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

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

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package org.cytoscape.cmdline.gui.internal;

/*
 * #%L
 * Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl)
 * $Id:$
 * $HeadURL:$
 * %%
 * Copyright (C) 2010 - 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 java.util.Properties;

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.cytoscape.application.CyShutdown;
import org.cytoscape.application.CyVersion;
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 Properties props;

    public Parser(String[] args, CyShutdown shutdown, CyVersion version, StartupConfig startupConfig,
            Properties props) {
        this.args = args;
        this.shutdown = shutdown;
        this.version = version;
        this.startupConfig = startupConfig;
        this.props = props;
        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("session").withDescription("Load a cytoscape session (.cys) file.")
                .withValueSeparator('\0').withArgName("file").hasArg() // only allow one session!!!
                .create("s"));

        opt.addOption(OptionBuilder.withLongOpt("network").withDescription("Load a network file (any format).")
                .withValueSeparator('\0').withArgName("file").hasArgs().create("N"));

        opt.addOption(OptionBuilder.withLongOpt("props").withDescription(
                "Load cytoscape properties file (Java properties format) or individual property: -P name=value.")
                .withValueSeparator('\0').withArgName("file").hasArgs().create("P"));

        opt.addOption(OptionBuilder.withLongOpt("vizmap")
                .withDescription("Load vizmap properties file (Cytoscape VizMap format).").withValueSeparator('\0')
                .withArgName("file").hasArgs().create("V"));

        opt.addOption(OptionBuilder.withLongOpt("script").withDescription("Execute commands from script file")
                .withValueSeparator('\0').withArgName("file").hasArgs().create("S"));

        opt.addOption(OptionBuilder.withLongOpt("rest").withDescription("Start a rest service")
                .withValueSeparator('\0').withArgName("port").hasArgs().create("R"));

        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.getMessage());
            printHelp();
            props.setProperty("tempHideWelcomeScreen", "true");
            shutdown.exit(1);
            return;
        }

        if (line.hasOption("h")) {
            printHelp();
            shutdown.exit(0);
            props.setProperty("tempHideWelcomeScreen", "true");
            return;
        }

        if (line.hasOption("v")) {
            logger.info("Cytoscape version: " + version.getVersion());
            System.out.println("Cytoscape version: " + version.getVersion());
            props.setProperty("tempHideWelcomeScreen", "true");
            shutdown.exit(0);
            return;
        }

        // always load any properties specified
        if (line.hasOption("P"))
            startupConfig.setProperties(line.getOptionValues("P"));

        // it the only argument is a session file, load it
        if (line.getOptions().length == 0 && line.getArgs().length == 1 && line.getArgs()[0].endsWith(".cys")) {
            startupConfig.setSession(line.getArgs()[0]);
            return;
        }

        // Either load the session ...      
        if (line.hasOption("s")) {
            startupConfig.setSession(line.getOptionValue("s"));

            // ... or all the rest.
        } else {
            if (line.hasOption("N"))
                startupConfig.setNetworks(line.getOptionValues("N"));

            if (line.hasOption("V"))
                startupConfig.setVizMapProps(line.getOptionValues("V"));
        }

        // Do we have any command scripts requested?
        if (line.hasOption("S"))
            startupConfig.setCommandScript(line.getOptionValue("S"));

        // Do we want a rest server?
        if (line.hasOption("R"))
            startupConfig.setRestPort(line.getOptionValue("R"));
    }

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