module.script.emtab365.ImportSamplesEMTAB365.java Source code

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Here is the source code for module.script.emtab365.ImportSamplesEMTAB365.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.emtab365;

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

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;
import service.MongoService;

public class ImportSamplesEMTAB365 extends BaseModule {

    private MongoService mongoService = new MongoService();
    private ExcelService excelService = new ExcelService();

    public ImportSamplesEMTAB365() {

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

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

        // ===== Collections ======
        MongoCollection<Document> collectionPlatforms = db.getCollection("platforms");
        MongoCollection<Document> collectionSeries = db.getCollection("series");
        MongoCollection<Document> collectionSamples = db.getCollection("samples");

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

        String inputfile = this.getInputDirectory() + this.getDirSeparator() + "E-MTAB-365.sdrf.xlsx";
        System.out.println("LOADING \t " + inputfile);
        excelService.load(inputfile);

        // ===== Init values ======

        String idSeries = "E-MTAB-365";
        List<String> listSeries = new ArrayList<String>();
        listSeries.add(idSeries);
        Document docSeries = collectionSeries.find(Filters.eq("_id", idSeries)).first();
        String organism = "Homo sapiens";

        // ==== Header processing ====

        Map<Integer, String> mapHeader = new HashMap<Integer, String>();
        for (int i = 0; i < excelService.getHeader().size(); i++) {
            String headerItem = (String) excelService.getHeader().get(i);
            if (headerItem != null && headerItem.contains("[")) {
                String[] parts = headerItem.split("[\\[\\]]");
                headerItem = parts[1];
                headerItem = headerItem.replaceAll("[:_\\.]", " ");
            }
            mapHeader.put(i, headerItem.trim());
        }
        System.out.println(mapHeader);

        for (int i = 0; i < excelService.getData().size(); i++) {
            // for (int i=0; i<1; i++) {

            List<Object> dataline = excelService.getData().get(i);
            String idSample = (String) dataline.get(0);

            if (!idSample.equals("pool XX")) {

                String idPlatform = ((String) dataline.get(54)).trim();
                if (idPlatform.contains("A-AFFY-44")) {
                    idPlatform = "GPL570";
                } else {
                    Document docPlatform = mongoService.createPlatform(idPlatform, null, "9606", "Homo sapiens",
                            null, null, null, null);
                    UpdateResult res = collectionPlatforms.updateOne(
                            Filters.eq("_id", docPlatform.getString("_id")), new Document("$set", docPlatform));
                    if (res.getMatchedCount() == 0) {
                        collectionPlatforms.insertOne(docPlatform);
                    }
                }

                Document docSample = mongoService.createSample(idSample, idSeries, listSeries, organism,
                        (Date) docSeries.get("submission_date"), (Date) docSeries.get("last_update"), false);

                // === exp_group ===

                Document expgroup = mongoService.createExpGroup(docSample, idPlatform, null, null, organism);
                docSample.append("exp_group", expgroup);

                // === parameters ===

                Map<String, Object> mapParameters = new HashMap<String, Object>();

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

                    String key = mapHeader.get(j);
                    Object value = dataline.get(j);

                    if (value instanceof String) {
                        String valueString = ((String) value).trim();
                        if (valueString != null && !valueString.isEmpty() && !valueString.equals("NA")
                                && !valueString.equals("ND")) {
                            value = valueString;
                        } else {
                            value = null;
                        }
                    }

                    if (key != null && value != null) {
                        mapParameters.put(key, value);
                        // System.out.println(key + "='" + value+"'");
                    }
                }

                Document parameters = mongoService.createParameters(docSample, mapParameters);
                docSample.append("parameters", parameters);

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

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

                System.out.println(docSample);

            }
        }

        mongoClient.close();
    }

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

    public static void main(String[] args) {
        new ImportSamplesEMTAB365();
    }

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

}