_id", gsmNumber), new Document("$push", pro12));
            }

        }

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

        mongoClient.close();
    }

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

    public static void main(String[] args) {
        new TransferPro12();
    }

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

}