com.act.lcms.db.io.DB.java Source code

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Here is the source code for com.act.lcms.db.io.DB.java

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/*************************************************************************
*                                                                        *
*  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));
        }
    }
}