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

Introduction

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

Source

/*************************************************************************
*                                                                        *
*  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.ConstructAnalysisFileParser;
import com.act.lcms.db.model.ChemicalAssociatedWithPathway;
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.tuple.Pair;

import java.io.File;
import java.util.List;

public class LoadConstructAnalysisTableIntoDB {
    public static void main(String[] args) throws Exception {
        Options opts = new Options();
        opts.addOption(Option.builder("i").argName("path").desc("The TSV file to read").hasArg().required()
                .longOpt("input-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());
            HelpFormatter fmt = new HelpFormatter();
            fmt.printHelp(LoadConstructAnalysisTableIntoDB.class.getCanonicalName(), opts, true);
            System.exit(1);
        }

        if (cl.hasOption("help")) {
            new HelpFormatter().printHelp(LoadConstructAnalysisTableIntoDB.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(LoadConstructAnalysisTableIntoDB.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);

            ConstructAnalysisFileParser parser = new ConstructAnalysisFileParser();
            parser.parse(inputFile);

            List<Pair<Integer, DB.OPERATION_PERFORMED>> results = ChemicalAssociatedWithPathway
                    .insertOrUpdateChemicalsAssociatedWithPathwayFromParser(db, parser);
            if (results != null) {
                for (Pair<Integer, DB.OPERATION_PERFORMED> r : results) {
                    System.out.format("%d: %s\n", r.getLeft(), r.getRight());
                }
            }
            // 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();
        }

    }
}