module.UpdateNumberSamples.java Source code

Introduction

Here is the source code for module.UpdateNumberSamples.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.List;

import org.bson.Document;
import org.bson.conversions.Bson;

import com.mongodb.MongoClient;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Filters;

import config.MongoUtil;

public class UpdateNumberSamples extends BaseModule {

    public UpdateNumberSamples() {

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

        MongoClient mongoClient = MongoUtil.buildMongoClient();
        MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

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

        // String [] listIdSeries = {"TISSUE_SPECIFIC_GENES_MM"};
        // List<Document> listSeries = collectionSeries.find(Filters.in("_id", listIdSeries)).into(new ArrayList<Document>());

        List<Document> listSeries = collectionSeries.find().into(new ArrayList<Document>());

        for (Document ser : listSeries) {
            System.out.println(ser);

            String idSeries = ser.getString("_id");
            Bson filter = Filters.in("series", idSeries);

            Long nbSamples = collectionSamples.count(filter);

            System.out.println(idSeries + " " + nbSamples);

            ser.append("nb_samples", nbSamples);
            collectionSeries.updateOne(Filters.eq("_id", idSeries), new Document("$set", ser));

        }

        mongoClient.close();

    }

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

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

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

}