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

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Here is the source code for com.act.lcms.db.io.ExportPlateCompositionFromDB.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 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();
            }
        }
    }
}