module.test.ImportProbesets.java Source code

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Here is the source code for module.test.ImportProbesets.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.test;

import java.util.List;

import org.bson.Document;
import org.hibernate.Session;
import org.hibernate.SessionFactory;

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

import config.HibernateUtil;
import config.MongoUtil;
import module.BaseModule;
import service.FileService;
import service.FormatService;
import service.MongoService;

public class ImportProbesets extends BaseModule {

    private MongoService mongoService = new MongoService();
    private FileService fileService = new FileService();
    private FormatService formatService = new FormatService();

    public ImportProbesets() {

        // === Display ===
        System.out.println("\n================ BEGIN Module " + this.getClass().getName() + "================");

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

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

        // ===== Session PostgreSQL =====
        SessionFactory sessionFactory = HibernateUtil
                .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
        Session session = sessionFactory.openSession();

        String idPlatform = "GPL570";
        String gpl = idPlatform.toLowerCase();

        // ===== Load file =====

        String inputfile = this.getInputDirectory() + this.getDirSeparator() + "HG-U133_Plus_2.na36.annot.csv";

        System.out.println("ID Platform " + gpl);
        System.out.println("LOADING \t " + inputfile);
        System.out.println("Please wait... ");
        List<String> listRows = fileService.loadTextFile(inputfile);
        System.out.println("File sucessfully LOADED");

        // ===== Recognize header =====

        List<String> header = fileService.readHeader(listRows, "\",\"");
        System.out.println("Header " + header);
        List<List<String>> data = fileService.readData(listRows, "\",\"");
        System.out.println(
                "The data are sucessfully loaded: rows " + data.size() + ", columns " + data.get(0).size());

        Integer indProbeset = fileService.findIndex(header, "Probe Set ID");
        Integer indGenes = fileService.findIndex(header, "Entrez Gene");
        Integer indUnigenes = fileService.findIndex(header, "UniGene ID");
        Integer indTranscripts = fileService.findIndex(header, "RefSeq Transcript ID");
        Integer indGb = fileService.findIndex(header, "Representative Public ID");

        for (int i = 0; i < 5; i++) {
            List<String> dataline = data.get(i);

            String probeset = dataline.get(indProbeset);
            String genes = dataline.get(indGenes);
            String unigenes = dataline.get(indUnigenes);
            String transcripts = dataline.get(indTranscripts);
            String gb = dataline.get(indGb);

            System.out.println(probeset + "\t" + genes + "\t" + formatService.splitInArray(unigenes, "///") + "\t"
                    + gb + "\t" + transcripts);

            Document docProbeset = mongoService.createProbeset(idPlatform, probeset);
            docProbeset.put("genes", formatService.splitInArray(genes, "///"));
            docProbeset.put("unigenes", formatService.splitInArray(unigenes, "///"));

            List<String> listTranscripts = formatService.splitInArray(transcripts, "///");
            listTranscripts.addAll(formatService.splitInArray(gb, "///"));

            docProbeset.put("transcripts", listTranscripts);

            collectionProbesets.insertOne(docProbeset);

            /*
            for (int j=0; j<dataline.size(); j++) {
               String key = header.get(j);
               String value = dataline.get(j);
               System.out.println(key + ": " + value);
            }
            */
        }

        /*
        String tableProbe = "hs.om_probe_" + gpl;
        String tableGP = "hs.om_gp_" + gpl;
        List<Object []> listProbesets = session.createNativeQuery("select * from " + tableProbe + " order by id_probe").getResultList();
        for (int i=0; i<10; i++) {
            
           Object[] line = listProbesets.get(i);
            
           System.out.println(Arrays.toString(line));
           // Document docProbeset = mongoService.createProbeset(idPlatform, "1007_s_at");
           // collectionProbesets.insertOne(docProbeset);
        }
         */

        // === Close connections ===

        if (session.isOpen()) {
            session.close();
        }
        sessionFactory.close();
        mongoClient.close();

        // === Display ===
        System.out.println("================ END Module " + this.getClass().getName() + "================");

    }

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

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

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

}