Program: 133684
Project: 133684
Buggy source:
/** 
 * This operations loads a MOOSE GetPot file at the specified path and returns a fully-configured set of ICE TreeComposites.
 * @param filePath The file path from which the MOOSE blocks written in GetPot should be read. If the path is null or empty, the operation returns without doing any work.
 * @return The MOOSE input file specification as read from the GetPot inputand stored in TreeComposites. Each TreeComposite contains both parameters and exemplar children. Any parameters in a TreeComposite are contained in a DataComponent. The id of the data component is 1.
 */
public ArrayList<TreeComposite> loadFromGetPot(String filePath){
  ArrayList<TreeComposite> trees=new ArrayList<TreeComposite>();
  byte[] fileByteArray=null;
  String mooseFileString=null, potLine=null;
  if (filePath == null || filePath.isEmpty()) {
    return null;
  }
  if (debugFlag) {
    System.out.println("String_Node_Str" + "String_Node_Str" + filePath);
  }
  try {
    RandomAccessFile mooseFile=new RandomAccessFile(filePath,"String_Node_Str");
    fileByteArray=new byte[(int)mooseFile.length()];
    mooseFile.read(fileByteArray);
    mooseFileString=new String(fileByteArray);
    mooseFile.close();
    if (debugFlag) {
      System.out.println("String_Node_Str");
    }
  }
 catch (  IOException e) {
    System.err.println("String_Node_Str" + "String_Node_Str");
    e.printStackTrace();
  }
  if (mooseFileString != null && !mooseFileString.isEmpty()) {
    ArrayList<String> potLines=new ArrayList<String>(Arrays.asList(mooseFileString.split("String_Node_Str")));
    String trimmedPotLine="String_Node_Str";
    for (int i=0; i < potLines.size(); i++) {
      trimmedPotLine=potLines.get(i).trim();
      if (trimmedPotLine.startsWith("String_Node_Str") && !trimmedPotLine.contains("String_Node_Str") && !trimmedPotLine.contains("String_Node_Str")&& !trimmedPotLine.contains("String_Node_Str")) {
        potLines.remove(i);
        --i;
      }
 else       if (potLines.get(i).isEmpty()) {
        potLines.remove(i);
        --i;
      }
 else {
        potLines.set(i,potLines.get(i).trim());
      }
    }
    int counter=0, endCounter=1;
    while (counter < potLines.size()) {
      potLine=potLines.get(counter);
      ++counter;
      if (potLine.contains("String_Node_Str") && potLine.contains("String_Node_Str")) {
        potLine=potLines.get(endCounter);
        while (!potLine.contains("String_Node_Str")) {
          potLine=potLines.get(endCounter);
          ++endCounter;
        }
        Block block=new Block();
        ArrayList<String> blockLines=new ArrayList<String>(potLines.subList(counter - 1,endCounter));
        StringBuilder stringBuilder=new StringBuilder(blockLines.get(0));
        blockLines.set(0,stringBuilder.toString());
        block.fromGetPot(blockLines);
        trees.add(block.toTreeComposite());
        counter=endCounter;
        if (debugFlag) {
          System.out.println("String_Node_Str" + "String_Node_Str" + filePath + "String_Node_Str");
          for (          String line : blockLines) {
            System.out.println(line);
          }
        }
      }
    }
  }
 else   if (debugFlag) {
    System.err.println("String_Node_Str" + "String_Node_Str" + filePath + "String_Node_Str");
  }
  return trees;
}

Fixed version (ground truth):
/** 
 * This operations loads a MOOSE GetPot file at the specified path and returns a fully-configured set of ICE TreeComposites.
 * @param filePath The file path from which the MOOSE blocks written in GetPot should be read. If the path is null or empty, the operation returns without doing any work.
 * @return The MOOSE input file specification as read from the GetPot inputand stored in TreeComposites. Each TreeComposite contains both parameters and exemplar children. Any parameters in a TreeComposite are contained in a DataComponent. The id of the data component is 1.
 */
public ArrayList<TreeComposite> loadFromGetPot(String filePath){
  ArrayList<TreeComposite> trees=new ArrayList<TreeComposite>();
  byte[] fileByteArray=null;
  String mooseFileString=null, potLine=null;
  if (filePath == null || filePath.isEmpty()) {
    return null;
  }
  if (debugFlag) {
    System.out.println("String_Node_Str" + "String_Node_Str" + filePath);
  }
  try {
    RandomAccessFile mooseFile=new RandomAccessFile(filePath,"String_Node_Str");
    fileByteArray=new byte[(int)mooseFile.length()];
    mooseFile.read(fileByteArray);
    mooseFileString=new String(fileByteArray);
    mooseFile.close();
    if (debugFlag) {
      System.out.println("String_Node_Str");
    }
  }
 catch (  IOException e) {
    System.err.println("String_Node_Str" + "String_Node_Str");
    e.printStackTrace();
  }
  if (mooseFileString != null && !mooseFileString.isEmpty()) {
    ArrayList<String> potLines=new ArrayList<String>(Arrays.asList(mooseFileString.split("String_Node_Str")));
    String trimmedPotLine="String_Node_Str";
    for (int i=0; i < potLines.size(); i++) {
      trimmedPotLine=potLines.get(i).trim();
      if (trimmedPotLine.startsWith("String_Node_Str") && !trimmedPotLine.contains("String_Node_Str") && !trimmedPotLine.contains("String_Node_Str")&& !trimmedPotLine.contains("String_Node_Str")) {
        potLines.remove(i);
        --i;
      }
 else       if (potLines.get(i).isEmpty()) {
        potLines.remove(i);
        --i;
      }
 else {
        if (trimmedPotLine.startsWith("String_Node_Str") && trimmedPotLine.contains("String_Node_Str")) {
          String[] splitTrimmedPotLine=trimmedPotLine.split("String_Node_Str");
          if (splitTrimmedPotLine.length > 4) {
            potLines.remove(i);
            --i;
            continue;
          }
        }
        potLines.set(i,potLines.get(i).trim());
      }
    }
    int counter=0, endCounter=1;
    while (counter < potLines.size()) {
      potLine=potLines.get(counter);
      ++counter;
      if (potLine.contains("String_Node_Str") && potLine.contains("String_Node_Str")) {
        potLine=potLines.get(endCounter);
        while (!potLine.contains("String_Node_Str")) {
          potLine=potLines.get(endCounter);
          ++endCounter;
        }
        Block block=new Block();
        ArrayList<String> blockLines=new ArrayList<String>(potLines.subList(counter - 1,endCounter));
        StringBuilder stringBuilder=new StringBuilder(blockLines.get(0));
        blockLines.set(0,stringBuilder.toString());
        block.fromGetPot(blockLines);
        trees.add(block.toTreeComposite());
        counter=endCounter;
        if (debugFlag) {
          System.out.println("String_Node_Str" + "String_Node_Str" + filePath + "String_Node_Str");
          for (          String line : blockLines) {
            System.out.println(line);
          }
        }
      }
    }
  }
 else   if (debugFlag) {
    System.err.println("String_Node_Str" + "String_Node_Str" + filePath + "String_Node_Str");
  }
  return trees;
}