module.script.AddSeriesToSamples.java Source code

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Here is the source code for module.script.AddSeriesToSamples.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.script;

import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

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;
import module.BaseModule;
import service.FormatService;

public class AddSeriesToSamples extends BaseModule {

    public AddSeriesToSamples() {

        // ===== Service =====
        FormatService formatService = new FormatService();

        // ===== Session Mongo =====

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

        Set<String> setProjects = new HashSet<String>();

        MongoCollection<Document> collection = db.getCollection("sample");

        Bson filters = Filters.and(Filters.in("series", "PRJNA270632"));

        List<Document> listDocuments = collection.find(filters).into(new ArrayList<Document>());

        for (int i = 0; i < listDocuments.size(); i++) {

            Document doc = listDocuments.get(i);
            Document expgroup = doc.get("exp_group", Document.class);

            if (expgroup.get("exp_Mcount") != null) {

                List<String> projects = doc.get("series", ArrayList.class);
                setProjects.clear();
                setProjects.addAll(projects);
                setProjects.add("TISSUE_SPECIFIC_GENES_HS");
                doc.put("series", setProjects);
                System.out.println(doc.getString("_id") + " " + projects + " -> " + setProjects);

                collection.updateOne(Filters.eq("_id", doc.getString("_id")), new Document("$set", doc));
            }

        }

        mongoClient.close();
    }

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

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

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

    public void display(List<Document> list) {

        for (Document document : list) {
            System.out.println(document);
        }
    }

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

    public void displayMatrix(List<Object> list) {
        for (Object item : list) {
            Object[] line = (Object[]) item;
            System.out.println(Arrays.toString(line));
        }
    }

}