module.ImportPlatform.java Source code

Introduction

Here is the source code for module.ImportPlatform.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;

import java.util.ArrayList;
import java.util.Date;
import java.util.List;

import org.bson.Document;

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.MongoUtil;
import model.bind.NcbiGeoGpl;
import service.MongoService;
import service.WebService;

public class ImportPlatform {

    private WebService webService = new WebService();
    private MongoService mongoService = new MongoService();
    private Date today = new Date();

    public ImportPlatform() {

        // ===== Connection =====

        MongoClient mongoClient = MongoUtil.buildMongoClient();
        MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
        MongoCollection<Document> collectionPlatforms = db.getCollection("platforms");
        MongoCollection<Document> collectionSamples = db.getCollection("samples");
        MongoCollection<Document> collectionSeries = db.getCollection("series");

        // ===== Platforms =====

        List<String> listGpl = collectionSamples.distinct("exp_group.id_platform", String.class)
                .into(new ArrayList<String>());

        for (String idPlatform : listGpl) {
            Document doc = collectionPlatforms.find(Filters.in("_id", idPlatform)).first();
            if (doc.getString("type") == null) {
                System.out.println(idPlatform + ": " + doc);
            }
        }

        mongoClient.close();
    }

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

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

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

}