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 org.apache.commons.cli.CommandLine;
  import org.apache.commons.cli.Option;
  
  import java.sql.Connection;
  import java.sql.DriverManager;
  import java.sql.SQLException;
  import java.util.ArrayList;
  import java.util.List;
  
  public class DB implements AutoCloseable {
    public enum OPERATION_PERFORMED {
      CREATE,
      READ,
      UPDATE,
      DELETE,
      ERROR,
    }
  
    public static final String DEFAULT_HOST = "localhost";
    public static final Integer DEFAULT_PORT = 5432;
    public static final String DEFAULT_DB_NAME = "lcms";
  
    public static final String DB_OPTION_URL = "db-url";
    public static final String DB_OPTION_HOST = "db-host";
    public static final String DB_OPTION_PORT = "db-port";
    public static final String DB_OPTION_USERNAME = "db-user";
    public static final String DB_OPTION_PASSWORD = "db-pass";
    public static final String DB_OPTION_DB_NAME = "db-name";
  
  
    public static final List<Option.Builder> DB_OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
      // DB connection options.
      add(Option.builder()
              .argName("database url")
              .desc("The url to use when connecting to the LCMS db")
              .hasArg()
              .longOpt(DB_OPTION_URL)
      );
      add(Option.builder("H")
              .argName("database host")
              .desc(String.format("The LCMS DB host (default = %s)", DEFAULT_HOST))
              .hasArg()
              .longOpt(DB_OPTION_HOST)
      );
      add(Option.builder("P")
              .argName("database port")
              .desc(String.format("The LCMS DB port (default = %d)", DEFAULT_PORT))
              .hasArg()
              .longOpt(DB_OPTION_PORT)
      );
      add(Option.builder()
              .argName("database user")
              .desc("The LCMS DB user")
              .hasArg()
              .longOpt(DB_OPTION_USERNAME)
      );
      add(Option.builder()
              .argName("database password")
              .desc("The LCMS DB password")
              .hasArg()
              .longOpt(DB_OPTION_PASSWORD)
      );
      add(Option.builder("db")
              .argName("database name")
              .desc(String.format("The LCMS DB name (default = %s)", DEFAULT_DB_NAME))
              .hasArg()
              .longOpt(DB_OPTION_DB_NAME)
      );
    }};
  
    Connection conn;
  
    public DB connectToDB(String connStr) throws ClassNotFoundException, SQLException {
      /* Explicitly load the PostgreSQL driver class before trying to connect.
       * See https://jdbc.postgresql.org/documentation/94/load.html. */
      Class.forName("org.postgresql.Driver");
      this.conn = DriverManager.getConnection(connStr);
      return this;
    }
  
    public DB connectToDB(String host, Integer port, String databaseName, String user, String password)
        throws ClassNotFoundException, SQLException {
      Class.forName("org.postgresql.Driver");
      String url = String.format("jdbc:postgresql://%s:%d/%s",
          host == null ? DEFAULT_HOST : host,
          port == null ? DEFAULT_PORT : port,
          databaseName == null ? DEFAULT_DB_NAME : databaseName);
      this.conn = DriverManager.getConnection(url, user, password);
      return this;
    }
  
    public Connection getConn() {
      return conn;
    }
  
    @Override
    public void close() throws SQLException {
      if (conn != null && !conn.isClosed()) {
        conn.close();
      }
    }
  
    public static DB openDBFromCLI(CommandLine cl) throws ClassNotFoundException, SQLException {
      if (cl.hasOption(DB_OPTION_URL)) {
        return new DB().connectToDB(cl.getOptionValue(DB_OPTION_URL));
      } else {
        Integer port = null;
        if (cl.getOptionValue(DB_OPTION_PORT) != null) {
          port = Integer.parseInt(cl.getOptionValue(DB_OPTION_PORT));
        }
        return new DB().connectToDB(cl.getOptionValue(DB_OPTION_HOST), port, cl.getOptionValue(DB_OPTION_DB_NAME),
            cl.getOptionValue(DB_OPTION_USERNAME), cl.getOptionValue(DB_OPTION_PASSWORD));
      }
    }
  }
  