module.script.QueryAvailableData.java Source code

Introduction

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

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.bson.Document;

import com.mongodb.client.model.Aggregates;
import com.mongodb.client.model.Accumulators;
import com.mongodb.client.model.Projections;
import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Sorts;
import com.mongodb.Block;
import com.mongodb.MongoClient;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;

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

public class QueryAvailableData extends BaseModule {

    public QueryAvailableData() {

        // ===== Service =====
        FormatService formatService = new FormatService();

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

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

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

        // ===== Print block =====
        Block<Document> printBlock = new Block<Document>() {
            public void apply(final Document document) {
                System.out.println(document.toJson());
            }
        };

        // ===== Group by topology =====
        // db.getCollection('samples').aggregate({ $group: { "_id" : "$exp_group.topology", "total" : {$sum : 1} }}, {$sort : {total : -1}} )
        /*
        List<Document> listDocuments = collectionSamples.aggregate(
        Arrays.asList(
              Aggregates.group("$exp_group.topology", Accumulators.sum("total", 1)),
              Aggregates.sort(Sorts.orderBy(Sorts.descending("total")))
              ))
        .into(new ArrayList<Document>());
         */

        // ===== Group by sample =====
        /*
        List<Document> listSeries = collectionSeries
        .find()
        .projection(Projections.fields(Projections.include("title")))
        .sort(Sorts.ascending("_id"))
        .into(new ArrayList<Document>());
            
        for (Document doc : listSeries) {
            
           String idSeries = doc.getString("_id");
           Long nbSamples = collectionSamples.count((Filters.eq("series", idSeries)));
           doc.append("nbSamples", nbSamples);
        } 
        display(listSeries);
        */

        // === Export Geo for a list of idSeries ===

        // String[] listIdSeries = {"GSE11092","GSE13309", "GSE13159"};

        /*
        List<Document> docExpGroup = collectionSamples
        .find(Filters.in("series", listIdSeries))
        .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
        .into(new ArrayList<Document>());
        // display(docExpGroup);
            
        List<String> header = formatService.extractHeader(docExpGroup, "exp_group");
        List<Object> data = formatService.extractData(docExpGroup, header, "exp_group");
        System.out.println(header);
        displayMatrix(data);
            
        */
        // List<Object> listObjects = formatService.convertHeterogeneousMongoDocuments(docExpGroup, "exp_group");
        // displayMatrix(listObjects);

        // List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments);

        // === Find series ===

        String[] listIdSamples = { "GSM80908", "GSM274639", "GSM274638", "GSM280213" };
        List<Document> listDocuments = collectionSamples
                .aggregate(Arrays.asList(Aggregates.match(Filters.in("_id", listIdSamples)),
                        Aggregates.group("$main_gse_number"),
                        Aggregates.sort(Sorts.orderBy(Sorts.ascending("main_gse_numbe")))))
                .into(new ArrayList<Document>());
        List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments);
        displayMatrix(listObjects);

        mongoClient.close();
    }

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

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

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

    public void display(List<Document> list) {

        for (Document document : list) {
            System.out.println(document);
        }
    }

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

    public void displayMatrix(List<Object> list) {
        for (Object item : list) {
            Object[] line = (Object[]) item;
            System.out.println(Arrays.toString(line));
        }
    }

}