/*--------------------------------------------------------------------------
 *  Copyright 2008 utgenome.org
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *--------------------------------------------------------------------------*/
//--------------------------------------
// utgb-shell Project
//
// Repair.java
// Since: Feb 1, 2008
//
// $URL$ 
// $Author$
//--------------------------------------
package org.utgenome.shell;

import java.io.IOException;

import org.utgenome.config.TrackConfiguration;
import org.utgenome.shell.Create.ScaffoldFileFilter;
import org.xerial.util.cui.OptionHandler;
import org.xerial.util.cui.OptionParser;
import org.xerial.util.cui.OptionParserException;
import org.xerial.util.log.Logger;

public class Repair extends UTGBShellSubCommandBase {
	private static Logger _logger = Logger.getLogger(Repair.class);

	private enum Opt {
		PACKAGE_NAME, GROUP, TARGET_FILE
	}

	private OptionParser<Opt> optionParser = new OptionParser<Opt>();
	private String packageName = null;
	private String group = "org.utgenome.track";
	private String repairTargetFile = null;
	private ScaffoldFileFilter scaffoldFilter = new Create.CreateAllScaffoldFileFilter();

	public Repair() {
		optionParser.addOptionWithArgument(Opt.PACKAGE_NAME, "p", "package", "PACKAGE_NAME", "specify the java package name, e.g. org.yourdomain.track",
				new OptionHandler<Opt>() {
					public void handle(OptionParser<Opt> parser) throws OptionParserException {
						packageName = parser.getValue(Opt.PACKAGE_NAME);
					}
				});
		optionParser.addOptionWithArgument(Opt.GROUP, "g", "group", "GROUP_NAME", "specify the maven group name of this project. default = org.utgenome.track",
				new OptionHandler<Opt>() {
					public void handle(OptionParser<Opt> parser) throws OptionParserException {
						group = parser.getValue(Opt.GROUP);
					}
				});
		optionParser.addOptionWithArgument(Opt.TARGET_FILE, "f", "file", "FILENAME", "repair specified file only", new OptionHandler<Opt>() {
			public void handle(OptionParser<Opt> parser) throws OptionParserException {
				repairTargetFile = parser.getValue(Opt.TARGET_FILE);
				scaffoldFilter = new Create.ScaffoldFileFilter() {
					public boolean accept(String pathname) {
						return pathname.equals(repairTargetFile);
					}
				};
			}
		});
	}

	@Override
	public void execute(String[] args) throws UTGBShellException {
		try {
			optionParser.parse(args);
			try {
				TrackConfiguration config = loadTrackConfiguration();
				Create.createScaffold(config.getProjectName(), config.getPackage(), config.getGroup(), "./", scaffoldFilter);
			}
			catch (UTGBShellException e) {
				_logger.info("No config/track-config.xml file found or the config file is collapsed");
				// create from scratch
				if (optionParser.getArgumentLength() < 1)
					throw new UTGBShellException("please specify your package name with -p option and the project name as a command line argument.");
				String projectName = optionParser.getArgument(0);
				if (packageName == null)
					packageName = projectName;
				Create.createScaffold(projectName, packageName, group, "./", scaffoldFilter);
			}
		}
		catch (IOException e) {
			throw new UTGBShellException(e);
		}
		catch (OptionParserException e) {
			throw new UTGBShellException(e);
		}
	}

	@Override
	public String name() {
		return "repair";
	}

	public String getDetailedDescription() {
		return loadUsage("help-repair.txt");
	}

	public String getOneLinerDescription() {
		return "repair or restore template files";
	}

	public String getOptionList() {
		return optionParser.helpMessage();
	}
}