Program: 39776
Project: 39776
Buggy source:
public Graph importGraphFromFile(String s){
  Graph gtna=new Graph(s);
  ProjectController pc=Lookup.getDefault().lookup(ProjectController.class);
  pc.newProject();
  Workspace workspace=pc.getCurrentWorkspace();
  ImportController importController=Lookup.getDefault().lookup(ImportController.class);
  Container container;
  try {
    File file=new File(getClass().getResource(s).toURI());
    container=importController.importFile(file);
    container.getLoader().setEdgeDefault(EdgeDefault.UNDIRECTED);
    container.setAllowAutoNode(true);
  }
 catch (  Exception e) {
    System.out.println("String_Node_Str" + s);
    return null;
  }
  importController.process(container,new DefaultProcessor(),workspace);
  GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getModel();
  UndirectedGraph gephi=graphModel.getUndirectedGraph();
  gtna.graph.Node[] nodes=new gtna.graph.Node[gephi.getNodeCount()];
  for (  Node n : gephi.getNodes()) {
    gtna.graph.Node node=new gtna.graph.Node(n.getId(),gtna);
    nodes[n.getId() - 1]=node;
  }
  int importedEdges=0;
  for (  Edge e : gephi.getEdges()) {
    importedEdges++;
    System.out.println("String_Node_Str" + importedEdges + "String_Node_Str"+ e.toString());
    int src=e.getSource().getId() - 1;
    int dst=e.getTarget().getId() - 1;
    System.out.println("String_Node_Str" + src + "String_Node_Str"+ dst);
    nodes[src].addOut(dst);
    nodes[dst].addIn(src);
  }
  gtna.setNodes(nodes);
  gtna.generateEdges();
  System.out.println("String_Node_Str" + gtna.getNodes().length + "String_Node_Str"+ gtna.getEdges().size()+ "String_Node_Str");
  for (  gtna.graph.Node n : gtna.getNodes()) {
    n.generateAllEdges();
    System.out.println("String_Node_Str" + n.toString() + "String_Node_Str"+ gephi.getNeighbors(gephi.getNode(n.getIndex())).toArray().length);
  }
  return gtna;
}

Fixed version (ground truth):
public Graph importGraphFromFile(String s){
  Graph gtnaGraph=new Graph(s);
  ProjectController pc=Lookup.getDefault().lookup(ProjectController.class);
  pc.newProject();
  Workspace workspace=pc.getCurrentWorkspace();
  ImportController importController=Lookup.getDefault().lookup(ImportController.class);
  Container container;
  try {
    File file=new File(getClass().getResource(s).toURI());
    container=importController.importFile(file);
    container.getLoader().setEdgeDefault(EdgeDefault.UNDIRECTED);
    container.setAllowAutoNode(true);
  }
 catch (  Exception e) {
    System.out.println("String_Node_Str" + s);
    return null;
  }
  importController.process(container,new DefaultProcessor(),workspace);
  GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getModel();
  gephi=graphModel.getUndirectedGraph();
  gtna.graph.Node[] nodes=gtna.graph.Node.init(gephi.getNodeCount(),gtnaGraph);
  int importedEdges=0;
  Edges edges=new Edges(nodes,gephi.getEdgeCount() * 2);
  for (  Edge e : gephi.getEdges()) {
    importedEdges++;
    System.out.println("String_Node_Str" + importedEdges + "String_Node_Str"+ e.toString());
    int src=e.getSource().getId() - 1;
    int dst=e.getTarget().getId() - 1;
    System.out.println("String_Node_Str" + src + "String_Node_Str"+ dst);
    edges.add(src,dst);
    edges.add(dst,src);
  }
  edges.fill();
  gtnaGraph.setNodes(nodes);
  System.out.println("String_Node_Str" + gtnaGraph.getNodes().length + "String_Node_Str"+ gtnaGraph.getEdges().size()+ "String_Node_Str");
  return gtnaGraph;
}