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.sars;
  
  import act.server.MongoDB;
  import com.act.biointerpretation.Utils.ReactionProjector;
  import com.act.biointerpretation.mechanisminspection.ErosCorpus;
  import org.apache.commons.cli.CommandLine;
  import org.apache.commons.cli.CommandLineParser;
  import org.apache.commons.cli.DefaultParser;
  import org.apache.commons.cli.HelpFormatter;
  import org.apache.commons.cli.Option;
  import org.apache.commons.cli.Options;
  import org.apache.commons.cli.ParseException;
  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.Arrays;
  import java.util.List;
  
  public class SarGenerationDriver {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(SarGenerationDriver.class);
  
    private static final String OPTION_DB = "db";
    private static final String OPTION_OUTPUT_PATH = "o";
    private static final String OPTION_HELP = "h";
    private static final String OPTION_REACTION_LIST = "r";
    private static final String OPTION_REACTIONS_FILE = "f";
  
    public static final String HELP_MESSAGE =
        "This class is used to generate SARs from a set of reactions or chemicals.  It has several modes of operation, " +
            "which are described in more detail along with the operations that run them.";
  
    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
      add(Option.builder(OPTION_DB)
          .argName("db name")
          .desc("The name of the mongo DB to use.")
          .hasArg()
          .longOpt("db-name")
          .type(String.class)
          .required(true)
      );
      add(Option.builder(OPTION_OUTPUT_PATH)
          .argName("output file path")
          .desc("The absolute path to the file to which to write the json file of the sar corpus.")
          .hasArg()
          .longOpt("output-file-path")
          .required(true)
      );
      add(Option.builder(OPTION_REACTION_LIST)
          .argName("specific reactions")
          .desc("A list of reaction IDs to build a SAR from.")
          .hasArgs()
          .valueSeparator(',')
          .longOpt("specific reactions")
      );
      add(Option.builder(OPTION_REACTIONS_FILE)
          .argName("reactions file")
          .desc("Absolute path to file from which to read reaction groups.  File should either be a ReactionGroupCorpus " +
              "in json format, or a file with one reaction group per line, where each line has comma separate values, " +
              "with the first value being the name of the group, and the subsequent values being reaction ids.")
          .hasArg()
          .longOpt("reactions-file")
      );
      add(Option.builder(OPTION_HELP)
          .argName("help")
          .desc("Prints this help message.")
          .longOpt("help")
      );
    }};
  
    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();
  
    static {
      HELP_FORMATTER.setWidth(100);
    }
  
    private static final String LOCAL_HOST = "localhost";
    private static final Integer MONGO_PORT = 27017;
  
    public static void main(String[] args) throws Exception {
      // Build command line parser.
      Options opts = new Options();
      for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());
      }
  
      CommandLine cl = null;
      try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
      } catch (ParseException e) {
        LOGGER.error("Argument parsing failed: %s", e.getMessage());
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
  
      // Print help.
      if (cl.hasOption(OPTION_HELP)) {
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
      }
  
      // Create DB and DbAPI
      MongoDB mongoDB = new MongoDB(LOCAL_HOST, MONGO_PORT, cl.getOptionValue(OPTION_DB));
      DbAPI dbApi = new DbAPI(mongoDB);
  
      // Handle output file
      File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH));
      if (outputFile.isDirectory() || outputFile.exists()) {
        LOGGER.error("Supplied output file is a directory or already exists.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
      outputFile.createNewFile();
  
      // Check that there is exactly one reaction group input option
      if (cl.hasOption(OPTION_REACTION_LIST) && cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.error("Cannot process both a reaction list and a reactions file as input.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
      if (!cl.hasOption(OPTION_REACTION_LIST) && !cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.error("Must supply either a reaction list or a reactions file as input.");
        HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
  
      // Build input reaction group corpus.
      Iterable<ReactionGroup> groups = null;
      if (cl.hasOption(OPTION_REACTION_LIST)) {
        LOGGER.info("Using specific input reactions.");
        ReactionGroup group = new ReactionGroup("ONLY_GROUP", "NO_DB");
        for (String idString : cl.getOptionValues(OPTION_REACTION_LIST)) {
          group.addReactionId(Long.parseLong(idString));
        }
        groups = Arrays.asList(group);
      }
      if (cl.hasOption(OPTION_REACTIONS_FILE)) {
        LOGGER.info("Using reactions file.");
        File inputFile = new File(cl.getOptionValue(OPTION_REACTIONS_FILE));
        try {
          groups = ReactionGroupCorpus.loadFromJsonFile(inputFile);
          LOGGER.info("Successfully parsed input as json file.");
        } catch (IOException e) {
          LOGGER.info("Input file not json file. Trying txt format.");
          try {
            groups = ReactionGroupCorpus.loadFromTextFile(inputFile);
            LOGGER.info("Successfully parsed input as text file.");
          } catch (IOException f) {
            LOGGER.error("Reactions input file not parseable. %s", f.getMessage());
            throw f;
          }
        }
      }
  
      // Build all pieces of SAR generator
      ReactionProjector projector = new ReactionProjector();
      ExpandedReactionSearcher generalizer = new ExpandedReactionSearcher(projector);
  
      McsCalculator reactionMcsCalculator = new McsCalculator(McsCalculator.REACTION_BUILDING_OPTIONS);
      McsCalculator sarMcsCalculator = new McsCalculator(McsCalculator.SAR_OPTIONS);
  
      FullReactionBuilder reactionBuilder = new FullReactionBuilder(reactionMcsCalculator, generalizer, projector);
  
      SarFactory substructureSarFactory = new OneSubstrateSubstructureSar.Factory(sarMcsCalculator);
      SarFactory carbonCountSarFactory = new OneSubstrateCarbonCountSar.Factory();
      List<SarFactory> sarFactories = Arrays.asList(carbonCountSarFactory, substructureSarFactory);
  
      ErosCorpus roCorpus = new ErosCorpus();
      roCorpus.loadValidationCorpus();
  
      ReactionGroupCharacterizer reactionGroupCharacterizer =
          new OneSubstrateOneRoCharacterizer(dbApi, sarFactories, reactionBuilder, roCorpus);
      SarCorpusBuilder corpusBuilder = new SarCorpusBuilder(groups, reactionGroupCharacterizer);
      LOGGER.info("Parsed arguments and constructed SAR corpus builder. Building corpus.");
  
      SarCorpus sarCorpus = corpusBuilder.build();
      LOGGER.info("Built sar corpus. Printing to file in json format.");
  
      sarCorpus.printToJsonFile(outputFile);
      LOGGER.info("Complete!");
    }
  }
  