module.CreateStudy.java Source code

Introduction

Here is the source code for module.CreateStudy.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.Date;
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 com.mongodb.client.result.UpdateResult;

import config.MongoUtil;
import service.ExcelService;

public class CreateStudy extends BaseModule {

    private Date today = new Date();
    private Set<String> setGpl = new HashSet<String>();

    @SuppressWarnings("unchecked")
    public CreateStudy() {

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

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

        // === Excel data loader ===

        String inputfile = this.getInputDirectory() + this.getDirSeparator() + "prolung2_expgrp4.xlsx";
        System.out.println("LOADING \t " + inputfile);
        ExcelService excelService = new ExcelService();
        excelService.load(inputfile);
        List<Object> listCel = excelService.extractColumn(0);

        Integer indCel = excelService.getHeaderMap().get("gse8894_sample_cel");

        // ===  New Series === 
        MongoCollection<Document> collectionSeries = db.getCollection("series");
        Document docSeries = new Document();
        docSeries.append("_id", "PROLUNG").append("title", "Lung cancerous and non-cancerous samples")
                .append("platforms", null).append("submission_date", today).append("last_update", today)
                .append("import_date", today);

        UpdateResult updateResult = collectionSeries.updateOne(Filters.eq("_id", docSeries.get("_id")),
                new Document("$set", docSeries));
        if (updateResult.getMatchedCount() == 0) {
            collectionSeries.insertOne(docSeries);
        }

        // === Add samples to new series ===
        MongoCollection<Document> collectionSamples = db.getCollection("samples");
        for (int i = 0; i < listCel.size(); i++) {

            String gsm = this.getGsm(listCel.get(i));

            Document docSample = collectionSamples.find(Filters.eq("_id", gsm)).first();

            if (docSample == null) {
                System.err.println("ERROR! Sample " + gsm + "doesn't exist. Try another column.");

                gsm = this.getGsm(excelService.getData().get(i).get(indCel));
                docSample = collectionSamples.find(Filters.eq("_id", gsm)).first();

                if (docSample == null) {
                    System.err.println("ERROR! Sample " + gsm + " doesn't exist. Exit.");
                    System.exit(0);
                } else {
                    System.err.println("Found " + gsm);
                }
            }

            Document expGroup = (Document) docSample.get("exp_group");
            setGpl.add(expGroup.get("id_platform").toString());

            List<String> listSeries = (List<String>) docSample.get("series");
            listSeries.add(docSeries.getString("_id"));
            docSample.put("series", listSeries);

            System.out.println(docSample);
            // updateResult = collectionSamples.updateOne(Filters.eq("_id", docSample.get("_id")), new Document("$set", docSample));
        }

        // === Update platforms of the series ===

        System.out.println(setGpl);

        docSeries.put("platforms", setGpl);
        updateResult = collectionSeries.updateOne(Filters.eq("_id", docSeries.get("_id")),
                new Document("$set", docSeries));
        if (updateResult.getMatchedCount() == 0) {
            collectionSeries.insertOne(docSeries);
        }

    }

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

    private String getGsm(Object obj) {
        String cel = obj.toString();
        String gsm = cel.toString().trim();
        if (gsm.contains(".") || gsm.contains("_")) {
            gsm = gsm.split("[\\._]")[0];
        }
        return gsm;
    }

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

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

    /** ============================================================== */
}