module.script.epimed_ontology.UpdateFetalAdultOvary.java Source code

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Here is the source code for module.script.epimed_ontology.UpdateFetalAdultOvary.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.bson.conversions.Bson;
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.ClTopology;

public class UpdateFetalAdultOvary {

    public UpdateFetalAdultOvary() {

        // ===== Session PostgreSQL =====
        SessionFactory sessionFactory = HibernateUtil
                .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
        Session session = sessionFactory.openSession();
        ClTopologyDao topologyDao = new ClTopologyDao(session);
        ClTopology adultOvary = topologyDao.find("C56.9");
        ClTopology fetalOvary = topologyDao.find("E56.9");

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

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

        Bson filters = Filters.and(Filters.eq("exp_group.id_topology", "C56.9"), // ovary
                Filters.eq("exp_group.id_tissue_stage", 1) // adult
        );

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

        for (Document sample : samples) {
            Document expgroup = sample.get("exp_group", Document.class);
            expgroup.append("id_topology", adultOvary.getIdTopology());
            expgroup.append("topology", adultOvary.getName());
            sample.append("exp_group", expgroup);
            collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")), new Document("$set", sample));
        }
        System.out.println(samples.size());

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

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

        mongoClient.close();
    }

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

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

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

}