org.cytoscape.cmdline.headless.internal.Parser.java Source code

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Here is the source code for org.cytoscape.cmdline.headless.internal.Parser.java

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package org.cytoscape.cmdline.headless.internal;

/*
 * #%L
 * Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl)
 * $Id:$
 * $HeadURL:$
 * %%
 * Copyright (C) 2006 - 2013 The Cytoscape Consortium
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as 
 * published by the Free Software Foundation, either version 2.1 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 Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-2.1.html>.
 * #L%
 */

import org.cytoscape.application.CyShutdown;
import org.cytoscape.application.CyVersion;
import org.cytoscape.command.AvailableCommands;

import java.util.Properties;

import java.awt.Dimension;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class Parser {
    private static final Logger logger = LoggerFactory.getLogger(Parser.class);

    private final String[] args;
    private final Options options;
    private final CyShutdown shutdown;
    private final CyVersion version;
    private final StartupConfig startupConfig;
    private final AvailableCommands availableCommands;

    public Parser(String[] args, CyShutdown shutdown, CyVersion version, StartupConfig startupConfig,
            AvailableCommands availableCommands) {
        this.args = args;
        this.shutdown = shutdown;
        this.version = version;
        this.startupConfig = startupConfig;
        this.availableCommands = availableCommands;
        options = initOptions();
        parseCommandLine(args);
    }

    private Options initOptions() {
        Options opt = new Options();

        opt.addOption("h", "help", false, "Print this message.");
        opt.addOption("v", "version", false, "Print the version number.");

        opt.addOption(OptionBuilder.withLongOpt("command").withDescription("Cytoscape command file to be executed.")
                .withValueSeparator('\0').withArgName("file").hasArgs().create("c"));

        return opt;
    }

    private void parseCommandLine(String[] args) {

        // try to parse the cmd line
        CommandLineParser parser = new PosixParser();
        CommandLine line = null;

        // first load the simple exit options
        try {
            line = parser.parse(options, args);
        } catch (ParseException e) {
            logger.error("Parsing command line failed.", e);
            printHelp();
            shutdown.exit(1);
            return;
        }

        if (line.hasOption("h")) {
            printHelp();
        } else if (line.hasOption("v")) {
            System.out.println("Cytoscape version: " + version.getVersion());
        } else if (line.hasOption("c")) {
            startupConfig.setCommandFile(line.getOptionValue("c"));
        } else {
            logger.error("No arguments specified. See usage for details.");
            printHelp();
        }
    }

    private void printHelp() {
        HelpFormatter formatter = new HelpFormatter();
        System.out.println();
        formatter.printHelp("cytoscape.{sh|bat} [OPTIONS]", options);
        printAvailableCommands();
    }

    private void printAvailableCommands() {
        StringBuilder sb = new StringBuilder();
        sb.append(System.getProperty("line.separator"));
        sb.append(" available commands:");
        sb.append(System.getProperty("line.separator"));
        sb.append(System.getProperty("line.separator"));
        for (String namespace : availableCommands.getNamespaces()) {
            for (String command : availableCommands.getCommands(namespace)) {
                sb.append("  ");
                sb.append(namespace);
                sb.append(" ");
                sb.append(command);
                sb.append(" ");
                for (String arg : availableCommands.getArguments(namespace, command)) {
                    sb.append(arg);
                    sb.append(" ");
                }
                sb.append(System.getProperty("line.separator"));
            }
        }
        System.out.println(sb.toString());
    }
}