module.test.CustomExport.java Source code

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Here is the source code for module.test.CustomExport.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.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import org.bson.Document;
import org.bson.conversions.Bson;

import com.mongodb.MongoClient;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Projections;

import config.MongoUtil;
import module.BaseModule;
import service.FileService;

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

    private FileService fileService = new FileService();
    private SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy.MM.dd");

    public CustomExport() {

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

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

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

        // ===== Find exp_group in the database =====

        // === Query 1 ===
        /*
        String queryName = "breast_cancer_GPL570";
        List<Bson> filters = new ArrayList<Bson>();
        filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
        filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
        filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral
         */

        // === Query 2 ===
        /*
        String queryName = "breast_normal_GPL570";
        List<Bson> filters = new ArrayList<Bson>();
        filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
        filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
        filters.add(Filters.eq("exp_group.id_tissue_status", 1)); // normal
        */

        // === Query 3 ===
        String queryName = "breast_cancer_with_survival_GPL570";
        List<Bson> filters = new ArrayList<Bson>();
        filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
        filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
        filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral
        filters.add(Filters.or(Filters.ne("exp_group.os_months", null), Filters.ne("exp_group.dfss_months", null),
                Filters.ne("exp_group.relapsed", null), Filters.ne("exp_group.dead", null)));

        Bson filter = Filters.and(filters);
        Long nbSamples = collection.count(filter);
        List<String> listSeries = collection.distinct("exp_group.main_gse_number", filter, String.class)
                .into(new ArrayList<String>());
        queryName = queryName + "_" + nbSamples + "_samples_" + listSeries.size() + "_series";

        List<Document> docExpGroup = collection.find(filter)
                .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
                .into(new ArrayList<Document>());

        List<Document> docParam = collection.find(filter)
                .projection(Projections.fields(Projections.include("parameters"), Projections.excludeId()))
                .into(new ArrayList<Document>());

        mongoClient.close();

        // ===== Load Exp Group into a matrix =====

        List<String> headerExpGroup = new ArrayList<String>();
        List<Object> dataExpGroup = new ArrayList<Object>();

        for (int i = 0; i < docExpGroup.size(); i++) {
            Map<String, String> expGroup = (Map<String, String>) docExpGroup.get(i).get("exp_group");
            if (i == 0) {
                headerExpGroup.addAll(expGroup.keySet());
            }

            Object[] dataLine = new Object[headerExpGroup.size()];
            for (int j = 0; j < headerExpGroup.size(); j++) {
                dataLine[j] = expGroup.get(headerExpGroup.get(j));
            }
            dataExpGroup.add(dataLine);
        }

        // ===== Load Params into a matrix =====

        Set<String> headerParamSet = new HashSet<String>();
        List<String> headerParam = new ArrayList<String>();
        List<Object> dataParam = new ArrayList<Object>();

        for (int i = 0; i < docParam.size(); i++) {
            Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
            headerParamSet.addAll(param.keySet());
        }
        headerParam.addAll(headerParamSet);
        Collections.sort(headerParam);

        for (int i = 0; i < docParam.size(); i++) {
            Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
            Object[] dataLine = new Object[headerParam.size()];
            for (int j = 0; j < headerParam.size(); j++) {
                dataLine[j] = param.get(headerParam.get(j));
            }
            // System.out.println(Arrays.toString(dataLine));
            dataParam.add(dataLine);

        }

        // === Output ===

        String fileName = this.getOutputDirectory() + this.getDirSeparator() + "EpiMed_database_" + queryName + "_"
                + dateFormat.format(new Date()) + ".xlsx";
        System.out.println(fileName);
        XSSFWorkbook workbook = fileService.createWorkbook();
        fileService.addSheet(workbook, "exp_group_" + dateFormat.format(new Date()), headerExpGroup, dataExpGroup);
        fileService.addSheet(workbook, "parameters_" + dateFormat.format(new Date()), headerParam, dataParam);
        fileService.writeWorkbook(workbook, fileName);

    }

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

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

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

}