private boolean expandMetaChoice(
      Writer output,
      DbObject object,
      MetaChoice choice,
      boolean state[],
      MetaClass childrenMetaClass,
      RuleOptions options)
      throws DbException, IOException, RuleException {

    boolean expanded = false;
    Object child = object.get(choice);

    if (child instanceof DbObject) {
      DbObject dbChild = (DbObject) child;
      MetaClass metaClass = dbChild.getMetaClass();
      String className = metaClass.getGUIName();
      boolean excluded = false;

      // check if child's class is excluded
      if (options != null) {
        excluded = options.isExcluded(className);

        // if not, check if parent's connection is excluded
        if (!excluded) {
          MetaClass metaClass2 = object.getMetaClass();
          String parentClassName = metaClass2.getGUIName();
          String connectionName = parentClassName + "." + choice.getGUIName();
          excluded = options.isExcluded(connectionName);
        } // end if
      } // end if

      if (!excluded) {
        if (childrenMetaClass.isAssignableFrom(metaClass)) {
          expanded |= expandChild(output, object, dbChild, 1, state, options);
        } // end if
      } // end if
    } // end if

    if ((!expanded) && (nullModifier != null)) {
      expanded |= nullModifier.expand(output, object, options);
    } // end if

    return expanded;
  } // end expandMetaChoice
  private MetaClass getChildrenMetaClass() {
    MetaClass childrenMetaClass = m_childrenMetaClass;

    if (childrenMetaClass == null) {
      m_childrenMetaClass = MetaClass.find(sChildrenMetaClass);
      childrenMetaClass = m_childrenMetaClass;
    }

    return childrenMetaClass;
  }
 /**
  * Reads the POST contents of the request and parses it into an Annotation object, ready to be
  * annotated. This method can also read a serialized document, if the input format is set to be
  * serialized.
  *
  * @param props The properties we are annotating with. This is where the input format is retrieved
  *     from.
  * @param httpExchange The exchange we are reading POST data from.
  * @return An Annotation representing the read document.
  * @throws IOException Thrown if we cannot read the POST data.
  * @throws ClassNotFoundException Thrown if we cannot load the serializer.
  */
 private Annotation getDocument(Properties props, HttpExchange httpExchange)
     throws IOException, ClassNotFoundException {
   String inputFormat = props.getProperty("inputFormat", "text");
   switch (inputFormat) {
     case "text":
       return new Annotation(
           IOUtils.slurpReader(new InputStreamReader(httpExchange.getRequestBody())));
     case "serialized":
       String inputSerializerName =
           props.getProperty("inputSerializer", ProtobufAnnotationSerializer.class.getName());
       AnnotationSerializer serializer = MetaClass.create(inputSerializerName).createInstance();
       Pair<Annotation, InputStream> pair = serializer.read(httpExchange.getRequestBody());
       return pair.first;
     default:
       throw new IOException("Could not parse input format: " + inputFormat);
   }
 }
  // 'official' constructor
  // new param: childrenMetaClass
  public Connector(
      String ruleName,
      MetaRelationship aConnector,
      String childRule,
      String[] optionalRules,
      MetaClass childrenMetaClass,
      Modifier[] someModifiers) {
    this(ruleName, aConnector, (Rule) null, childrenMetaClass, someModifiers);
    int nbRules = optionalRules.length;
    m_childStrRule = childRule;
    m_oneChildStrRule = optionalRules[0];
    m_whenCond = (nbRules > 1) ? optionalRules[1] : null;
    m_childrenMetaClass = childrenMetaClass;

    // store m_childrenMetaClass because it is transient
    if (m_childrenMetaClass != null) {
      sChildrenMetaClass = m_childrenMetaClass.getJClass().getName();
    }
  } // end Connector()
  public Connector(
      String ruleName,
      MetaRelationship aConnector,
      Rule aChildRule,
      MetaClass childrenMetaClass,
      Modifier[] someModifiers) {
    super(ruleName, someModifiers);
    m_connector = aConnector;
    m_childrenMetaClass = childrenMetaClass; // doesn't work
    childRule = aChildRule;

    // store m_connector because it is transient
    sConnector = m_connector.getJName();

    // store m_childrenMetaClass because it is transient
    if (m_childrenMetaClass != null) {
      sChildrenMetaClass = m_childrenMetaClass.getJClass().getName();
    }
  } // end Connector()
  public void generate(String inputFileName) throws Exception {
    List<MetaClass> metaClasses = new ArrayList<>();
    List<LifeLine> lifeLines = new ArrayList<>();
    List<MethodInvocation> rootMessages = new ArrayList<>();
    MethodInvocation parentMessage = new MethodInvocation();
    GsonBuilder builder = new GsonBuilder();
    List<MethodInvocation> methodInvocations = new ArrayList<>();
    Package mainPackage = new Package();
    List<Guard> listOfGuards = new ArrayList<>();
    Map<Guard, Instruction> guardToCFMap = new HashMap<>();
    List<Instruction> combinedFragments = new ArrayList<Instruction>();
    List<Operation> operationsList = new ArrayList<>();

    builder.registerTypeAdapter(RefObject.class, new RefObjectJsonDeSerializer());
    Gson gson = builder.create();

    Element myTypes = gson.fromJson(new FileReader(inputFileName), Element.class);
    if (myTypes._type.equals("Project")) {
      List<Element> umlElements =
          myTypes
              .ownedElements
              .stream()
              .filter(f -> f._type.equals("UMLModel"))
              .collect(Collectors.toList());
      if (umlElements.size() > 0) { // There has be to atleast one UMLModel package
        Element element = umlElements.get(0);
        // package that the classes are supposed to be in
        mainPackage.setName(element.name);
        List<Element> umlPackages =
            element
                .ownedElements
                .stream()
                .filter(g -> g._type.equals("UMLPackage"))
                .collect(Collectors.toList());
        if (umlPackages.size()
            > 1) { // There has to be two packages- one for class one for behaviour
          Element classes = umlPackages.get(0);
          Element behaviour = umlPackages.get(1);
          // *--------------------------CLASSES-------------------------------*//
          // in the first pass, get all classes that are defined in the diagram
          // get details that can be directly inferred from the json like, fields and operations,
          // which do not refer to other classes
          for (Element umlClass : classes.getOwnedElements()) {
            MetaClass metaClass = new MetaClass(umlClass.name, umlClass._id);

            // check if class is interface or not because there is no distinction in json
            if (umlClass._type.equals("UMLClass")) {
              metaClass.setInterface(false);
            } else {
              metaClass.setInterface(true);
            }
            if (umlClass.operations != null) {
              metaClass.setOperations(umlClass.operations);
              operationsList.addAll(metaClass.operations);
            }
            if (umlClass.attributes != null) {
              metaClass.setFields(umlClass.attributes);
            }
            metaClasses.add(metaClass);
          }

          // in second pass, define associations and generalizations for these classes
          for (Element umlClass : classes.getOwnedElements()) {
            if (umlClass.ownedElements != null) {
              // find corresponding metaclass, then populate the secondary inferences
              List<MetaClass> correspondingMetaClassList =
                  metaClasses
                      .stream()
                      .filter(f -> f._id.equals(umlClass._id))
                      .collect(Collectors.toList());
              MetaClass correspondingMetaClass = correspondingMetaClassList.get(0);
              List<Element> umlAssociations =
                  umlClass
                      .ownedElements
                      .stream()
                      .filter(f -> f._type.equals("UMLAssociation"))
                      .collect(Collectors.toList());

              if (umlAssociations.size() > 0) {
                correspondingMetaClass.setAssociations(metaClasses, umlAssociations);
              }
              List<Element> umlGeneralization =
                  umlClass
                      .ownedElements
                      .stream()
                      .filter(f -> f._type.equals("UMLGeneralization"))
                      .collect(Collectors.toList());
              if (umlGeneralization.size() > 0) {
                correspondingMetaClass.setGeneralizations(metaClasses, umlGeneralization);
              }
              List<Element> umlRealization =
                  umlClass
                      .ownedElements
                      .stream()
                      .filter(f -> f._type.equals("UMLInterfaceRealization"))
                      .collect(Collectors.toList());
              if (umlRealization.size() > 0) {
                correspondingMetaClass.setInterfaceRealization(metaClasses, umlRealization);
              }
            }
          }

          // *--------------------------CLASSES-------------------------------*//

          // *-----------------------  BEHAVIOUR---------------------------------*//
          for (Element umlCollaboration : behaviour.getOwnedElements()) {
            // Role to Class mapping
            ArrayList<Element> attributes = umlCollaboration.attributes;
            HashMap<String, MetaClass> roleToClassMap = new HashMap<>();
            if (attributes != null) {
              for (Element attribute : attributes) {
                List<MetaClass> roleClass =
                    metaClasses
                        .stream()
                        .filter(f -> f._id.equals(attribute.type.$ref))
                        .collect(Collectors.toList());
                roleToClassMap.put(attribute._id, roleClass.get(0));
              }
            }

            for (Element umlInteraction : umlCollaboration.ownedElements) {

              // mapping lifelines to the classes they correspond
              ArrayList<Element> participants = umlInteraction.participants;
              if (participants != null && participants.size() > 0) {
                for (Element participant : participants) {
                  MetaClass participantClass = roleToClassMap.get(participant.represent.$ref);
                  LifeLine lifeLine = new LifeLine();
                  lifeLine.setName(participant.name);
                  lifeLine.setId(participant._id);
                  lifeLine.setMetaClass(participantClass);
                  lifeLines.add(lifeLine);
                }
              }
              // first parse all the combined fragments and get ready
              if (umlInteraction.fragments != null) {
                for (Element fragment :
                    umlInteraction.fragments) { // depending on the fragment set the class
                  Instruction instruction = null;
                  if (fragment.interactionOperator.equals("loop")) {
                    Loop loop = new Loop();
                    loop.setId(fragment._id);
                    loop.setWeight(0);
                    Guard guard = new Guard(fragment.operands.get(0)._id);
                    // loop can have only one condition--- one condition-- condition is made up of
                    // AND or OR's
                    guard.setCondition(fragment.operands.get(0).guard);
                    loop.setGuard(guard);
                    instruction = loop;
                    combinedFragments.add(loop);
                    listOfGuards.add(guard);
                    guardToCFMap.put(guard, loop);
                  }

                  if (fragment.interactionOperator.equals("alt")) {
                    Conditional c = new Conditional();
                    c.setId(fragment._id);
                    c.setWeight(0);
                    instruction = c;
                    combinedFragments.add(c);

                    Guard consequence = new Guard(fragment.operands.get(0)._id);
                    consequence.setCondition(fragment.operands.get(0).guard);
                    c.setCons(consequence);
                    listOfGuards.add(consequence);
                    guardToCFMap.put(consequence, c);
                    consequence.setConsequence(true);

                    if (fragment.operands.size() > 1) {
                      Guard alternate = new Guard(fragment.operands.get(1)._id);
                      alternate.setCondition(fragment.operands.get(1).guard);
                      c.setAlt(alternate);
                      listOfGuards.add(alternate);
                      guardToCFMap.put(alternate, c);
                      alternate.setAlternative(true);
                    }
                  }

                  if (fragment.tags != null) {
                    for (Element tag : fragment.tags) {
                      if (tag.name.equals("parent")) {
                        List<Instruction> instructionList =
                            combinedFragments
                                .stream()
                                .filter(e -> e.getId().equals(tag.reference.$ref))
                                .collect(Collectors.toList());
                        if (instructionList.size() > 0) {
                          instructionList.get(0).getBlock().add(instruction);
                          instruction.setParent(instructionList.get(0));
                        }
                      }
                    }
                  }
                }
              }

              // parsing the messages and make nodes out them to later build a tree from the
              // lifelines
              ArrayList<Element> messages = umlInteraction.messages;
              Element startMessage = messages.get(0);
              String sourceRef = startMessage.source.$ref;
              String targetRef = startMessage.target.$ref;
              Element endMessage = null;

              LifeLine sourceLifeLine = getLifeLine(lifeLines, sourceRef);
              LifeLine targetLifeLine = getLifeLine(lifeLines, targetRef);

              // First message processing
              parentMessage = new MethodInvocation();
              parentMessage.setAssignmentTarget(startMessage.assignmentTarget);
              parentMessage.setMessageSort(startMessage.messageSort);
              parentMessage.setSource(sourceLifeLine.getMetaClass());
              parentMessage.setTarget(targetLifeLine.getMetaClass());
              parentMessage.setName(startMessage.name);
              parentMessage.setId(startMessage._id);
              if (sourceLifeLine.getId().equals(targetLifeLine.getId())) {
                parentMessage.setCallerObject("this");
              } else {
                parentMessage.setCallerObject(targetLifeLine.getName());
              }
              int weight = 0;
              parentMessage.setWeight(weight++);
              if (startMessage.signature != null) {
                parentMessage.setSignature(startMessage.signature.$ref);
              }

              if (startMessage.tags != null) {
                for (Element tag : startMessage.tags) {
                  //                                    if (tag.name.equals("CF")) {
                  //                                        parentMessage.setInCF(true);
                  //
                  // parentMessage.setCfID(tag.reference.$ref);
                  //                                    }
                  if (tag.name.equals("operand")) {
                    parentMessage.setOperandId(tag.reference.$ref);
                  }
                }
              }

              MethodInvocation rootMessage = parentMessage;
              methodInvocations.add(rootMessage);
              rootMessages.add(rootMessage);
              Iterator<Element> iter = messages.iterator();
              while (iter.hasNext()) {
                if (iter.next() == endMessage) {
                  continue;
                }

                iter.remove();
                List<Element> childMessages = getChildMessages(messages, targetRef);
                for (Element child : childMessages) {

                  LifeLine childSource = getLifeLine(lifeLines, child.source.$ref);
                  LifeLine childTarget = getLifeLine(lifeLines, child.target.$ref);

                  MethodInvocation childMessage = new MethodInvocation();
                  childMessage.setMessageSort(child.messageSort);
                  childMessage.setSource(childSource.getMetaClass());
                  childMessage.setTarget(childTarget.getMetaClass());
                  childMessage.setAssignmentTarget(child.assignmentTarget);
                  childMessage.setName(child.name);
                  childMessage.setId(child._id);
                  childMessage.setWeight(weight++);
                  childMessage.setArguments(child.arguments);

                  if (childSource.getId().equals(childTarget.getId())) {
                    childMessage.setCallerObject("this");
                  } else {
                    childMessage.setCallerObject(childTarget.getName());
                  }

                  if (child.signature != null) {
                    childMessage.setSignature(child.signature.$ref);
                  }

                  if (child.tags != null) {
                    for (Element tag : child.tags) {
                      //                                            if (tag.name.equals("CF")) {
                      //                                                childMessage.setInCF(true);
                      //
                      // childMessage.setCfID(tag.reference.$ref);
                      //                                            }
                      if (tag.name.equals("operand")) {
                        childMessage.setOperandId(tag.reference.$ref);
                      }
                    }
                  }

                  parentMessage.childNodes.add(childMessage);
                  methodInvocations.add(childMessage);
                }

                if (childMessages.size() > 0) {
                  List<MethodInvocation> nextMessage =
                      parentMessage
                          .childNodes
                          .stream()
                          .filter(f -> !f.source.equals(f.target))
                          .collect(Collectors.toList());
                  List<Element> startMessageNext =
                      childMessages
                          .stream()
                          .filter(f -> !f.source.$ref.equals(f.target.$ref))
                          .collect(Collectors.toList());
                  startMessage = startMessageNext.get(0);
                  targetRef = startMessage.target.$ref;
                  sourceRef = startMessage.source.$ref;

                  parentMessage = nextMessage.get(0);

                  if (childMessages.size() > 1) {
                    endMessage = childMessages.get(childMessages.size() - 1);
                  }
                }
              }
            }

            for (MethodInvocation methodInvocation : methodInvocations) {
              List<Operation> matchingOperation =
                  operationsList
                      .stream()
                      .filter(f -> f._id.equals(methodInvocation.getSignature()))
                      .collect(Collectors.toList());
              if (matchingOperation.size() > 0) {
                operationMap.put(methodInvocation, matchingOperation.get(0)._id);
                methodInvocation.setOperation(matchingOperation.get(0));
              }
            }

            Stack stack = new Stack();
            for (MethodInvocation root : methodInvocations) {
              stack.push(root);
              while (!stack.empty()) {
                MethodInvocation methodInvocation = (MethodInvocation) stack.pop();
                Operation currentOperation = methodInvocation.getOperation();

                if (currentOperation != null) {
                  // all child nodes of this node make up its body
                  List<MethodInvocation> childNodes = methodInvocation.childNodes;
                  for (MethodInvocation child : childNodes) {
                    stack.push(child);
                  }
                  for (MethodInvocation childNode : childNodes) {
                    if (childNode.getOperandId() != null) {
                      List<Instruction> combinedFragmentsList =
                          combinedFragments
                              .stream()
                              .filter(f -> f.getId().equals(childNode.getCfID()))
                              .collect(Collectors.toList());

                      List<Guard> guardList =
                          listOfGuards
                              .stream()
                              .filter(f -> f.id.equals(childNode.getOperandId()))
                              .collect(Collectors.toList());

                      if (guardList.size() > 0) {
                        Guard currentGuard = guardList.get(0);
                        Instruction instruction = guardToCFMap.get(guardList.get(0));
                        // get the topmost CF if it is in a tree
                        Instruction parent = instruction.getParent();

                        while (instruction.getParent() != null) {
                          instruction = instruction.getParent();
                        }

                        if (currentGuard.isConsequence) {
                          Conditional conditional = (Conditional) instruction;
                          if (!conditional.getConsequence().contains(childNode)) {
                            conditional.getConsequence().add(childNode);
                          }
                        }
                        if (currentGuard.isAlternative) {
                          Conditional conditional = (Conditional) instruction;
                          if (!conditional.getAlternative().contains(childNode)) {
                            conditional.getAlternative().add(childNode);
                          }
                        }
                        if (!currentGuard.isAlternative && !currentGuard.isConsequence) {
                          Loop loop = (Loop) instruction;
                          loop.getBlock().add(childNode);
                        } else {
                          if (!currentOperation.getBlock().contains(instruction)) {
                            currentOperation.getBlock().add(instruction);
                          }
                        }
                      }
                    } else {
                      if (!currentOperation.getBlock().contains(childNode)) {
                        currentOperation.getBlock().add(childNode);
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
    //
    ////        printAllData(metaClasses);
    //        while (parentMessage.childNodes != null || parentMessage.childNodes.size() > 0) {
    //            System.out.println("parent " + parentMessage.name);
    //            for (com.cbpro.main.MethodInvocation child : parentMessage.childNodes) {
    //                System.out.println("child " + child.name);
    //            }
    //            if (parentMessage.childNodes.size() > 0) {
    //                parentMessage = parentMessage.childNodes.get(0);
    //            } else {
    //                break;
    //            }
    //        }

    mainPackage.print();
    File dir = new File("/home/ramyashenoy/Desktop/DemoFolder/" + mainPackage.getName());

    boolean successful = dir.mkdir();
    if (successful) {
      System.out.println("directory was created successfully");
      for (MetaClass metaClass : metaClasses) {
        if (metaClass.name.equals("Main")) {
          continue;
        } else {
          String data = metaClass.print();
          BufferedWriter out = null;
          try {
            FileWriter fstream =
                new FileWriter(
                    dir.getPath() + "/" + metaClass.name + ".java",
                    true); // true tells to append data.
            out = new BufferedWriter(fstream);
            out.write(data);
          } catch (IOException e) {
            System.err.println("Error: " + e.getMessage());
          } finally {
            if (out != null) {
              out.close();
            }
          }
        }
      }
    } else {
      // creating the directory failed
      System.out.println("failed trying to create the directory");
    }

    mainPackage.setClasses(metaClasses);
  }
  // add childrenMetaClass to filter only children of that class
  // if null, scan each child
  protected boolean expandMetaRelationN(
      Writer output,
      DbObject object,
      MetaRelationship metaRelation,
      boolean state[],
      MetaClass childrenMetaClass,
      RuleOptions options)
      throws DbException, IOException, RuleException {

    boolean expanded = false;
    DbEnumeration dbEnumChildren = null;
    DbRelationN relationN = (DbRelationN) object.get(metaRelation);
    if (childrenMetaClass == null) {
      dbEnumChildren = relationN.elements();
    } else {
      dbEnumChildren = relationN.elements(childrenMetaClass);
    }

    // a first pass to find out the number of children
    int nbChildren = 0;
    try {
      while (dbEnumChildren.hasMoreElements()) {
        dbEnumChildren.nextElement();
        nbChildren++;

        // Cancel everything if the user has decided to stop the
        // operation
        if (options != null) {
          Controller controller = options.m_controller;
          if (controller != null) {
            boolean can_continue = controller.checkPoint();
            if (!can_continue) {
              throw new RuleException(controller.getAbortedString());
            }
          }
        } // end if
      } // end while
    } finally {
      dbEnumChildren.close();
    }

    // cannot rollback to the first element, so recreate the enumeration
    if (childrenMetaClass == null) {
      dbEnumChildren = relationN.elements();
    } else {
      dbEnumChildren = relationN.elements(childrenMetaClass);
    }

    try {
      while (dbEnumChildren.hasMoreElements()) {
        DbObject child = (DbObject) dbEnumChildren.nextElement();
        MetaClass metaClass = child.getMetaClass();
        String className = metaClass.getGUIName();
        boolean excluded = false;

        // check if child's class is excluded
        if (options != null) {
          excluded = options.isExcluded(className);

          // if not, check if parent's connection is excluded
          if (!excluded) {
            metaClass = object.getMetaClass();
            String parentClassName = metaClass.getGUIName();
            String connectionName = parentClassName + "." + metaRelation.getGUIName();
            excluded = options.isExcluded(connectionName);
          } // end if
        } // end if

        if (!excluded) {
          expanded |= expandChild(output, object, child, nbChildren, state, options);
        } // end if
      } // end while
    } finally {
      dbEnumChildren.close();
    }

    boolean atLeastOneChildPrinted = state[1];

    if ((atLeastOneChildPrinted) && (suffixModifier != null)) {
      expanded |= suffixModifier.expand(output, object, options);
    } else if ((!atLeastOneChildPrinted) && (nullModifier != null)) {
      expanded |= nullModifier.expand(output, object, options);
    }

    return expanded;
  } // end expandMetaRelationN
  private boolean expandMetaRelation1(
      Writer output,
      DbObject object,
      MetaRelation1 metaRelation1,
      boolean state[],
      MetaClass childrenMetaClass,
      RuleOptions options)
      throws DbException, IOException, RuleException {

    boolean expanded = false;
    Object child;
    if (childrenMetaClass != null) {
      if (metaRelation1 == DbObject.fComposite) {
        child = object.getCompositeOfType(childrenMetaClass);
      } else {
        child = object.get(metaRelation1);
        if (child instanceof DbObject) {
          DbObject dbChild = (DbObject) child;
          MetaClass mc = dbChild.getMetaClass();
          if (mc != childrenMetaClass) {
            child = null;
          }
        }
      }
    } else {
      child = object.get(metaRelation1);
    } // end if

    if (child != null) {
      if (child instanceof DbObject) {
        DbObject dbChild = (DbObject) child;
        MetaClass metaClass = dbChild.getMetaClass();
        String className = metaClass.getGUIName();
        boolean excluded = false;

        // check if child's class is excluded
        if (options != null) {
          excluded = options.isExcluded(className);

          // if not, check if parent's connection is excluded
          if (!excluded) {
            metaClass = object.getMetaClass();
            String parentClassName = metaClass.getGUIName();
            String connectionName = parentClassName + "." + metaRelation1.getGUIName();
            excluded = options.isExcluded(connectionName);
          } // end if
        } // end if

        if (!excluded) {
          expanded |= expandChild(output, object, dbChild, 1, state, options);
        } // end if
      } // end if
    } // end if

    // if a SUF modifier has to be expanded
    if ((expanded) && (suffixModifier != null)) {
      suffixModifier.expand(output, object, options);
    }

    // if a NULL modifier has to be expanded
    if ((!expanded) && (nullModifier != null)) {
      expanded |= nullModifier.expand(output, object, options);
    }

    return expanded;
  } // end expandMetaRelation1