module.script.epilung.SearchSamples.java Source code

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Here is the source code for module.script.epilung.SearchSamples.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.epilung;

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

import org.bson.Document;
import org.bson.conversions.Bson;

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

import config.MongoUtil;
import module.BaseModule;

public class SearchSamples extends BaseModule {

    public SearchSamples() {

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

        MongoClient mongoClient = MongoUtil.buildMongoClient();
        MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
        MongoCollection<Document> collectionSamples = db.getCollection("samples");
        MongoCollection<Document> collectionPlatforms = db.getCollection("platforms");

        Bson filters = Filters.and(
                Filters.in("exp_group.id_platform", new String[] { "GPL13534", "GPL8490", "GPL21145" }),
                Filters.eq("exp_group.id_tissue_status", 1), Filters.ne("exp_group.id_topology", null));

        /*
        List<Document> list = collectionSamples
        .find(filters)
        .into(new ArrayList<Document>());
        */

        List<Document> list = collectionSamples.aggregate(Arrays.asList(Aggregates.match(filters),
                Aggregates.group("$exp_group.topology", Accumulators.sum("total", 1)),
                Aggregates.sort(Sorts.orderBy(Sorts.descending("total"))))).into(new ArrayList<Document>());

        for (int i = 0; i < list.size(); i++) {
            System.out.println((i + 1) + " " + list.get(i));
        }

        collectionPlatforms.find(Filters.regex("title", ".*ethyl.*")).forEach(printBlock);

        mongoClient.close();

    }

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

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

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

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

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

}