module.script.TransferBrbAnnotations.java Source code

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Here is the source code for module.script.TransferBrbAnnotations.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;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.bson.Document;
import org.hibernate.Criteria;
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 com.mongodb.client.result.UpdateResult;

import config.HibernateUtil;
import config.MongoUtil;
import model.entity.ClPathology;
import model.entity.ClTissueStatus;
import module.BaseModule;

public class TransferBrbAnnotations extends BaseModule {

    @SuppressWarnings({ "unused", "unchecked" })
    public TransferBrbAnnotations() {

        // ===== 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, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
                + "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
                + "where exposed=true group by id_sample";

        List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

        for (Object item : list) {

            Map<String, Object> map = (HashMap<String, Object>) item;

            String gsmNumber = (String) map.get("id_sample");
            String gseNumber = (String) map.get("main_gse_number");

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

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

            if (doc != null) {
                Document expGroup = (Document) doc.get("exp_group");
                expGroup.put("exposure", map.get("list_substances"));
                System.out.println(expGroup);

                // Update Mongo document
                doc.put("exp_group", expGroup);
                doc.put("analyzed", true);
                UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                        new Document("$set", doc));
            }

        }

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

        mongoClient.close();
    }

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

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

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

}