module.script.ImportSupplementaryGSE25219.java Source code

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Here is the source code for module.script.ImportSupplementaryGSE25219.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;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.bson.Document;
import org.hibernate.Criteria;
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.ClPathology;
import model.entity.ClTissueStatus;
import module.BaseModule;
import service.ExcelService;

public class ImportSupplementaryGSE25219 extends BaseModule {

    @SuppressWarnings({ "unused", "unchecked" })
    public ImportSupplementaryGSE25219() {

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

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

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

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

        // ===== Excel data loader =====

        String inputfile = this.getInputDirectory() + this.getDirSeparator() + "NIHMS321722-supplement-7.xlsx";
        System.out.println("LOADING \t " + inputfile);
        ExcelService excelService = new ExcelService();
        excelService.load(inputfile);

        // ===== Format raw data into data structures ======

        List<Map<String, String>> listMap = new ArrayList<Map<String, String>>();
        List<String> headerMap = new ArrayList<String>();
        Map<String, String> mapBrain = new HashMap<String, String>();

        for (int i = 0; i < excelService.getData().size(); i++) {
            List<Object> dataLine = excelService.getData().get(i);

            String brainCode = (String) dataLine.get(0);
            if (brainCode != null) {
                mapBrain = new HashMap<String, String>();
            }

            // Existing brain code
            if (dataLine != null && dataLine.size() > 2 && dataLine.get(1) != null && dataLine.get(2) != null) {
                // System.out.println(dataLine.get(1) + " = " + dataLine.get(2));
                mapBrain.put(dataLine.get(1).toString().trim(), dataLine.get(2).toString().trim());
            }

            if (brainCode != null) {
                // New Brain code

                // System.out.println("brain code " + brainCode);
                headerMap.add(brainCode);
                listMap.add(mapBrain);
            }
        }

        // ===== Recognize data =====

        for (int i = 0; i < headerMap.size(); i++) {
            System.out.println("----------------------------");
            String code = headerMap.get(i);
            System.out.println(i + " " + code);
            Map<String, String> map = listMap.get(i);

            Map<String, String> updatedMap = new HashMap<String, String>();

            for (Map.Entry<String, String> entry : map.entrySet()) {
                String key = entry.getKey();
                String value = entry.getValue();

                if (!key.toLowerCase().equals("age")
                        // && !key.toLowerCase().equals("ethnicity")
                        // && !key.toLowerCase().equals("sex")
                        && !value.toLowerCase().equals("no data")) {
                    updatedMap.put(key, value);
                }

                // System.out.println(key + " -> " + value);
            }

            List<Document> listDocuments = collection
                    .find(Filters.and(Filters.eq("exp_group.main_gse_number", "GSE25219"),
                            Filters.eq("parameters.brain code", code)))
                    .into(new ArrayList<Document>());
            System.out.println("Number of corresponding Mongo documents " + listDocuments.size());
            System.out.println(updatedMap);

            for (int j = 0; j < listDocuments.size(); j++) {
                Document doc = listDocuments.get(j);

                Document parameters = (Document) doc.get("parameters");
                parameters.putAll(updatedMap);
                System.out.println("\t" + parameters);

                // Update Mongo document
                doc.put("parameters", parameters);
                doc.put("analyzed", true);
                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 ImportSupplementaryGSE25219();
    }

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

}