content: /*************************************************************************
  *                                                                        *
  *  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;
    }
  }
  