module.script.probcp.UpdateSamplesProbcp.java Source code

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Here is the source code for module.script.probcp.UpdateSamplesProbcp.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.probcp;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
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 com.mongodb.client.model.Filters;
import com.mongodb.client.result.UpdateResult;

import config.HibernateUtil;
import config.MongoUtil;
import model.entity.ClMorphology;
import model.entity.ClTopology;
import module.BaseModule;

@SuppressWarnings("unchecked")
public class UpdateSamplesProbcp extends BaseModule {

    private Date today = new Date();

    public UpdateSamplesProbcp() {

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

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

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

        String[] studies = { "tya16" };
        List<String> series = new ArrayList<String>();

        for (int l = 0; l < studies.length; l++) {

            String idStudy = studies[l];
            String studyName = idStudy.toUpperCase();

            series.clear();
            series.add(studyName);
            series.add("PROBCP");

            String sql = "select * from st_bcp." + idStudy + "_sample order by id_sample";

            List<Object> listSamples = session.createSQLQuery(sql).list();

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

                Object[] lineSample = (Object[]) listSamples.get(i);

                String idSample = (String) lineSample[0];
                String clinicalClassification = (String) lineSample[1];
                String tnmStage = (String) lineSample[2];
                Integer grade = (Integer) lineSample[3];
                String type = (String) lineSample[4];

                System.out.println(Arrays.toString(lineSample));

                String id = studyName + "_" + idSample;

                Document docSample = collectionSamples.find(Filters.eq("_id", id)).first();
                Document expgroup = (Document) docSample.get("exp_group");
                expgroup.append("tnm_grade", grade);
                expgroup.append("tnm_stage", null);
                docSample.append("exp_group", expgroup);

                UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", id),
                        new Document("$set", docSample));

                System.out.println(docSample);

            }

        }

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

        mongoClient.close();

    }

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

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

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

    public Document generateExpGroup(String idSample, String mainGse, String tnmStage, Integer grade, String type,
            String collectionMethod, ClTopology topology, ClMorphology morphology) {

        Document expGroup = new Document();

        expGroup.append("id_sample", idSample).append("main_gse_number", mainGse)
                .append("id_platform", "proteomics").append("sample_title", null).append("sample_source", null)
                .append("sex", null).append("ethnic_group", null).append("age_min", null).append("age_max", null)
                .append("id_tissue_stage", 1).append("tissue_stage", "adult").append("id_tissue_status", 3)
                .append("tissue_status", "Pathological tumoral").append("id_pathology", "C80.9")
                .append("pathology", "Cancer").append("collection_method", collectionMethod)
                .append("id_topology", topology.getIdTopology()).append("topology", topology.getName())
                .append("id_topology_group", topology.getClTopologyGroup().getIdGroup())
                .append("topology_group", topology.getClTopologyGroup().getName())
                .append("id_morphology", morphology.getIdMorphology()).append("morphology", morphology.getName())
                .append("histology_type", type).append("histology_subtype", null).append("t", null)
                .append("n", null).append("m", null).append("tnm_stage", tnmStage).append("tnm_grade", grade)
                .append("dfs_months", null).append("os_months", null).append("relapsed", null).append("dead", null)
                .append("treatment", null).append("exposure", null);

        return expGroup;
    }

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

    public Document generateParameters(String idSample) {
        Document parameters = new Document();
        parameters.append("id_sample", idSample);
        ;
        return parameters;
    }

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

}