act.installer.reachablesexplorer.ReachablesProjectionUpdate.java Source code

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Here is the source code for act.installer.reachablesexplorer.ReachablesProjectionUpdate.java

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/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  This program is distributed in the hope that it will be useful,       *
*  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
*  GNU General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package act.installer.reachablesexplorer;

import com.act.biointerpretation.l2expansion.sparkprojectors.utility.ProjectionResult;
import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.mongodb.BasicDBList;
import com.mongodb.BasicDBObject;
import com.mongodb.DBCollection;
import scala.collection.JavaConversions;

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

public class ReachablesProjectionUpdate {

    public static final String PRECURSOR_KEY = "prediction_precursors";
    public static final String INCHI_KEY = "InChI";
    public static final String SUBSTRATES_KEY = "substrates";
    public static final String RO_KEY = "ro";

    private static final Boolean UPSERT = true;
    private static final Boolean NO_MULTI = false;

    @JsonProperty("substrates")
    private final List<String> substrates;

    @JsonProperty("products")
    private final List<String> products;

    @JsonProperty("ros")
    private final List<String> ros;

    @JsonCreator
    public ReachablesProjectionUpdate(@JsonProperty("substrates") List<String> substrates,
            @JsonProperty("products") List<String> products, @JsonProperty("ros") List<String> ros) {
        this.substrates = substrates;
        this.products = products;
        this.ros = ros;
    }

    public ReachablesProjectionUpdate(ProjectionResult projectionResult) {
        this.ros = Arrays.asList(projectionResult.ros());
        this.substrates = JavaConversions.asJavaList(projectionResult.substrates());
        this.products = JavaConversions.asJavaList(projectionResult.products());
    }

    public ReachablesProjectionUpdate(ReachablesProjectionResult projectionResult) {
        this.ros = Arrays.asList(projectionResult.getRos());
        this.substrates = projectionResult.getSubstrates();
        this.products = projectionResult.getProducts();
    }

    public void updateDatabase(DBCollection reachables) {
        for (String product : products) {
            // The query object for this product
            BasicDBObject newProductQuery = new BasicDBObject().append(INCHI_KEY, product);

            // DB list of the substrates of this projection
            BasicDBList substrateList = new BasicDBList();
            substrateList.addAll(substrates);

            // DB list of the one RO associated with this projection
            BasicDBList roList = new BasicDBList();
            roList.addAll(ros);

            // The full entry to be added to the product's precursor list
            BasicDBObject precursorEntry = new BasicDBObject().append(SUBSTRATES_KEY, substrateList).append(RO_KEY,
                    roList);

            // The command to push the precursor entry onto the precursor list
            BasicDBObject precursors = new BasicDBObject();
            precursors.append("$push", new BasicDBObject(PRECURSOR_KEY, precursorEntry));

            // Do the update!
            reachables.update(newProductQuery, precursors, UPSERT, NO_MULTI);
        }
    }

    public void updateByLoader(Loader loader) {
        loader.updateFromProjection(this);
    }

    /**
     * Get the products associated with this projection. This is especially needed since the Precursor data associated
     * with this ProjectionResult will need to be associated with every product of the projection.
     * @return The products of the projection.
     */
    public List<String> getProducts() {
        return products;
    }

    public List<String> getSubstrates() {
        return substrates;
    }

    public List<String> getRos() {
        return ros;
    }
}