Java tutorial
/* The MIT License (MIT) Copyright (c) 2015 Pierre Lindenbaum Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package com.github.lindenb.jvarkit.util.command; import java.awt.Image; import java.awt.image.BufferedImage; import java.io.InputStream; import java.io.PrintStream; import java.io.PrintWriter; import java.net.InetAddress; import java.net.URL; import java.text.DecimalFormat; import java.util.Collection; import java.util.Date; import java.util.Enumeration; import java.util.jar.Manifest; import javax.swing.AbstractAction; import javax.swing.Icon; import javax.swing.ImageIcon; import javax.xml.stream.XMLStreamException; import javax.xml.stream.XMLStreamWriter; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.OptionGroup; import org.apache.commons.cli.Options; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import com.github.lindenb.jvarkit.util.htsjdk.HtsjdkVersion; import com.github.lindenb.jvarkit.util.log.Logging; @Deprecated public abstract class CommandFactory { protected enum Status { OK, EXIT_SUCCESS, EXIT_FAILURE }; private static final Log LOG = Logging.getLog(CommandFactory.class); private String version = null; private String compileDate; /** error stream */ private java.io.PrintStream _errStream = System.err; /** stdout stream */ private java.io.PrintStream _outStream = System.out; /** stdin stream */ private java.io.InputStream _inStream = System.in; public CommandFactory() { } public String getMessageBundle(String s) { return s == null ? "" : s; } public java.io.PrintStream stderr() { return this._errStream; } public void stderr(final java.io.PrintStream stream) { this._errStream = stream; } public java.io.PrintStream stdout() { return this._outStream; } public void stdout(final java.io.PrintStream stream) { this._outStream = stream; } public java.io.InputStream stdin() { return this._inStream; } public void stdin(final java.io.InputStream stream) { this._inStream = stream; } protected static final int ICON_SIZE = 64; private Icon _icon = null; protected Image getImageIcon() { BufferedImage img = new BufferedImage(ICON_SIZE, ICON_SIZE, BufferedImage.TYPE_INT_ARGB); return img; } public Icon getIcon() { if (_icon == null) { _icon = new ImageIcon(getImageIcon()); } return _icon; } public String getName() { return getClass().getName(); } public String getLabel() { return getName(); } public String getDescription() { return getLabel(); } protected Option createHelpOption() { return Option.builder("h").longOpt("help").hasArg(false).desc("show help (this screen)").build(); } protected Option createVersionOption() { return Option.builder("version").longOpt("version").hasArg(false).desc("show version and exit").build(); } protected void fillOptions(final Options opts) { final OptionGroup g = new OptionGroup(); g.addOption(createHelpOption()); g.addOption(createVersionOption()); g.addOption(Option.builder("proxy").required(false).longOpt("proxy").hasArg(true).argName("HOST:PORT") .desc("set the http and the https proxy.").build()); opts.addOptionGroup(g); } public abstract Command createCommand(); protected Status visit(final Option opt) { if (opt.getOpt().equals("version")) { stdout().println(getVersion()); return Status.EXIT_SUCCESS; } else if (opt.getOpt().equals("h")) { usage(stdout()); return Status.EXIT_SUCCESS; } else if (opt.getOpt().equals("proxy")) { String proxy = opt.getValue(); int colon = proxy.lastIndexOf(':'); if (colon == -1) { LOG.error("bad proxy \"" + proxy + "\""); return Status.EXIT_FAILURE; } LOG.debug("setting proxy " + proxy); System.setProperty("http.proxyHost", proxy.substring(0, colon)); System.setProperty("http.proxyPort", proxy.substring(colon + 1)); System.setProperty("https.proxyHost", proxy.substring(0, colon)); System.setProperty("https.proxyPort", proxy.substring(colon + 1)); return Status.OK; } LOG.fatal("Unknown option " + opt.getOpt()); return Status.EXIT_FAILURE; } protected void printOptions(final PrintStream out) { final Options opts = new Options(); fillOptions(opts); final HelpFormatter fmt = new HelpFormatter(); final PrintWriter w = new PrintWriter(out); fmt.setSyntaxPrefix(""); fmt.printOptions(w, 80, opts, 4, 5); w.flush(); } protected void printStandardPreamble(PrintStream out) { String prg = getName(); out.println(prg); for (int i = 0; i < prg.length(); ++i) out.print('='); out.println(); out.print("\nDescription: "); out.println(getDescription()); out.println(); out.println("Author : " + getAuthorName()); out.println("Mail : " + getAuthorMail()); out.println("WWW : " + getOnlineDocUrl()); out.println("Compilation : " + getCompileDate()); out.println("Git-Hash : " + getVersion()); out.println("Htsjdk-version : " + HtsjdkVersion.getVersion()); out.println("Htsjdk-home : " + HtsjdkVersion.getHome()); } private void loadManifest() { try { Enumeration<URL> resources = getClass().getClassLoader().getResources("META-INF/MANIFEST.MF");//not '/META-INF' while (resources.hasMoreElements()) { URL url = resources.nextElement(); InputStream in = url.openStream(); if (in == null) { continue; } Manifest m = new Manifest(in); in.close(); in = null; java.util.jar.Attributes attrs = m.getMainAttributes(); if (attrs == null) { continue; } String s = attrs.getValue("Git-Hash"); if (s != null && !s.isEmpty() && !s.contains("$")) //ant failed { this.version = s; } s = attrs.getValue("Compile-Date"); if (s != null && !s.isEmpty()) //ant failed { this.compileDate = s; } } } catch (Exception err) { } } public String getCompileDate() { if (this.compileDate == null) { this.compileDate = "undefined"; loadManifest(); } return compileDate; } public String getVersion() { if (this.version == null) { this.version = "1.0"; loadManifest(); } return version; } public String getOnlineDocUrl() { return "https://github.com/lindenb/jvarkit/wiki/" + getName(); } public String getAuthorName() { return "Pierre Lindenbaum PhD."; } public String getAuthorMail() { return "plinden" + "baum" + '@' + "yahoo" + '.' + "fr"; } protected void printSynopsis(PrintStream out) { out.println("\tjava -cp jar1.jar:jar2.jar:jar3.jar " + getClass().getName() + " [options] (files)"); } public void usage(PrintStream out) { out.println(); printStandardPreamble(out); out.println(); out.println("Usage:"); printSynopsis(out); out.println(); out.println("Options:"); printOptions(out); out.println(); } protected void writeHtmlDoc(final XMLStreamWriter w) throws XMLStreamException { w.writeStartElement("div"); w.writeComment("no doc available for " + getName()); w.writeEndElement(); } public int instanceMain(final String args[]) { /* create a new empty Command */ Command cmd = null; try { /* cmd line */ final StringBuilder sb = new StringBuilder(); for (String s : args) { if (sb.length() != 0) sb.append(" "); sb.append(s); } /* create new options */ final Options options = new Options(); /* get all options and add it to options */ fillOptions(options); /* create a new CLI parser */ final CommandLineParser parser = new DefaultParser(); final CommandLine cli = parser.parse(options, args); /* loop over the processed options */ for (final Option opt : cli.getOptions()) { if (opt.hasArg() && !opt.hasOptionalArg() && opt.getValue() == null) { LOG.warn("OPTION ####" + opt); } final Status status = visit(opt); switch (status) { case EXIT_FAILURE: return -1; case EXIT_SUCCESS: return 0; default: break; } } cmd = createCommand(); final Date startDate = new Date(); LOG.info("Starting JOB at " + startDate + " " + getClass().getName() + " version=" + getVersion() + " " + " built=" + getCompileDate()); LOG.info("Command Line args : " + (cmd.getProgramCommandLine().isEmpty() ? "(EMPTY/NO-ARGS)" : cmd.getProgramCommandLine())); String hostname = ""; try { hostname = InetAddress.getLocalHost().getHostName(); } catch (Exception err) { hostname = "host"; } LOG.info("Executing as " + System.getProperty("user.name") + "@" + hostname + " on " + System.getProperty("os.name") + " " + System.getProperty("os.version") + " " + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") + " " + System.getProperty("java.runtime.version")); LOG.debug("initialize " + cmd); final Collection<Throwable> initErrors = cmd.initializeKnime(); if (!(initErrors == null || initErrors.isEmpty())) { for (Throwable err : initErrors) { LOG.error(err); } LOG.fatal("Command initialization failed "); return -1; } LOG.debug("calling " + cmd); final Collection<Throwable> errors = cmd.call(); if (!(errors == null || errors.isEmpty())) { for (Throwable err : errors) { LOG.error(err); } LOG.fatal("Command failed "); return -1; } LOG.debug("success " + cmd); cmd.disposeKnime(); final Date endDate = new Date(); final double elapsedMinutes = (endDate.getTime() - startDate.getTime()) / (1000d * 60d); final String elapsedString = new DecimalFormat("#,##0.00").format(elapsedMinutes); LOG.info("End JOB [" + endDate + "] " + getName() + " done. Elapsed time: " + elapsedString + " minutes."); return 0; } catch (org.apache.commons.cli.UnrecognizedOptionException err) { LOG.fatal("Unknown command (" + err.getOption() + ") , please check your input.", err); return -1; } catch (Throwable err) { LOG.fatal("cannot build command", err); return -1; } finally { if (cmd != null) cmd.cleanup(); } } public void instanceMainWithExit(final String args[]) { int ret = instanceMain(args); System.exit(ret); } }