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.lcms.db.io;
  
  import com.act.lcms.db.io.parser.PlateCompositionParser;
  import com.act.lcms.db.model.DeliveredStrainWell;
  import com.act.lcms.db.model.FeedingLCMSWell;
  import com.act.lcms.db.model.InductionWell;
  import com.act.lcms.db.model.LCMSWell;
  import com.act.lcms.db.model.Plate;
  import com.act.lcms.db.model.PregrowthWell;
  import com.act.lcms.db.model.StandardWell;
  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.commons.lang3.StringUtils;
  
  import java.io.File;
  import java.util.Arrays;
  import java.util.List;
  
  public class LoadPlateCompositionIntoDB {
  
    // TODO: add argument parser and/or usage message.
    public static void main(String[] args) throws Exception {
      Options opts = new Options();
      opts.addOption(Option.builder("t")
              .argName("type")
              .desc("The type of plate composition in this file, valid options are: " +
                  StringUtils.join(Arrays.asList(Plate.CONTENT_TYPE.values()), ", "))
              .hasArg()
              .longOpt("plate-type")
              .required()
              .build()
      );
      opts.addOption(Option.builder("i")
              .argName("path")
              .desc("The plate composition file to read")
              .hasArg()
              .longOpt("input-file")
              .required()
              .build()
      );
  
      // DB connection options.
          opts.addOption(Option.builder()
              .argName("database url")
              .desc("The url to use when connecting to the LCMS db")
              .hasArg()
              .longOpt("db-url")
              .build()
      );
      opts.addOption(Option.builder("u")
              .argName("database user")
              .desc("The LCMS DB user")
              .hasArg()
              .longOpt("db-user")
              .build()
      );
      opts.addOption(Option.builder("p")
              .argName("database password")
              .desc("The LCMS DB password")
              .hasArg()
              .longOpt("db-pass")
              .build()
      );
      opts.addOption(Option.builder("H")
              .argName("database host")
              .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST))
              .hasArg()
              .longOpt("db-host")
              .build()
      );
      opts.addOption(Option.builder("P")
              .argName("database port")
              .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT))
              .hasArg()
              .longOpt("db-port")
              .build()
      );
      opts.addOption(Option.builder("N")
              .argName("database name")
              .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME))
              .hasArg()
              .longOpt("db-name")
              .build()
      );
  
      // Everybody needs a little help from their friends.
      opts.addOption(Option.builder("h")
              .argName("help")
              .desc("Prints this help message")
              .longOpt("help")
              .build()
      );
  
      CommandLine cl = null;
      try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
      } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HelpFormatter fmt = new HelpFormatter();
        fmt.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
      }
  
      if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        return;
      }
  
      File inputFile = new File(cl.getOptionValue("input-file"));
      if (!inputFile.exists()) {
        System.err.format("Unable to find input file at %s\n", cl.getOptionValue("input-file"));
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
      }
  
      PlateCompositionParser parser = new PlateCompositionParser();
      parser.processFile(inputFile);
  
      Plate.CONTENT_TYPE contentType = null;
      try {
        contentType = Plate.CONTENT_TYPE.valueOf(cl.getOptionValue("plate-type"));
      } catch (IllegalArgumentException e) {
        System.err.format("Unrecognized plate type '%s'\n", cl.getOptionValue("plate-type"));
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
      }
  
      DB db;
      if (cl.hasOption("db-url")) {
        db = new DB().connectToDB(cl.getOptionValue("db-url"));
      } else {
        Integer port = null;
        if (cl.getOptionValue("P") != null) {
          port = Integer.parseInt(cl.getOptionValue("P"));
        }
        db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"),
            cl.getOptionValue("u"), cl.getOptionValue("p"));
      }
  
      try {
        db.getConn().setAutoCommit(false);
  
        Plate p = Plate.getOrInsertFromPlateComposition(db, parser, contentType);
  
        switch (contentType) {
          case LCMS:
            List<LCMSWell> LCMSWells = LCMSWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (LCMSWell LCMSWell : LCMSWells) {
              System.out.format("%d: %d x %d  %s  %s\n", LCMSWell.getId(),
                  LCMSWell.getPlateColumn(), LCMSWell.getPlateRow(), LCMSWell.getMsid(), LCMSWell.getComposition());
            }
            break;
          case STANDARD:
            List<StandardWell> standardWells = StandardWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (StandardWell standardWell : standardWells) {
              System.out.format("%d: %d x %d  %s\n", standardWell.getId(),
                  standardWell.getPlateColumn(), standardWell.getPlateRow(), standardWell.getChemical());
            }
            break;
          case DELIVERED_STRAIN:
            List<DeliveredStrainWell> deliveredStrainWells =
                DeliveredStrainWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (DeliveredStrainWell deliveredStrainWell : deliveredStrainWells) {
              System.out.format("%d: %d x %d (%s) %s %s \n", deliveredStrainWell.getId(),
                  deliveredStrainWell.getPlateColumn(), deliveredStrainWell.getPlateRow(), deliveredStrainWell.getWell(),
                  deliveredStrainWell.getMsid(), deliveredStrainWell.getComposition());
            }
            break;
          case INDUCTION:
            List<InductionWell> inductionWells = InductionWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (InductionWell inductionWell : inductionWells) {
              System.out.format("%d: %d x %d %s %s %s %d\n", inductionWell.getId(),
                  inductionWell.getPlateColumn(), inductionWell.getPlateRow(),
                  inductionWell.getMsid(), inductionWell.getComposition(),
                  inductionWell.getChemical(), inductionWell.getGrowth());
            }
            break;
          case PREGROWTH:
            List<PregrowthWell> pregrowthWells = PregrowthWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (PregrowthWell pregrowthWell : pregrowthWells) {
              System.out.format("%d: %d x %d (%s @ %s) %s %s %d\n", pregrowthWell.getId(),
                  pregrowthWell.getPlateColumn(), pregrowthWell.getPlateRow(),
                  pregrowthWell.getSourcePlate(), pregrowthWell.getSourceWell(),
                  pregrowthWell.getMsid(), pregrowthWell.getComposition(), pregrowthWell.getGrowth());
            }
            break;
          case FEEDING_LCMS:
            List<FeedingLCMSWell> feedingLCMSWells =
                FeedingLCMSWell.getInstance().insertFromPlateComposition(db, parser, p);
            for (FeedingLCMSWell feedingLCMSWell : feedingLCMSWells) {
              System.out.format("%d: %d x %d (%s @ %s) %s %s %f\n", feedingLCMSWell.getId(),
                  feedingLCMSWell.getPlateColumn(), feedingLCMSWell.getPlateRow(),
                  feedingLCMSWell.getMsid(), feedingLCMSWell.getComposition(),
                  feedingLCMSWell.getExtract(), feedingLCMSWell.getChemical(), feedingLCMSWell.getConcentration());
            }
            break;
          default:
            System.err.format("Unrecognized/unimplemented data type '%s'\n", contentType);
            break;
        }
        // If we didn't encounter an exception, commit the transaction.
        db.getConn().commit();
      } catch (Exception e) {
        System.err.format("Caught exception when trying to load plate composition, rolling back. %s\n", e.getMessage());
        db.getConn().rollback();
        throw(e);
      } finally {
        db.getConn().close();
      }
  
    }
  }
  