module.script.proallchen.ImportProallChenSupplementary.java Source code

Introduction

Here is the source code for module.script.proallchen.ImportProallChenSupplementary.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.proallchen;

import static com.mongodb.client.model.Filters.eq;

import java.util.ArrayList;
import java.util.Date;
import java.util.List;

import org.bson.Document;

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

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

public class ImportProallChenSupplementary extends BaseModule {

    private Date today = new Date();

    public ImportProallChenSupplementary() {

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

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

        // ===== Samples ======

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

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

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

        System.out.println(excelService.getHeader());

        String idSeries = "PROALL_CHEN";
        List<String> listSeries = new ArrayList<String>();
        listSeries.add(idSeries);

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

            List<Object> line = excelService.getData().get(i);

            String idSample = "ESM" + line.get(0);

            System.out.println(idSample + " " + line);

            // ===== Sample Document =====

            Document docSample = new Document();

            docSample.append("_id", idSample).append("main_gse_number", idSeries).append("series", listSeries)
                    .append("organism", "Homo sapiens").append("submission_date", today)
                    .append("last_update", today).append("import_date", today).append("analyzed", false);

            // ===== Mandatory parameters =====
            Document expGroup = generateExpGroup(idSeries, idSample);
            docSample.append("exp_group", expGroup);

            // ===== Supplementary parameters =====

            Document parameters = new Document();
            parameters.append("id_sample", idSample);

            // === Attributes ===

            for (int j = 0; j < excelService.getHeader().size(); j++) {

                String header = (String) excelService.getHeader().get(j);
                Object value = line.get(j);
                // System.out.println(header + " = " + value);

                parameters.append(header, value);

            }
            docSample.append("parameters", parameters);

            System.out.println(docSample);

            // === Delete if already exist ===
            collectionSamples.deleteOne(eq("_id", idSample));

            // ===== Insert data =====
            collectionSamples.insertOne(docSample);

        }

        mongoClient.close();
    }

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

    public Document generateExpGroup(String gse, String gsm) {

        Document expGroup = new Document();

        expGroup.append("id_sample", gsm).append("main_gse_number", gse).append("id_platform", null)
                .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", null).append("tissue_stage", null).append("id_tissue_status", null)
                .append("tissue_status", null).append("id_pathology", null).append("pathology", null)
                .append("collection_method", null).append("id_topology", null).append("topology", null)
                .append("id_topology_group", null).append("topology_group", null).append("id_morphology", null)
                .append("morphology", null).append("histology_type", null).append("histology_subtype", null)
                .append("t", null).append("n", null).append("m", null).append("tnm_stage", null)
                .append("tnm_grade", null).append("dfs_months", null).append("os_months", null)
                .append("relapsed", null).append("dead", null).append("treatment", null).append("exposure", null);

        return expGroup;
    }

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

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

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

}