/**
   * Process and loop until told to stop. A callback_done will stop the loop and will return a
   * result. Otherwise null is returned.
   */
  public Object run() throws CommandException {
    Object result = null;
    boolean shutdown = false;
    boolean closeWhenDone = true;
    Commands.ValueObject valueObject =
        new Commands.ValueObject(); // Working value object so not continually recreated.
    InvokableValueSender valueSender =
        new InvokableValueSender(); // Working valuesender so not continually recreated.
    try {
      boolean doLoop = true;

      /**
       * Note: In the cases below you will see a lot of finally clauses that null variables out.
       * This is because this is a long running loop, and variables declared within blocks are not
       * garbage collected until the method is terminated, so these variables once set would never
       * be GC'd. The nulling at the end of the case makes sure that any of those objects set are
       * now available for garbage collection when necessary.
       */
      while (doLoop && isConnected()) {
        byte cmd = 0;
        try {
          if (LINUX_1_3) socket.setSoTimeout(1000); // Linux 1.3 bug, see comment on LINUX_1_3
          cmd = in.readByte();
          if (LINUX_1_3 && isConnected())
            socket.setSoTimeout(0); // Linux 1.3 bug, see comment on LINUX_1_3
        } catch (InterruptedIOException e) {
          continue; // Timeout, try again
        }
        switch (cmd) {
          case Commands.QUIT_CONNECTION:
            doLoop = false;
            break; // Close this connection

          case Commands.TERMINATE_SERVER:
            doLoop = false;
            shutdown = true; // Shutdown everything
            break;

          case Commands.GET_CLASS:
            String className = in.readUTF();
            Class aClass = null;
            Class superClass = null;
            String superClassName = null;
            boolean added = false;
            try {
              aClass =
                  Class.forName(
                      className); // Turns out using JNI format for array type will work fine.

              added = server.getIdentityID(aClass, valueObject);
              boolean isInterface = aClass.isInterface();
              boolean isAbstract = java.lang.reflect.Modifier.isAbstract(aClass.getModifiers());
              superClass = aClass.getSuperclass();
              superClassName = (superClass != null) ? superClass.getName() : ""; // $NON-NLS-1$
              out.writeByte(Commands.GET_CLASS_RETURN);
              out.writeInt(valueObject.objectID);
              out.writeBoolean(isInterface);
              out.writeBoolean(isAbstract);
              out.writeUTF(superClassName);
              out.flush();
            } catch (ClassNotFoundException e) {
              valueObject.set();
              Commands.sendErrorCommand(out, Commands.GET_CLASS_NOT_FOUND, valueObject);
            } catch (ExceptionInInitializerError e) {
              sendException(e.getException(), valueObject, out);
            } catch (LinkageError e) {
              sendException(e, valueObject, out);
            } catch (Throwable e) {
              // Something bad, did we add a class? If we did remove it from the table.
              if (added) server.removeObject(server.getObject(valueObject.objectID));
              throw e;
            } finally {
              // clear out for GC to work.
              className = null;
              aClass = null;
              superClass = null;
              superClassName = null;
              valueObject.set();
            }
            break;

          case Commands.GET_CLASS_FROM_ID:
            int classID = in.readInt();
            try {
              aClass = (Class) server.getObject(classID);
              boolean isInterface = aClass.isInterface();
              boolean isAbstract = java.lang.reflect.Modifier.isAbstract(aClass.getModifiers());
              superClass = aClass.getSuperclass();
              superClassName = (superClass != null) ? superClass.getName() : ""; // $NON-NLS-1$
              out.writeByte(Commands.GET_CLASS_ID_RETURN);
              out.writeUTF(aClass.getName());
              out.writeBoolean(isInterface);
              out.writeBoolean(isAbstract);
              out.writeUTF(superClassName);
              out.flush();
            } catch (ClassCastException e) {
              valueObject.set();
              Commands.sendErrorCommand(out, Commands.CLASS_CAST_EXCEPTION, valueObject);
            } finally {
              // clear out for GC to work.
              aClass = null;
              superClass = null;
              superClassName = null;
              valueObject.set();
            }
            break;

          case Commands.GET_OBJECT_DATA:
            int objectID = in.readInt();
            Object anObject = null;
            try {
              anObject = server.getObject(objectID);
              valueObject.setObjectID(objectID, server.getIdentityID(anObject.getClass()));
              Commands.writeValue(out, valueObject, true);
            } catch (ClassCastException e) {
              valueObject.set();
              Commands.sendErrorCommand(out, Commands.CLASS_CAST_EXCEPTION, valueObject);
            } finally {
              anObject = null; // Clear out for GC to work
              valueObject.set();
            }
            break;

          case Commands.RELEASE_OBJECT:
            int id = in.readInt();
            server.removeObject(server.getObject(id));
            break;

          case Commands.NEW_INIT_STRING:
            classID = in.readInt(); // ID Of class to do new upon.
            String initString = in.readUTF(); // The init string.
            Object newValue = null;
            Class theClass = null;
            try {
              theClass = (Class) server.getObject(classID);
              if (theClass == null) {
                // The class wasn't found. So imply ClassNotFound exception.
                throw new ClassNotFoundException();
              }

              InitializationStringParser parser = null;
              try {
                parser = InitializationStringParser.createParser(initString);
                newValue = parser.evaluate();
                boolean primitive = parser.isPrimitive();
                // If expected class is Void.TYPE, that means don't test the type of the result
                // to verify if correct type, just return what it really is.
                if (theClass != Void.TYPE && primitive != theClass.isPrimitive()) {
                  valueObject.set();
                  Commands.sendErrorCommand(out, Commands.CLASS_CAST_EXCEPTION, valueObject);
                  continue; // Goto next command.
                }
                if (primitive) {
                  try {
                    // Need to do special tests for compatibility and assignment.
                    sendObject(
                        newValue,
                        classID != Commands.VOID_TYPE
                            ? classID
                            : server.getIdentityID(parser.getExpectedType()),
                        valueObject,
                        out,
                        true); // This will make sure it goes out as the correct primitive type
                  } catch (ClassCastException e) {
                    // The returned type is not of the correct type for what is expected.
                    valueObject.set();
                    Commands.sendErrorCommand(out, Commands.CLASS_CAST_EXCEPTION, valueObject);
                    continue; // Goto next command
                  }
                } else {
                  if (newValue != null) {
                    // Test to see if they are compatible. (Null can be assigned to any object,
                    // so that is why it was tested out above).
                    // If expected class is Void.TYPE, that means don't test the type of the result
                    // to verify if correct type, just return what it really is.
                    if (theClass != Void.TYPE && !theClass.isInstance(newValue)) {
                      // The returned type is not of the correct type for what is expected.
                      valueObject.set();
                      Commands.sendErrorCommand(out, Commands.CLASS_CAST_EXCEPTION, valueObject);
                      continue; // Goto next command
                    }
                  }
                  sendObject(
                      newValue, NOT_A_PRIMITIVE, valueObject, out, true); // Send out as an object.
                }
              } catch (InitializationStringEvaluationException e) {
                if (e instanceof EvaluationException) {
                  // Want to return the real exception.
                  sendException(e.getOriginalException(), valueObject, out);
                } else {
                  // Couldn't be evaluated, return an error for this.
                  setExceptionIntoValue(e.getOriginalException(), valueObject);
                  Commands.sendErrorCommand(out, Commands.CANNOT_EVALUATE_STRING, valueObject);
                }
              } finally {
                parser = null; // Clear out for GC to work
              }
            } catch (Throwable e) {
              sendException(e, valueObject, out);
            } finally {
              // Clear out for GC to work
              initString = null;
              theClass = null;
              newValue = null;
              valueObject.set();
            }
            break;

          case Commands.INVOKE:
            Object target = null;
            Object[] parms = null;
            Class returnType = null;
            java.lang.reflect.Method aMethod = null;
            try {
              int methodID = in.readInt(); // ID of method to invoke
              aMethod = (java.lang.reflect.Method) server.getObject(methodID); // Method to invoke
              Commands.readValue(in, valueObject);
              target = getInvokableObject(valueObject);
              Commands.readValue(in, valueObject);
              if (valueObject.type == Commands.ARRAY_IDS) {
                // It is an array containing IDs, as it normally would be.
                valueSender.initialize(valueObject);
                Commands.readArray(in, valueObject.anInt, valueSender, valueObject, false);
                parms = (Object[]) valueSender.getArray();
              } else {
                // It is all objects or null, so it should be an Object[] or null. If not, then this
                // is an error.
                parms = (Object[]) valueObject.anObject;
              }

              if (!aMethod.isAccessible())
                aMethod.setAccessible(
                    true); // We will allow all to occur. Let access control be handled by IDE and
                           // compiler.
              newValue = aMethod.invoke(target, parms);
              returnType = aMethod.getReturnType();
              if (returnType.isPrimitive()) {
                int returnTypeID = server.getIdentityID(returnType);
                // Need to tell sendObject the correct primitive type.
                sendObject(newValue, returnTypeID, valueObject, out, true);

              } else {
                sendObject(
                    newValue,
                    NOT_A_PRIMITIVE,
                    valueObject,
                    out,
                    true); // Just send the object back. sendObject knows how to iterpret the type
              }
            } catch (CommandException e) {
              throw e; // Throw it again. These we don't want to come up as an exception proxy.
                       // These should end the thread.
            } catch (java.lang.reflect.InvocationTargetException e) {
              // This is a wrappered exception. Return the wrappered one so it looks like
              // it was the real one. (Sometimes the method being invoked is on a
              // java.lang.reflect.Constructor.newInstance,
              // which in turn is an InvocationTargetException, so we will go until we don't have an
              // InvocationTargetException.
              Throwable t = e;
              do {
                t = ((java.lang.reflect.InvocationTargetException) t).getTargetException();
              } while (t instanceof java.lang.reflect.InvocationTargetException);
              sendException(t, valueObject, out);
            } catch (Throwable e) {
              sendException(e, valueObject, out); // Turn it into a exception proxy on the client.
            } finally {
              // Clear out for GC to work
              valueObject.set();
              parms = null;
              target = null;
              aMethod = null;
              returnType = null;
              newValue = null;
              valueSender.clear();
            }
            break;

          case Commands.INVOKE_WITH_METHOD_PASSED:
            aClass = null;
            String methodName = null;
            Class[] parmTypes = null;
            target = null;
            parms = null;
            returnType = null;
            aMethod = null;

            try {
              Commands.readValue(in, valueObject);
              aClass = (Class) getInvokableObject(valueObject); // The class that has the method.
              methodName = in.readUTF();
              Commands.readValue(in, valueObject);
              if (valueObject.type == Commands.ARRAY_IDS) {
                // It is an array containing IDs, as it normally would be.
                valueSender.initialize(valueObject);
                Commands.readArray(in, valueObject.anInt, valueSender, valueObject, false);
                parmTypes = (Class[]) valueSender.getArray();
              } else {
                // It null, so it should be an null. If not, then this is an error.
                parmTypes = null;
              }
              aMethod = aClass.getMethod(methodName, parmTypes);

              // Now we get the info for the invocation of the method and execute it.
              Commands.readValue(in, valueObject);
              target = getInvokableObject(valueObject);
              Commands.readValue(in, valueObject);
              if (valueObject.type == Commands.ARRAY_IDS) {
                // It is an array containing IDs, as it normally would be.
                valueSender.initialize(valueObject);
                Commands.readArray(in, valueObject.anInt, valueSender, valueObject, false);
                parms = (Object[]) valueSender.getArray();
              } else {
                // It is all objects or null, so it should be an Object[] or null. If not, then this
                // is an error.
                parms = (Object[]) valueObject.anObject;
              }

              if (!aMethod.isAccessible())
                aMethod.setAccessible(
                    true); // We will allow all to occur. Let access control be handled by IDE and
                           // compiler.
              newValue = aMethod.invoke(target, parms);
              returnType = aMethod.getReturnType();
              if (returnType.isPrimitive()) {
                int returnTypeID = server.getIdentityID(returnType);
                // Need to tell sendObject the correct primitive type.
                sendObject(newValue, returnTypeID, valueObject, out, true);

              } else {
                sendObject(
                    newValue,
                    NOT_A_PRIMITIVE,
                    valueObject,
                    out,
                    true); // Just send the object back. sendObject knows how to iterpret the type
              }
            } catch (CommandException e) {
              throw e; // Throw it again. These we don't want to come up as an exception proxy.
                       // These should end the thread.
            } catch (java.lang.reflect.InvocationTargetException e) {
              // This is a wrappered exception. Return the wrappered one so it looks like
              // it was the real one. (Sometimes the method being invoked is on a
              // java.lang.reflect.Constructor.newInstance,
              // which in turn is an InvocationTargetException, so we will go until we don't have an
              // InvocationTargetException.
              Throwable t = e;
              do {
                t = ((java.lang.reflect.InvocationTargetException) t).getTargetException();
              } while (t instanceof java.lang.reflect.InvocationTargetException);
              sendException(t, valueObject, out);

            } catch (Throwable e) {
              sendException(e, valueObject, out); // Turn it into a exception proxy on the client.
            } finally {
              aClass = null;
              methodName = null;
              parmTypes = null;
              // Clear out for GC to work
              valueObject.set();
              parms = null;
              target = null;
              aMethod = null;
              returnType = null;
              newValue = null;
              valueSender.clear();
            }
            break;

          case Commands.GET_ARRAY_CONTENTS:
            try {
              target = server.getObject(in.readInt()); // Array to get the ids for.
              valueObject.setArrayIDS(
                  new ArrayContentsRetriever(target),
                  Array.getLength(target),
                  Commands.OBJECT_CLASS);
              Commands.writeValue(out, valueObject, true); // Write it back as a value command.
            } catch (CommandException e) {
              throw e; // Throw it again. These we don't want to come up as an exception proxy.
                       // These should end the thread.
            } catch (Throwable e) {
              sendException(e, valueObject, out); // Turn it into a exception proxy on the client.
            } finally {
              target = null;
              valueObject.set();
            }
            break;

          case Commands.CALLBACK_DONE:
            try {
              if (connectionThread != null) {
                valueObject.set();
                Commands.sendErrorCommand(out, Commands.UNKNOWN_COMMAND_SENT, valueObject);
              } else {
                try {
                  Commands.readBackValue(in, valueObject, Commands.NO_TYPE_CHECK);
                  if (valueObject.type == Commands.ARRAY_IDS) {
                    // It is an array containing IDs, as it normally would be.
                    valueSender.initialize(valueObject);
                    Commands.readArray(in, valueObject.anInt, valueSender, valueObject, false);
                    result = valueSender.getArray();
                  } else {
                    result = getInvokableObject(valueObject);
                  }
                  doLoop = false; // We need to terminate and return result
                  closeWhenDone = false; // Don't close, we will continue.
                } catch (CommandErrorException e) {
                  // There was an command error on the other side. This means
                  // connection still good, but don't continue the callback processing.
                  doLoop = false; // We need to terminate and return result
                  closeWhenDone = false; // Don't close, we will continue.
                  throw e; // Let it go on out.
                }
              }
            } finally {
              valueObject.set();
              valueSender.clear();
            }
            break;

          case Commands.ERROR:
            try {
              // Got an error command. Don't know what to do but read the
              // value and simply print it out.
              Commands.readValue(in, valueObject);
              result = getInvokableObject(valueObject);
              System.out.println("Error sent to server: Result=" + result); // $NON-NLS-1$
            } finally {
              valueObject.set();
            }
            break;

          case Commands.EXPRESSION_TREE_COMMAND:
            try {
              processExpressionCommand(valueObject, valueSender);
            } finally {
              valueObject.set();
              valueSender.clear();
            }
            break;

          default:
            // Unknown command. We don't know how long it is, so we need to shut the connection
            // down.
            System.err.println("Error: Invalid cmd send to server: Cmd=" + cmd); // $NON-NLS-1$
            doLoop = false;
            closeWhenDone = true;
            break;
        }
      }
    } catch (EOFException e) {
      // This is ok. It means that the connection on the other side was terminated.
      // So just accept this and go down.
    } catch (CommandException e) {
      throw e;
    } catch (SocketException e) {
      if (socket != null)
        throw new UnexpectedExceptionCommandException(
            false, e); // socket null means a valid close request
    } catch (Throwable e) {
      e.printStackTrace();
    } finally {
      if (closeWhenDone) {
        try {
          for (Iterator itr = expressionProcessors.values().iterator(); itr.hasNext(); ) {
            ExpressionProcesserController exp = (ExpressionProcesserController) itr.next();
            exp.close();
          }
        } finally {
          expressionProcessors.clear();
        }

        if (in != null)
          try {
            in.close();
          } catch (Exception e) {
          }
        in = null;
        if (out != null)
          try {
            out.close();
          } catch (Exception e) {
          }
        out = null;
        close();
      }
    }

    if (closeWhenDone && connectionThread != null) server.removeConnectionThread(connectionThread);
    if (shutdown) server.requestShutdown();

    return result;
  }
  /**
   * Finds all classes inside the stated scope that implement TetradSerializable and serializes them
   * out to the getCurrentDirectory() directory. Abstract methods and interfaces are skipped over.
   * For all other classes C, it is assumed that C has a static constructor of the following form:
   *
   * <pre>
   *     public static C serializableInstance() {
   *         // Returns an instance of C. May be a mind-numbingly simple
   *         // instance, no need to get fancy.
   *     }
   * </pre>
   *
   * The instance returned may be mind-numbingly simple; there is no need to get fancy. It may
   * change over time. The point is to make sure that instances serialized out with earlier versions
   * load with the currentDirectory version.
   *
   * @throws RuntimeException if clazz cannot be serialized. This exception has an informative
   *     message and wraps the originally thrown exception as root cause.
   */
  public void serializeCurrentDirectory() throws RuntimeException {
    clearCurrentDirectory();
    @SuppressWarnings("Convert2Diamond")
    Map<String, List<String>> classFields = new TreeMap<>();

    // Get the classes that implement SerializationCanonicalizer.
    List classes = getAssignableClasses(new File(getSerializableScope()), TetradSerializable.class);

    System.out.println(
        "Serializing exemplars of instantiable TetradSerializable "
            + "in "
            + getSerializableScope()
            + ".");
    System.out.println("Writing serialized examplars to " + getCurrentDirectory());

    int index = -1;

    for (Object aClass : classes) {
      Class clazz = (Class) aClass;

      if (TetradSerializableExcluded.class.isAssignableFrom(clazz)) {
        continue;
      }

      if (Modifier.isAbstract(clazz.getModifiers())) {
        continue;
      }

      if (Modifier.isInterface(clazz.getModifiers())) {
        continue;
      }

      int numFields = getNumNonSerialVersionUIDFields(clazz);

      if (numFields > 0 && serializableInstanceMethod(clazz) == null) {
        throw new RuntimeException(
            "Class "
                + clazz
                + " does not "
                + "\nhave a public static serializableInstance constructor.");
      }

      if (++index % 50 == 0) {
        System.out.println(index);
      }

      System.out.print(".");

      serializeClass(clazz, classFields);
    }

    try {
      File file = new File(getCurrentDirectory(), "class_fields.ser");
      FileOutputStream out = new FileOutputStream(file);
      ObjectOutputStream objOut = new ObjectOutputStream(out);
      objOut.writeObject(classFields);
      out.close();
    } catch (IOException e) {
      e.printStackTrace();
    }

    System.out.println("\nFinished serializing exemplars.");
  }
  public static void main(String[] args) throws Exception {
    System.out.println(
        "Checking that all known MBeans that are "
            + "NotificationBroadcasters have sane "
            + "MBeanInfo.getNotifications()");

    System.out.println("Checking platform MBeans...");
    checkPlatformMBeans();

    URL codeBase = ClassLoader.getSystemResource("javax/management/MBeanServer.class");
    if (codeBase == null) {
      throw new Exception("Could not determine codeBase for " + MBeanServer.class);
    }

    System.out.println();
    System.out.println("Looking for standard MBeans...");
    String[] classes = findStandardMBeans(codeBase);

    System.out.println("Testing standard MBeans...");
    for (int i = 0; i < classes.length; i++) {
      String name = classes[i];
      Class<?> c;
      try {
        c = Class.forName(name);
      } catch (Throwable e) {
        System.out.println(name + ": cannot load (not public?): " + e);
        continue;
      }
      if (!NotificationBroadcaster.class.isAssignableFrom(c)) {
        System.out.println(name + ": not a NotificationBroadcaster");
        continue;
      }
      if (Modifier.isAbstract(c.getModifiers())) {
        System.out.println(name + ": abstract class");
        continue;
      }

      NotificationBroadcaster mbean;
      Constructor<?> constr;
      try {
        constr = c.getConstructor();
      } catch (Exception e) {
        System.out.println(name + ": no public no-arg constructor: " + e);
        continue;
      }
      try {
        mbean = (NotificationBroadcaster) constr.newInstance();
      } catch (Exception e) {
        System.out.println(name + ": no-arg constructor failed: " + e);
        continue;
      }

      check(mbean);
    }

    System.out.println();
    System.out.println("Testing some explicit cases...");

    check(new RelationService(false));
    /*
      We can't do this:
        check(new RequiredModelMBean());
      because the Model MBean spec more or less forces us to use the
      names GENERIC and ATTRIBUTE_CHANGE for its standard notifs.
    */
    checkRMIConnectorServer();

    System.out.println();
    if (!suspicious.isEmpty()) System.out.println("SUSPICIOUS CLASSES: " + suspicious);

    if (failed.isEmpty()) System.out.println("TEST PASSED");
    else {
      System.out.println("TEST FAILED: " + failed);
      System.exit(1);
    }
  }