module.script.proallchen.ImportProallChenOriginal.java Source code

Introduction

Here is the source code for module.script.proallchen.ImportProallChenOriginal.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 com.mongodb.client.model.Filters;
import com.mongodb.client.result.UpdateResult;

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

public class ImportProallChenOriginal extends BaseModule {

    private Date today = new Date();

    public ImportProallChenOriginal() {

        // ===== 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() + "PROALL_CHEN_clinical.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);

            Document docSample = collectionSamples.find(Filters.eq("_id", idSample.trim())).first();

            System.out.println(docSample);

            Document parameters = (Document) docSample.get("parameters");

            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);

            }

            System.out.println(parameters);

            // Update Mongo document
            docSample.put("parameters", parameters);
            UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", docSample.get("_id")),
                    new Document("$set", docSample));
        }

        mongoClient.close();
    }

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

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

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

}