module.ClearGeoExpGroup.java Source code

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Here is the source code for module.ClearGeoExpGroup.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;

import java.util.ArrayList;
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;

public class ClearGeoExpGroup extends BaseModule {

    private String gseNumber = "GSE47361";

    private boolean commit = true;

    public ClearGeoExpGroup() {

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

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

        MongoCollection<Document> collection = db.getCollection("samples");
        List<Document> listDocuments = collection.find(Filters.in("series", gseNumber))
                .into(new ArrayList<Document>());

        // ===== Analyse ======

        for (int i = 0; i < listDocuments.size(); i++) {

            Document doc = listDocuments.get(i);
            String id = doc.getString("_id");
            Document expGroup = (Document) doc.get("exp_group");
            this.clear(expGroup);
            expGroup.remove("er");
            expGroup.remove("pr");
            expGroup.remove("her2");
            expGroup.remove("triple_negative");

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", false);
            if (commit) {
                UpdateResult updateResult = collection.updateOne(Filters.eq("_id", id), new Document("$set", doc));

            }

        }

        mongoClient.close();
    }

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

    private void clear(Document doc) {
        doc.put("sex", null);
        doc.put("ethnic_group", null);
        doc.put("age_min", null);
        doc.put("age_max", null);
        doc.put("id_tissue_stage", null);
        doc.put("tissue_stage", null);
        doc.put("id_tissue_status", null);
        doc.put("tissue_status", null);
        doc.put("id_pathology", null);
        doc.put("pathology", null);
        doc.put("collection_method", null);
        doc.put("id_topology", null);
        doc.put("topology", null);
        doc.put("id_topology_group", null);
        doc.put("topology_group", null);
        doc.put("id_morphology", null);
        doc.put("morphology", null);
        doc.put("histology_type", null);
        doc.put("histology_subtype", null);
        doc.put("t", null);
        doc.put("n", null);
        doc.put("m", null);
        doc.put("tnm_stage", null);
        doc.put("tnm_grade", null);
        doc.put("dfs_months", null);
        doc.put("os_months", null);
        doc.put("relapsed", null);
        doc.put("dead", null);
        doc.put("treatment", null);
        doc.put("exposure", null);
    }

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

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

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

}