module.script.emtab365.UpdateSamplesEMTAB365.java Source code

Introduction

Here is the source code for module.script.emtab365.UpdateSamplesEMTAB365.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.script.emtab365;

import java.util.ArrayList;
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;

public class UpdateSamplesEMTAB365 extends BaseModule {

    private String gseNumber = "E-MTAB-365";
    private boolean commit = true;

    public UpdateSamplesEMTAB365() {

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

        // ===== INIT =====

        ClMorphology ductal = session.get(ClMorphology.class, "8500/3"); // 8500/3   Infiltrating duct carcinoma, NOS (C50._)
        ClMorphology lobular = session.get(ClMorphology.class, "8520/3"); // 8520/3   Lobular carcinoma, NOS (C50._)
        ClMorphology morphology = session.get(ClMorphology.class, "8010/3"); // Carcinoma

        ClTopology breast = session.get(ClTopology.class, "C50.9"); // Breast
        ClTopology blood = session.get(ClTopology.class, "C42.0"); // Blood
        ClTopology lymphNode = session.get(ClTopology.class, "C77.9"); // Lymph node

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

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

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

        List<Document> listDocuments = collection.find(Filters.in("series", gseNumber))
                .into(new ArrayList<Document>());

        for (int i = 0; i < listDocuments.size(); i++) {
            Document doc = listDocuments.get(i);
            Document expgroup = (Document) doc.get("exp_group");
            Document parameters = (Document) doc.get("parameters");

            String histoType = parameters.getString("Histology");
            String histoSubtype = parameters.getString("CIT classification");

            expgroup.put("histology_subtype", histoSubtype);

            if (histoType != null && histoType.toLowerCase().equals("lobular")) {
                morphology = lobular;
            }
            if (histoType != null && histoType.toLowerCase().equals("ductal")) {
                morphology = ductal;
            }

            expgroup.put("id_morphology", morphology.getIdMorphology());
            expgroup.put("morphology", morphology.getName());

            expgroup.put("sample_source", parameters.getString("Source Name"));

            String organismPart = parameters.getString("OrgansimPart");

            ClTopology topology = null;
            if (organismPart != null) {

                if (organismPart.toLowerCase().contains("breast")) {
                    topology = breast;
                }

                if (organismPart.toLowerCase().contains("blood")) {
                    topology = blood;
                }
                if (organismPart.toLowerCase().contains("lymph")) {
                    topology = lymphNode;
                }

            } else {
                topology = breast;
            }

            expgroup.put("id_topology", topology.getIdTopology());
            expgroup.put("topology", topology.getName());
            expgroup.put("id_topology_group", topology.getClTopologyGroup().getIdGroup());
            expgroup.put("topology_group", topology.getClTopologyGroup().getName());

            // ==== Survival =====

            Object dfs_months = parameters.get("Delay Metastasis Free Survival months");
            if (dfs_months != null) {
                expgroup.put("dfs_months", dfs_months);
            }

            Object os_months = parameters.get("Delay Overall Survival months");
            if (os_months != null) {
                expgroup.put("os_months", os_months);
            }

            Double os = (Double) expgroup.get("os_months");
            Double dfs = (Double) expgroup.get("dfs_months");
            if (os != null && dfs != null && dfs.equals(os)) {
                expgroup.put("relapsed", false);
            }

            if (os != null && dfs != null && dfs < os) {
                expgroup.put("relapsed", true);
            }

            if (os != null && dfs != null && dfs > os) {
                expgroup.put("relapsed", null);
            }

            Object relapseDate = parameters.get("Relapse  Metastasis Date");
            if (relapseDate != null) {
                expgroup.put("relapsed", true);
            }

            // ==== Grade ====
            expgroup.put("tnm_grade", parameters.get("Grade  Scarff Bloom Richardson"));

            // ==== Files =====

            expgroup.put("ftp", parameters.getString("ArrayExpress FTP file"));
            expgroup.put("file_name", parameters.getString("Array Data File"));

            expgroup.remove("individual");
            if (parameters.getString("Individual") != null) {
                expgroup.put("individual", parameters.getString("Individual"));
            }

            // ==== Biomarkers ====
            /*
            String p53 = parameters.getString("Phenotype - TP53  Gene mutation  Status");
            expgroup.put("p53", value)
                
            String pr = parameters.getString("PGR  Protein expression");
            String er = parameters.getString("ESR1  Protein expression");
            String her2 = parameters.getString("ERBB2  Protein expression");
             */

            doc.put("exp_group", expgroup);

            System.out.println(i + " " + doc.get("_id") + " " + doc.get("analyzed") + " " + expgroup);

            if (commit) {
                UpdateResult updateResult = collection.updateOne(Filters.eq("_id", doc.get("_id")),
                        new Document("$set", doc));
            }
        }

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

        mongoClient.close();
    }

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

    public static void main(String[] args) {
        new UpdateSamplesEMTAB365();
    }

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

}