module.script.proallchen.CreateProallChen.java Source code

Introduction

Here is the source code for module.script.proallchen.CreateProallChen.java

Source

/**
 * 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.proallchen;

import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;

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 config.HibernateUtil;
import config.MongoUtil;
import module.BaseModule;

public class CreateProallChen extends BaseModule {

    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");

    public CreateProallChen() {

        // ===== 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");
        // MongoDatabase db = mongoClient.getDatabase("geo");

        MongoCollection<Document> collectionSeries = db.getCollection("series");

        Date submissionDate = null;
        try {
            submissionDate = dateFormat.parse("2016-05-13");
        } catch (ParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

        // List<String> platforms = new ArrayList<String>();
        // platforms.add("GPL570");

        Document docSeries = new Document();
        docSeries.append("_id", "PROALL_CHEN")
                .append("title", "Genomic Profiling of Adult and Pediatric B-cell Acute Lymphoblastic Leukemia")
                .append("platforms", null).append("submission_date", submissionDate)
                .append("last_update", submissionDate).append("import_date", new Date());

        System.out.println(docSeries);
        collectionSeries.insertOne(docSeries);

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

        mongoClient.close();
    }

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

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

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

}