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 com.act.biointerpretation.networkanalysis;
  
  import act.server.MongoDB;
  import com.act.biointerpretation.l2expansion.L2PredictionCorpus;
  import com.act.jobs.FileChecker;
  import com.act.jobs.JavaRunnable;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.io.File;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.Optional;
  
  /**
   * Builds a metabolic network from any of several sources. Can take edges from an existing network,
   * a database of reactions, or prediction corpuses.
   */
  public class NetworkBuilder implements JavaRunnable {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(NetworkBuilder.class);
  
    private final Optional<File> seedNetwork;
  
    private final List<File> corpusFiles;
    private final Optional<MongoDB> db;
  
    private final File outputFile;
  
    // True if the builder should read in every valid input file even if some inputs are invalid.
    // False if builder should crash on even a single invalid input file.
    private final boolean skipInvalidInputs;
  
    public NetworkBuilder(
        File seedNetwork, List<File> corpusFiles, Optional<MongoDB> db, File outputFile, boolean skipInvalidInputs) {
      this.seedNetwork = Optional.ofNullable(seedNetwork);
      this.corpusFiles = corpusFiles;
      this.db = db;
      this.outputFile = outputFile;
      this.skipInvalidInputs = skipInvalidInputs;
    }
  
    @Override
    public void run() throws IOException {
      LOGGER.info("Starting NetworkBuilder run.");
  
      // Check input files for validity
      if (seedNetwork.isPresent()) {
        FileChecker.verifyInputFile(seedNetwork.get());
      }
      for (File file : corpusFiles) {
        FileChecker.verifyInputFile(file);
      }
      FileChecker.verifyAndCreateOutputFile(outputFile);
      LOGGER.info("Checked input files for validity.");
  
      // Read in input corpuses
      List<L2PredictionCorpus> corpuses = new ArrayList<>(corpusFiles.size());
      for (File file : corpusFiles) {
        try {
          corpuses.add(L2PredictionCorpus.readPredictionsFromJsonFile(file));
        } catch (IOException e) {
          LOGGER.warn("Couldn't read file of name %s as input corpus.", file.getName());
          if (!skipInvalidInputs) {
            throw new IOException("Couldn't read input corpus file " + file.getName() + ": " + e.getMessage());
          }
        }
      }
  
      // Set up network object, and load predictions and reactions into network edges.
      MetabolismNetwork network;
      if (seedNetwork.isPresent()) {
        network = MetabolismNetwork.getNetworkFromJsonFile(seedNetwork.get());
      } else {
        network = new MetabolismNetwork();
      }
      LOGGER.info("Created starting network! Loading edges from DB.");
  
      db.ifPresent(network::loadAllEdgesFromDb);
      LOGGER.info("Done loading edges from DB, if any. Loading edges from any supplied prediction corpuses.");
  
      corpuses.forEach(corpus -> network.loadPredictions(corpus));
      LOGGER.info("Done loading predictions from input corpuses. Writing network to file.");
  
      // Write network out
      network.writeToJsonFile(outputFile);
      LOGGER.info("Complete! Network has been written to %s", outputFile.getAbsolutePath());
    }
  }
  