Program: 9638
Project: 9638
Buggy source:
public static void main(String[] args) throws IOException, ComponentInitException, IllegalArgumentException, SecurityException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, LearningProblemUnsupportedException {
  SimpleLayout layout=new SimpleLayout();
  ConsoleAppender consoleAppender=new ConsoleAppender(layout);
  Logger.getRootLogger().setLevel(Level.WARN);
  Logger.getLogger("String_Node_Str").setLevel(Level.WARN);
  Logger.getRootLogger().removeAllAppenders();
  Logger.getRootLogger().addAppender(consoleAppender);
  OptionParser parser=new OptionParser();
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(Boolean.class).defaultsTo(false);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withRequiredArg().ofType(URL.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(URI.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(URI.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(File.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(String.class).defaultsTo("String_Node_Str");
  OptionSet options=null;
  try {
    options=parser.parse(args);
  }
 catch (  Exception e) {
    System.out.println("String_Node_Str" + e.getMessage() + "String_Node_Str");
    System.exit(0);
  }
  if (options.has("String_Node_Str")) {
    parser.printHelpOn(System.out);
    String addHelp="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
    System.out.println();
    System.out.println(addHelp);
  }
 else {
    URL endpoint=(URL)options.valueOf("String_Node_Str");
    URI graph=(URI)options.valueOf("String_Node_Str");
    LinkedList<String> defaultGraphURIs=new LinkedList<String>();
    if (graph != null) {
      defaultGraphURIs.add(graph.toString());
    }
    SparqlEndpoint se=new SparqlEndpoint(endpoint,defaultGraphURIs,new LinkedList<String>());
    Entity resource=null;
    if (options.valueOf("String_Node_Str") != null) {
      resource=new SPARQLTasks(se).guessResourceType(((URI)options.valueOf("String_Node_Str")).toString());
      if (resource == null) {
        throw new IllegalArgumentException("String_Node_Str" + options.valueOf("String_Node_Str"));
      }
    }
    if (!options.hasArgument("String_Node_Str")) {
      System.out.println("String_Node_Str");
    }
    boolean verbose=(Boolean)options.valueOf("String_Node_Str");
    Enrichment e=new Enrichment(se,resource,verbose);
    e.start();
    SparqlEndpointKS ks=new SparqlEndpointKS(se);
    File f=(File)options.valueOf("String_Node_Str");
    if (options.has("String_Node_Str")) {
      if (options.valueOf("String_Node_Str").equals("String_Node_Str")) {
        List<AlgorithmRun> runs=e.getAlgorithmRuns();
        List<OWLAxiom> axioms=new LinkedList<OWLAxiom>();
        for (        AlgorithmRun run : runs) {
          axioms.addAll(e.toRDF(run.getAxioms(),run.getAlgorithm(),run.getParameters(),ks));
        }
        Model model=e.getModel(axioms);
        if (options.has("String_Node_Str")) {
          model.write(new FileOutputStream(f));
        }
 else {
          System.out.println("String_Node_Str");
          model.write(System.out);
          System.out.println("String_Node_Str");
        }
      }
    }
  }
}

Fixed version (ground truth):
public static void main(String[] args) throws IOException, ComponentInitException, IllegalArgumentException, SecurityException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, LearningProblemUnsupportedException {
  SimpleLayout layout=new SimpleLayout();
  ConsoleAppender consoleAppender=new ConsoleAppender(layout);
  Logger.getRootLogger().setLevel(Level.WARN);
  Logger.getLogger("String_Node_Str").setLevel(Level.WARN);
  Logger.getRootLogger().removeAllAppenders();
  Logger.getRootLogger().addAppender(consoleAppender);
  OptionParser parser=new OptionParser();
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(Boolean.class).defaultsTo(false);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withRequiredArg().ofType(URL.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(URI.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(URI.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(File.class);
  parser.acceptsAll(asList("String_Node_Str","String_Node_Str"),"String_Node_Str").withOptionalArg().ofType(String.class).defaultsTo("String_Node_Str");
  OptionSet options=null;
  try {
    options=parser.parse(args);
  }
 catch (  Exception e) {
    System.out.println("String_Node_Str" + e.getMessage() + "String_Node_Str");
    System.exit(0);
  }
  if (options.has("String_Node_Str")) {
    parser.printHelpOn(System.out);
    String addHelp="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
    System.out.println();
    System.out.println(addHelp);
  }
 else {
    URL endpoint=(URL)options.valueOf("String_Node_Str");
    URI graph=(URI)options.valueOf("String_Node_Str");
    LinkedList<String> defaultGraphURIs=new LinkedList<String>();
    if (graph != null) {
      defaultGraphURIs.add(graph.toString());
    }
    SparqlEndpoint se=new SparqlEndpoint(endpoint,defaultGraphURIs,new LinkedList<String>());
    Entity resource=null;
    if (options.valueOf("String_Node_Str") != null) {
      resource=new SPARQLTasks(se).guessResourceType(((URI)options.valueOf("String_Node_Str")).toString());
      if (resource == null) {
        throw new IllegalArgumentException("String_Node_Str" + options.valueOf("String_Node_Str"));
      }
    }
    if (!options.hasArgument("String_Node_Str")) {
      System.out.println("String_Node_Str");
    }
    boolean verbose=(Boolean)options.valueOf("String_Node_Str");
    Enrichment e=new Enrichment(se,resource,verbose);
    e.start();
    SparqlEndpointKS ks=new SparqlEndpointKS(se);
    File f=(File)options.valueOf("String_Node_Str");
    if (options.has("String_Node_Str")) {
      if (options.valueOf("String_Node_Str").equals("String_Node_Str")) {
        List<AlgorithmRun> runs=e.getAlgorithmRuns();
        List<OWLAxiom> axioms=new LinkedList<OWLAxiom>();
        for (        AlgorithmRun run : runs) {
          axioms.addAll(e.toRDF(run.getAxioms(),run.getAlgorithm(),run.getParameters(),ks));
        }
        Model model=e.getModel(axioms);
        for (        Statement st : model.listStatements().toList()) {
          System.out.println("String_Node_Str");
          if (st.getSubject().isResource()) {
            System.out.println(st.getSubject());
          }
          System.out.println(st.getPredicate());
          if (st.getObject().isResource()) {
          }
          System.out.println(st.getObject());
        }
        if (options.has("String_Node_Str")) {
          model.write(new FileOutputStream(f));
        }
 else {
          System.out.println("String_Node_Str");
          model.write(System.out);
          System.out.println("String_Node_Str");
        }
      }
    }
  }
}