module.script.ImportSupplementaryGSE20711.java Source code

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Here is the source code for module.script.ImportSupplementaryGSE20711.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.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;
import service.ExcelService;

public class ImportSupplementaryGSE20711 extends BaseModule {

    public ImportSupplementaryGSE20711() {

        // ===== 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");

        // ===== Excel data loader =====

        String inputfile = this.getInputDirectory() + this.getDirSeparator() + "GSE20711_emmm0003-0726-SD2.xlsx";
        System.out.println("LOADING \t " + inputfile);
        ExcelService excelService = new ExcelService();
        excelService.load(inputfile);

        String gseNumber = "GSE20711";

        for (int i = 0; i < excelService.getData().size(); i++) {
            List<Object> dataLine = excelService.getData().get(i);

            String bcString = (String) dataLine.get(0);
            bcString = bcString.replaceAll("BC", "");

            Integer bcNumber = Integer.parseInt(bcString);

            Document docSample = collection
                    .find(Filters
                            .and(Filters.in("series", gseNumber),
                                    Filters.eq("exp_group.sample_title",
                                            "Breast tumor from patient P_" + bcNumber + " (expression data)")))
                    .first();

            System.out.println("-------------------------------------------");
            System.out.println(dataLine);
            System.out.println(docSample);

        }

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

        mongoClient.close();
    }

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

    public static void main(String[] args) {
        new ImportSupplementaryGSE20711();
    }

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

}