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.writer.PlateCompositionWriter;
  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 java.io.FileWriter;
  import java.io.OutputStreamWriter;
  import java.io.Writer;
  
  public class ExportPlateCompositionFromDB {
    public static void main(String[] args) throws Exception {
      Options opts = new Options();
      opts.addOption(Option.builder("b")
              .argName("barcode")
              .desc("The barcode of the plate to print")
              .hasArg()
              .longOpt("barcode")
              .build()
      );
      opts.addOption(Option.builder("n")
              .argName("name")
              .desc("The name of the plate to print")
              .hasArg()
              .longOpt("name")
              .build()
      );
  
      opts.addOption(Option.builder("o")
              .argName("output file")
              .desc("An output file to which to write this plate's composition table (writes to stdout if omitted")
              .hasArg()
              .longOpt("output-file")
              .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());
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
      }
  
      if (cl.hasOption("help")) {
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        return;
      }
  
      if (!cl.hasOption("b") && !cl.hasOption("n")) {
        System.err.format("Must specify either plate barcode or plate name.");
        new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true);
        System.exit(1);
      }
  
      DB db = null;
      try {
        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"));
        }
  
        Writer writer = null;
        if (cl.hasOption("o")) {
          writer = new FileWriter(cl.getOptionValue("o"));
        } else {
          writer = new OutputStreamWriter(System.out);
        }
  
        PlateCompositionWriter cw = new PlateCompositionWriter();
        if (cl.hasOption("b")) {
          cw.writePlateCompositionByBarcode(db, cl.getOptionValue("b"), writer);
        } else if (cl.hasOption("n")) {
          cw.writePlateCompositionByName(db, cl.getOptionValue("n"), writer);
        }
  
        writer.close();
      } finally {
        if (db != null) {
          db.close();
        }
      }
    }
  }
  