module.test.SearchSeries.java Source code

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Here is the source code for module.test.SearchSeries.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.test;

import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

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 config.MongoUtil;
import module.BaseModule;

public class SearchSeries extends BaseModule {

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

    public SearchSeries() throws ParseException {

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

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

        String[] listSeries = { "E-MTAB-365", "GSE3156", "GSE3744", "GSE4922", "GSE5764", "GSE6367", "GSE6883",
                "GSE8977", "GSE9014", "GSE9195", "GSE10885", "GSE11078", "GSE11352", "GSE12080", "GSE12237",
                "GSE12276", "GSE14017", "GSE16391", "GSE17215", "GSE17907", "GSE19615", "GSE21653", "GSE28681",
                "GSE38867" };

        List<Document> list = collectionSamples.find(Filters.in("_id", listSeries)).into(new ArrayList<Document>());

        Set<String> setGse = new HashSet<String>();
        List<String> listGse = new ArrayList<String>();
        for (int i = 0; i < list.size(); i++) {
            Document doc = list.get(i);
            setGse.add(doc.getString("_id"));
        }
        listGse.addAll(setGse);
        Collections.sort(listGse);

        System.out.println("Found " + list.size() + " samples");
        System.out.println("List GSE " + listGse);

        mongoClient.close();

    }

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

    public static void main(String[] args) {
        try {
            new SearchSeries();
        } catch (ParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }

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

}