module.script.TransferFromEpimedProd.java Source code

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Here is the source code for module.script.TransferFromEpimedProd.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 TransferFromEpimedProd extends BaseModule {

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

        // ===== 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 * from epimed_prod.view_exp_group order by main_gse_number, id_sample";
        List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

        String[] commonAttributes = { "pathology", "tnm_stage", "id_topology_group", "histology_subtype",
                "tissue_stage", "dead", "dfs_months", "age_max", "morphology", "id_tissue_stage", "topology", "sex",
                "age_min", "m", "topology_group", "n", "t", "collection_method", "id_morphology", "relapsed",
                "histology_type", "os_months", "id_topology" };

        List<ClPathology> listPathology = session.createCriteria(ClPathology.class).list();
        Map<String, ClPathology> mapPathology = new HashMap<String, ClPathology>();
        for (ClPathology p : listPathology) {
            mapPathology.put(p.getName(), p);
        }

        List<ClTissueStatus> listTissueStatus = session.createCriteria(ClTissueStatus.class).list();
        Map<Integer, ClTissueStatus> mapTissueStatus = new HashMap<Integer, ClTissueStatus>();
        for (ClTissueStatus t : listTissueStatus) {
            mapTissueStatus.put(t.getIdTissueStatus(), t);
        }

        System.out.println(listTissueStatus);

        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");
                for (int j = 0; j < commonAttributes.length; j++) {
                    String attr = commonAttributes[j];
                    expGroup.put(attr, map.get(attr));
                }

                // Treatment
                expGroup.put("treatment", map.get("treatment_type"));

                // Pathology
                String pathoString = (String) map.get("pathology");
                ClPathology pathology = mapPathology.get(pathoString);
                if (pathology != null) {
                    expGroup.put("id_pathology", pathology.getIdPathology());
                    expGroup.put("pathology", pathology.getName());
                }

                // Tissue status
                Integer idTissueStatus = (Integer) map.get("id_tissue_status");
                if (idTissueStatus != null && idTissueStatus > 3) {
                    idTissueStatus = 3;
                }
                ClTissueStatus tissueStatus = mapTissueStatus.get(idTissueStatus);
                if (tissueStatus != null) {
                    expGroup.put("id_tissue_status", tissueStatus.getIdTissueStatus());
                    expGroup.put("tissue_status", tissueStatus.getName());
                }

                System.out.println("idTissueStatus=" + tissueStatus + ", pathology=" + pathology);
                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 TransferFromEpimedProd();
    }

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

}