module.script.epilung.SearchSamplesLungAdenocarcinoma.java Source code

Introduction

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

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

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.Filters;

import config.MongoUtil;
import module.BaseModule;

public class SearchSamplesLungAdenocarcinoma extends BaseModule {

    public SearchSamplesLungAdenocarcinoma() {

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

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

        System.out.println("\n================== SUMMARY ==================");

        Bson[] pFilters = { Filters.eq("_id", "GPL570"), Filters.eq("type", "rna-seq") };

        for (Bson pFilter : pFilters) {

            // === Platforms ===
            List<String> platforms = new ArrayList<String>();
            List<String> platformstext = new ArrayList<String>();
            List<Document> list = collectionPlatforms.find(pFilter).into(new ArrayList<Document>());
            for (Document doc : list) {
                platforms.add(doc.getString("_id"));
                platformstext.add(doc.getString("_id") + " " + doc.getString("type"));
            }

            String lungAdenoFilterName = "Lung adenocarcinoma samples with survival";
            Bson lungAdenoFilter = Filters.and(Filters.in("exp_group.id_platform", platforms),
                    Filters.eq("exp_group.id_tissue_status", 3), Filters.eq("exp_group.id_topology_group", "C34"),
                    Filters.regex("exp_group.morphology", ".*denocarcinoma.*"),
                    Filters.or(Filters.ne("exp_group.os_months", null), Filters.ne("exp_group.dfs_months", null)));

            String ntlFilterName = "Normal lung samples";
            Bson ntlFilter = Filters.and(Filters.in("exp_group.id_platform", platforms),
                    Filters.eq("exp_group.id_tissue_status", 1), Filters.eq("exp_group.id_topology_group", "C34"));

            String[] filterNames = { lungAdenoFilterName, ntlFilterName };
            Bson[] sFilters = { lungAdenoFilter, ntlFilter };

            for (int i = 0; i < sFilters.length; i++) {

                Bson filter = sFilters[i];
                String filterName = filterNames[i];

                List<Document> docs = collectionSamples.find(filter).into(new ArrayList<Document>());

                Set<String> setGse = new HashSet<String>();
                for (Document doc : docs) {
                    setGse.add(doc.getString("main_gse_number"));
                    // System.out.println(doc);
                }

                System.out.println("-------------------------------------------");
                System.out.println("Query: " + filterName);
                System.out.println("Platforms: " + platformstext);
                System.out.println("Samples: " + docs.size());
                System.out.println("Series: " + setGse);

            }
        }
        /*      
         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>());
            
         */

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

        mongoClient.close();

    }

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

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

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

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

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

}