module.UpdateTissueStatus.java Source code

Introduction

Here is the source code for module.UpdateTissueStatus.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 com.mongodb.MongoClient;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Filters;

import config.MongoUtil;

public class UpdateTissueStatus extends BaseModule {

    public UpdateTissueStatus() {

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

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

        List<Document> samples = collectionSample.find().into(new ArrayList<Document>());
        ;

        for (Document sample : samples) {

            Document expgroup = sample.get("exp_group", Document.class);
            Integer idTissueStatus = expgroup.getInteger("id_tissue_status");
            if (idTissueStatus != null) {
                if (idTissueStatus.equals(1)) {
                    expgroup.put("tissue_status", "normal");
                }
                if (idTissueStatus.equals(2)) {
                    expgroup.put("tissue_status", "pathological_non_tumoral");
                }
                if (idTissueStatus.equals(3)) {
                    expgroup.put("tissue_status", "tumoral");
                }

                sample.put("exp_group", expgroup);

                System.out.println(sample.get("exp_group", Document.class));

                collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")),
                        new Document("$set", sample));

            }

        }

        mongoClient.close();

    }

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

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

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

}