module.ImportGeo.java Source code

Introduction

Here is the source code for module.ImportGeo.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 static com.mongodb.client.model.Filters.eq;

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 model.bind.NcbiGeoGpl;
import model.bind.NcbiGeoGse;
import model.bind.NcbiGeoGsm;
import service.MongoService;
import service.WebService;

public class ImportGeo {

    private String[] listGseNumber = { "GSE45484" };

    private WebService webService = new WebService();
    private MongoService mongoService = new MongoService();

    public ImportGeo() {

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

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

        // ===== Insert data =====

        for (int k = 0; k < listGseNumber.length; k++) {

            String gseNumber = listGseNumber[k];

            System.out.println("------------------------------------------");
            System.out.println(k + " Import " + gseNumber);

            // ===== Load GSE =====

            NcbiGeoGse gse = new NcbiGeoGse(webService.loadGeo(gseNumber));
            System.out.println(gse);

            // ===== Series =====

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

            Document docSeries = mongoService.createSeries(gse.getGseNumber(), gse.getTitle(), gse.getListGpl(),
                    gse.getSubmissionDate(), gse.getLastUpdate());

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

            // ===== Platforms =====

            MongoCollection<Document> collectionPlatforms = db.getCollection("platform");

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

                NcbiGeoGpl gpl = new NcbiGeoGpl(webService.loadGeo(gse.getListGpl().get(i)));

                System.out.println("\t Import platform " + gpl.getGplNumber());

                Document docPlatforms = mongoService.createPlatform(gpl.getGplNumber(), gpl.getTitle(),
                        gpl.getTaxid(), gpl.getOrganism(), gpl.getManufacturer(), gpl.getSubmissionDate(),
                        gpl.getLastUpdate(), gpl.getTechnology());

                UpdateResult res = collectionPlatforms.updateOne(Filters.eq("_id", gpl.getGplNumber()),
                        new Document("$set", docPlatforms));
                if (res.getMatchedCount() == 0) {
                    collectionPlatforms.insertOne(docPlatforms);
                }
            }

            // ===== Samples ======

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

            // for (int i=0; i<1; i++) {
            for (int i = 0; i < gse.getListGsm().size(); i++) {

                NcbiGeoGsm gsm = new NcbiGeoGsm(webService.loadGeo(gse.getListGsm().get(i)));

                Document docSampleExist = collectionSamples.find(Filters.eq("_id", gsm.getGsmNumber())).first();
                boolean docAlreadyExist = docSampleExist != null;

                boolean analysed = false;

                if (docAlreadyExist) {
                    analysed = (Boolean) docSampleExist.get("analyzed");
                    System.out.println(i + "/" + gse.getListGsm().size() + "\t " + gse.getGseNumber() + "\t "
                            + gsm.getGsmNumber() + ":  already exists in the database, analyzed=" + analysed);
                } else {
                    System.out.println(i + "/" + gse.getListGsm().size() + "\t " + gse.getGseNumber() + "\t "
                            + gsm.getGsmNumber());
                }

                // ===== Sample Document =====

                Document docSample = mongoService.createSample(gsm.getGsmNumber(), gse.getGseNumber(),
                        gsm.getListGse(), gsm.getOrganism(), gsm.getSubmissionDate(), gsm.getLastUpdate(),
                        analysed);

                // ===== Mandatory parameters =====

                // Preserve "exp_group" if the document exists already

                Document expGroup = null;
                if (docAlreadyExist) {
                    expGroup = (Document) docSampleExist.get("exp_group");
                } else {
                    expGroup = mongoService.createExpGroup(docSample, gsm.getGplNumber(), gsm.getTitle(),
                            gsm.getSourceName(), gsm.getOrganism());

                }
                docSample.append("exp_group", expGroup);

                // ===== Supplementary parameters =====

                Document parameters = generateParameters(gsm);
                docSample.append("parameters", parameters);

                // === Delete if already exist ===
                collectionSamples.deleteOne(eq("_id", gsm.getGsmNumber()));

                // ===== Insert data =====
                collectionSamples.insertOne(docSample);

            }

        }

        mongoClient.close();
    }

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

    public Document generateParameters(NcbiGeoGsm gsm) {
        Document parameters = new Document();
        parameters.append("id_sample", gsm.getGsmNumber());
        mongoService.append(parameters, gsm.getDescription());
        mongoService.append(parameters, gsm.getListCharacteristics());
        // parameters.append("extract_protocol", gsm.getExtractProtocol())
        ;
        return parameters;
    }

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

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

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

}