Examples of org.molgenis.util.cmdline.CmdLineParser

org.molgenis.util.cmdline.CmdLineParser

This class defines the commandline options parser. Based on a class filled with members annotated with the Option annotation-type the parser knows for which minus parameters to look and to convert the accompanying string to which type. After the parse-function is finished the annotated object is filled with the data passed with the command-line options.

 class Example { class Options { \@Option(name="t", param="integer", type=Option.OptionType.REQUIRED_ARGUMENT, usage= "a long description here ...") public int threshold = 500; \@option(name="f", param="filename", type=Option.OptionType.REQUIRED_ARGUMENT, usage= "a long description here ...") public String file = "std_file.txt"; \@option(name="fs", param="filename-list comma separated", type=Option.OptionType.REQUIRED_ARGUMENT, usage= "a long description here ...") public Vector files = new Vector(); \@option(name="d", param="", type=Option.OptionType.NO_ARGUMENT, usage= "a long description here ...") public boolean do_something = false;  } public static void main(String args[]) { Example m = new Example(); Options options = m.new Options(); CmdLineParser parser = new CmdLineParser(options); try { parser.parse(args); } catch(CmdLineException e) { parser.printUsage(System.err, e.toString()); } if (options.do_something) { ... } } }

TODO Although some support is in place, methods are still not supported. TODO Help-output should be nicely formatted. TODO Make the program description also an annotated type ? @author RA Scheltema @version 1.0.0

    finally
    {
      IOUtils.closeQuietly(is);
    }


    CmdLineParser parser = new CmdLineParser(this);
    parser.parse(props);
    this.molgenis_properties = propertiesFile;


    // parse passwordfile
    String passwordFile = propertiesFile.replace(".properties", ".passwd");
    this.molgenis_passwd = passwordFile;
    props = new Properties();
    is = null;
    try
    {
      // try to load from local files
      is = new FileInputStream(passwordFile.trim());
      props.load(is);
    }
    catch (FileNotFoundException e)
    {
      InputStream is2 = ClassLoader.getSystemResourceAsStream(passwordFile.trim());
      try
      {
        // try to load from classpath
        props.load(is2);
      }
      catch (Exception e2)
      {
        // no biggie
      }
      finally
      {
        IOUtils.closeQuietly(is2);
      }
    }
    finally
    {
      IOUtils.closeQuietly(is);
    }
    parser = new CmdLineParser(this);
    parser.parse(props);


    // warn if no password was provided
    if ("".equals(this.db_password)) System.err.println("WARNING: db_password was not provided in neither "
        + propertiesFile + " nor " + passwordFile);

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   * @throws FileNotFoundException
   * @throws CmdLineException
   */
  public MolgenisOptions(Properties properties)
  {
    CmdLineParser parser;
    try
    {
      parser = new CmdLineParser(this);
      parser.parse(properties);
      Logger.getLogger(this.getClass().getSimpleName()).debug("parsed properties file.");
    }
    catch (Exception e)
    {
      // TODO Auto-generated catch block

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  @Override
  public String toString()
  {
    try
    {
      return new CmdLineParser(this).toString(this);
    }
    catch (NullPointerException e)
    {
      e.printStackTrace();
    }

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Related Classes of org.molgenis.util.cmdline.CmdLineParser

org.molgenis.MolgenisOptions

java.lang.reflect.Field

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