Java tutorial
/** * Copyright (C) 2012 Selventa, Inc. * * This file is part of the OpenBEL Framework. * * 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 3 of the License, or * (at your option) any later version. * * The OpenBEL Framework 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 Lesser General Public * License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>. * * Additional Terms under LGPL v3: * * This license does not authorize you and you are prohibited from using the * name, trademarks, service marks, logos or similar indicia of Selventa, Inc., * or, in the discretion of other licensors or authors of the program, the * name, trademarks, service marks, logos or similar indicia of such authors or * licensors, in any marketing or advertising materials relating to your * distribution of the program or any covered product. This restriction does * not waive or limit your obligation to keep intact all copyright notices set * forth in the program as delivered to you. * * If you distribute the program in whole or in part, or any modified version * of the program, and you assume contractual liability to the recipient with * respect to the program or modified version, then you will indemnify the * authors and licensors of the program for any liabilities that these * contractual assumptions directly impose on those licensors and authors. */ package org.openbel.framework.tools; import static org.openbel.framework.common.BELUtilities.noItems; import static org.openbel.framework.common.Strings.SYSTEM_CONFIG_PATH; import static org.openbel.framework.common.enums.ExitCode.NO_XBEL_DOCUMENTS; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.net.MalformedURLException; import java.net.URI; import java.net.URISyntaxException; import java.net.URL; import java.util.LinkedList; import java.util.List; import javax.xml.bind.JAXBException; import org.apache.commons.cli.Option; import org.openbel.framework.common.enums.ExitCode; import org.openbel.framework.common.model.Document; import org.openbel.framework.core.CommandLineApplication; import org.openbel.framework.core.ConversionError; import org.openbel.framework.core.XBELConverterService; import org.openbel.framework.core.XBELConverterServiceImpl; import org.openbel.framework.core.XBELValidatorService; import org.openbel.framework.core.XBELValidatorServiceImpl; import org.openbel.framework.core.compiler.ValidationError; import org.xml.sax.SAXException; /** * The <tt>Backtrack</tt> BEL command-line application. */ public class Backtrack extends CommandLineApplication { private final XBELValidatorService validator; private final XBELConverterService converter; /** * System configuration command-line argument short option, * {@value #SHORT_OPT_SYSCFG}. */ protected final static String SHORT_OPT_SYSCFG = "s"; /** * System configuration command-line argument long option, * {@value #LONG_OPT_SYSCFG}. */ protected final static String LONG_OPT_SYSCFG = "system-config"; /** * Creates the application with the provided command-line arguments. * * @param args Command-line arguments * @throws JAXBException Thrown if an error was encountered during JAXB * processing * @throws SAXException Thrown if an error is found during processing the * specified schemas; the current API does not provide * {@link org.xml.sax.ErrorHandler SAX error handler} functionality * @throws MalformedURLException thrown if the schema file {@link URL}s * syntax is malformed * @throws URISyntaxException thrown if a {@link URL} in {@code schemas} has * invalid {@link URI} syntax * @throws IOException thrown if an i/o error occurs reading from the schema * url's {@link InputStream} */ private Backtrack(String[] args) throws MalformedURLException, SAXException, IOException, URISyntaxException, JAXBException { super(args); setReportable(null); initializeSystemConfiguration(); validator = new XBELValidatorServiceImpl(); converter = new XBELConverterServiceImpl(); List<String> extraargs = getExtraneousArguments(); // Quit now if no XBEL document was provided, or too many args. if (noItems(extraargs) || extraargs.size() > 1) { printUsage(); bail(NO_XBEL_DOCUMENTS); } // Quit now if file is not readable final File file = new File(extraargs.get(0)); if (!file.canRead()) { reportable.error("bad input " + file); printUsage(); bail(NO_XBEL_DOCUMENTS); } try { validate(file); } catch (ValidationError ve) { reportable.error(ve.getUserFacingMessage()); bail(ExitCode.NO_VALID_DOCUMENTS); } Document document = null; try { document = convert(file); } catch (ConversionError ce) { reportable.error("Failed converting file to BEL model"); reportable.error(ce.getUserFacingMessage()); bail(ExitCode.NO_CONVERTED_DOCUMENTS); } String output = ""; try { output = convert(document); } catch (ConversionError ce) { reportable.error("Failed converting BEL model to BEL document"); reportable.error(ce.getUserFacingMessage()); bail(ExitCode.NO_CONVERTED_DOCUMENTS); } reportable.output(output); } private void validate(final File f) throws ValidationError { validator.validate(f); } private String convert(final Document d) throws ConversionError { try { return converter.toXML(d); } catch (JAXBException e) { e.printStackTrace(); final String name = d.getName(); final String msg = e.getMessage(); final Throwable cause = e; throw new ConversionError(name, msg, cause); } catch (IOException e) { final String name = d.getName(); final String msg = e.getMessage(); final Throwable cause = e; throw new ConversionError(name, msg, cause); } } private Document convert(final File f) throws ConversionError { try { Document document = converter.toCommon(f); return document; } catch (JAXBException e) { final String name = f.getAbsolutePath(); final String msg = e.getMessage(); final Throwable cause = e; throw new ConversionError(name, msg, cause); } catch (IOException e) { final String name = f.getAbsolutePath(); final String msg = e.getMessage(); final Throwable cause = e; throw new ConversionError(name, msg, cause); } } /** * {@inheritDoc} */ @Override public List<Option> getCommandLineOptions() { final List<Option> ret = new LinkedList<Option>(); ret.add(new Option(SHORT_OPT_SYSCFG, LONG_OPT_SYSCFG, true, SYSTEM_CONFIG_PATH)); return ret; } /** * {@inheritDoc} */ @Override public String getUsage() { return "FILE"; } /** * Returns {@code "BEL Backtrack"}. */ @Override public String getApplicationName() { return "BEL Backtrack"; } /** * Returns {@code "Backtrack"}. * * @return String */ @Override public String getApplicationShortName() { return "Backtrack"; } /** * {@inheritDoc} */ @Override public String getApplicationDescription() { final StringBuilder bldr = new StringBuilder(); bldr.append("Converts a BEL document to the BEL model, "); bldr.append("then reconstitutes the BEL document."); return bldr.toString(); } /** * Backtrack {@code main()}. * * @param args Command-line arguments */ public static void main(String... args) { try { Backtrack b = new Backtrack(args); b.end(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (SAXException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (URISyntaxException e) { e.printStackTrace(); } catch (JAXBException e) { e.printStackTrace(); } } }