ModuleRunner.java

/**
 * 
 */
package net.sourceforge.seqware.pipeline.plugins;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.pipeline.module.ModuleInterface;
import net.sourceforge.seqware.pipeline.plugin.Plugin;
import net.sourceforge.seqware.pipeline.plugin.PluginInterface;
import net.sourceforge.seqware.pipeline.runner.Runner;
import org.openide.util.Lookup;
import org.openide.util.lookup.ServiceProvider;

/**
 * <p>
 * ModuleRunner class.
 * </p>
 * 
 * @author boconnor ProviderFor(PluginInterface.class)
 * 
 *         TODO: need to merge/migrate the Runner code into this plugin framework. For now I'm just calling the other object.
 * @version $Id: $Id
 */
@ServiceProvider(service = PluginInterface.class)
public class ModuleRunner extends Plugin {

    ReturnValue ret = new ReturnValue();
    Runner runner = new Runner();

    /**
     * <p>
     * Constructor for ModuleRunner.
     * </p>
     */
    public ModuleRunner() {
        super();
        // parser.acceptsAll(Arrays.asList("help", "h", "?"), "Provides this help message.");
        ret.setExitStatus(ReturnValue.SUCCESS);
    }

    /**
     * <p>
     * parse_parameters.
     * </p>
     * 
     * @return a {@link net.sourceforge.seqware.common.module.ReturnValue} object.
     */
    @Override
    public ReturnValue parse_parameters() {
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#init()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue init() {
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#do_test()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_test() {
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#do_run()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_run() {

        if (params == null || params.length == 0 || contains(params, "help")) {
            doHelp();
            Log.stdout("NOTE: This ModuleRunner will simply pass all parameters to the Runner object. To use one of the modules above simple execute:\n"
                    + "\n"
                    + "  java -jar seqware-pipeline-*.jar -p net.sourceforge.seqware.pipeline.plugins.ModuleRunner [RunnerParameters (see help message below)] --module [module from list above] -- [ModuleParameters]"
                    + "\n\nRunner Help Message:\n");
            runner.run(new String[0]);
        } else {
            runner.run(params);
        }

        return ret;

    }

    private boolean contains(String[] arr, String search) {
        for (String token : arr) {
            Log.debug("Array:" + token);
            if (token.contains(search)) {
                return (true);
            }
        }
        return (false);
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#clean_up()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue clean_up() {
        return ret;
    }

    /**
     * <p>
     * get_description.
     * </p>
     * 
     * @return a {@link java.lang.String} object.
     */
    @Override
    public String get_description() {
        return ("Description: A wrapper around Runner which will either list all Modules in the classpath (if no args are passed) or trigger a specific Module. Great for running Modules standalone.");
    }

    private void doHelp() {
        // then list all the modules in the classpath!
        Collection<? extends ModuleInterface> mods;
        mods = Lookup.getDefault().lookupAll(ModuleInterface.class);

        Log.stdout("\nAvailable Module List:");

        HashMap<String, ArrayList<String>> modules = new HashMap<>();

        for (ModuleInterface mod : mods) {

            if (modules.get(mod.getClass().getPackage().getName()) == null) {
                ArrayList<String> modulesInPackage = new ArrayList<>();
                modules.put(mod.getClass().getPackage().getName(), modulesInPackage);
            }
            ArrayList<String> modulesInPackage = modules.get(mod.getClass().getPackage().getName());
            modulesInPackage.add(mod.getClass().getPackage().getName() + "." + mod.getClass().getSimpleName());
        }

        for (String pack : modules.keySet()) {
            Log.stdout("\n  Package: " + pack + "\n");
            for (String mod : modules.get(pack)) {
                Log.stdout("    Module: " + mod);
            }
        }

    }

}