Program: 14586
Project: 14586
Buggy source:
public String generateTopology(){
  StringBuilder buf=new StringBuilder();
  Multimap<String,String> networks=ArrayListMultimap.create();
  Multimap<String,String> rules=ArrayListMultimap.create();
  EntityTransaction db=Entities.get(VmInstance.class);
  try {
    Predicate<VmInstance> filter=Predicates.and(VmState.TERMINATED.not(),VmState.STOPPED.not());
    for (    VmInstance vm : VmInstances.list(filter)) {
      try {
        for (        NetworkGroup ruleGroup : vm.getNetworkGroups()) {
          try {
            ruleGroup=Entities.merge(ruleGroup);
            networks.put(ruleGroup.getClusterNetworkName(),vm.getPrivateAddress());
            if (!rules.containsKey(ruleGroup.getNaturalId())) {
              for (              NetworkRule netRule : ruleGroup.getNetworkRules()) {
                try {
                  String rule=String.format("String_Node_Str",netRule.getProtocol(),(NetworkRule.Protocol.icmp.equals(netRule.getProtocol()) ? "String_Node_Str" : "String_Node_Str"),netRule.getLowPort(),(NetworkRule.Protocol.icmp.equals(netRule.getProtocol()) ? "String_Node_Str" : "String_Node_Str"),netRule.getHighPort());
                  for (                  NetworkPeer peer : netRule.getNetworkPeers()) {
                    String ruleString=String.format("String_Node_Str",rule,peer.getGroupName(),peer.getUserQueryKey());
                    if (!rules.get(ruleGroup.getClusterNetworkName()).contains(ruleString)) {
                      rules.put(ruleGroup.getClusterNetworkName(),ruleString);
                    }
                  }
                  for (                  String cidr : netRule.getIpRanges()) {
                    String ruleString=String.format("String_Node_Str",rule,cidr);
                    if (!rules.get(ruleGroup.getClusterNetworkName()).contains(ruleString)) {
                      rules.put(ruleGroup.getClusterNetworkName(),ruleString);
                    }
                  }
                }
 catch (                Exception ex) {
                  LOG.error(ex,ex);
                }
              }
            }
          }
 catch (          Exception ex) {
            LOG.error(ex,ex);
          }
        }
      }
 catch (      Exception ex) {
        LOG.error(ex,ex);
      }
    }
    buf.append(rulesToString(rules));
    buf.append(groupsToString(networks));
    db.rollback();
  }
 catch (  Exception ex) {
    LOG.error(ex,ex);
    db.rollback();
  }
  return buf.toString();
}

Fixed version (ground truth):
private static String generateTopology(){
  StringBuilder buf=new StringBuilder();
  Multimap<String,String> networks=ArrayListMultimap.create();
  Multimap<String,String> rules=ArrayListMultimap.create();
  EntityTransaction db=Entities.get(VmInstance.class);
  try {
    Predicate<VmInstance> filter=Predicates.and(VmState.TERMINATED.not(),VmState.STOPPED.not());
    for (    VmInstance vm : VmInstances.list(filter)) {
      try {
        for (        NetworkGroup ruleGroup : vm.getNetworkGroups()) {
          try {
            ruleGroup=Entities.merge(ruleGroup);
            networks.put(ruleGroup.getClusterNetworkName(),vm.getPrivateAddress());
            if (!rules.containsKey(ruleGroup.getNaturalId())) {
              for (              NetworkRule netRule : ruleGroup.getNetworkRules()) {
                try {
                  String rule=String.format("String_Node_Str",netRule.getProtocol(),(NetworkRule.Protocol.icmp.equals(netRule.getProtocol()) ? "String_Node_Str" : "String_Node_Str"),netRule.getLowPort(),(NetworkRule.Protocol.icmp.equals(netRule.getProtocol()) ? "String_Node_Str" : "String_Node_Str"),netRule.getHighPort());
                  for (                  NetworkPeer peer : netRule.getNetworkPeers()) {
                    String ruleString=String.format("String_Node_Str",rule,peer.getGroupName(),peer.getUserQueryKey());
                    if (!rules.get(ruleGroup.getClusterNetworkName()).contains(ruleString)) {
                      rules.put(ruleGroup.getClusterNetworkName(),ruleString);
                    }
                  }
                  for (                  String cidr : netRule.getIpRanges()) {
                    String ruleString=String.format("String_Node_Str",rule,cidr);
                    if (!rules.get(ruleGroup.getClusterNetworkName()).contains(ruleString)) {
                      rules.put(ruleGroup.getClusterNetworkName(),ruleString);
                    }
                  }
                }
 catch (                Exception ex) {
                  LOG.error(ex,ex);
                }
              }
            }
          }
 catch (          Exception ex) {
            LOG.error(ex,ex);
          }
        }
      }
 catch (      Exception ex) {
        LOG.error(ex,ex);
      }
    }
    buf.append(rulesToString(rules));
    buf.append(groupsToString(networks));
    db.rollback();
  }
 catch (  Exception ex) {
    LOG.error(ex,ex);
    db.rollback();
  }
  return buf.toString();
}