;; *************************************************
;; 1. add a precondition with a slot (is-possible)
;; *************************************************

(global-situation)

(is-possible has
	(instance-of (Slot))
	(domain (Change))
	(range (Boolean))
	(cardinality (N-to-1))
	(fluent-status (*Fluent))
	(situation-specific (t))
)

;; in case of TakeIn (such as Endocytosis), the virus should be near the cell
;; in case of other Move, the patient's location should be the same as the
;; source

(every Change has 
       (is-possible (((not (Self isa Move)) or 
		      ((Self isa TakeIn) and
          	       ((the location of (the patient of Self))= (the near of
			(the agent of Self)))) or
                      ((not (Self isa TakeIn)) and 
                       ((the source of Self) /= NIL) and
          	       ((the source of Self) = (the location of (the patient of Self))))))))
#|
(every Change has 
	(is-possible (t))) ;; default

(every Move has 
	(is-possible 
		((((the source of Self) /= NIL) and
          	  ((the source of Self) = (the location of (the patient of Self)))))))
(every TakeIn has
	(is-possible 
		(((the location of (the patient of Self))= 
		 (the near of (the agent of Self))))))
|#
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; additional slots for 'near' ;;;;;;

(near has
	(instance-of (Slot))
	(domain (TangibleThing))
	(range (TangibleThing))
	(inverse (near-of))
	(cardinality (N-to-1)))

(near-of has
	(instance-of (Slot))
	(domain (TangibleThing))
	(range (TangibleThing)))

;; *************************************************
;; 2. define Arrive
;; *************************************************

(Arrive has 
	(superclasses (Change)))

(every Arrive has
       (agent ((a TangibleThing)))
       (source (( a Space)))
;       (source ((the location of ((Self agent)))))
;	(destination ((a Space)))
       	(destination ((a TangibleThing)))
        (affect ((a Affect with
		   (affectedThing ((Self agent)))
		   (affectedSlot (location))
		   (expectedValue ((the near of (the destination of Self)))))))
)
;; *************************************************
;; 3. define new situation
;; *************************************************

    (*new-start-situation has
	(instance-of (Situation)))

(in-situation *new-start-situation)

    (a VirusInvadesCell with
  	 (agent (*virus))
	 (patient (*cell)))
    
    (*virus has 
	(contains ((the Dna parts of Self)))
        (location (*somewhere)))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Q: computing value of is-possible slot:
;;     the location of the virus has to be defined in global situation?
;;    message: (Don't re-evaluate inherited rules ((not (_Endocytosis11 isa TakeIn)) or
;;                                       ((the location of (the patient of _Endocytosis11)) =
;;                                        (the near of (the agent of _Endocytosis11)))) for _Endocytosis11 in this situation,
;;                as I don't know if this is the situation where this event will occur!)

;; *************************************************
;; 3. run simulation
;; *************************************************
;; in simulation, the system checks the preconditions

[*new-start-situation] KM> (forall (the actions of (thelast VirusInvadesCell))
              where (the is-possible of It) (do-and-next It))
 0: (do-action |_Fuse163| :change-to-next-situation t)
 0: returned |_Situation166|
 0: (do-action |_Degrade164| :change-to-next-situation t)
 0: returned |_Situation170|
 0: (do-action |_Release162| :change-to-next-situation t)
 0: returned |_Situation172|
 0: (do-action |_Deliver156| :change-to-next-situation t)
 0: returned |_Situation173|
 0: (do-action |_VirusInvadesCell149| :change-to-next-situation t)
 0: returned |_Situation174|
(_Situation166 _Situation170 _Situation172 _Situation173 _Situation174)
(1671 inferences and 33281 kb-accesses in 6.4 sec [260 lips, 5183 kaps])

;; what is the location now?
[_Situation174] KM> (the location of (the Virus))
(*somewhere)  ;; Virus didn't reach the cell !!!

;; what are not possible actions?
;(forall (the actions of (thelast VirusInvadesCell)) 
;	where ((the is-possible of It) = NIL) It)

;; find all the expected-effect where the result is not equal to the expected value
[_Situation174] (forall (the expected-effect of (thelast VirusInvadesCell))
 where ((the checkedValue of It) /= (the expectedValue of It))
 (the affectedSlot of It))
(location)

;; find all the subclasses of Change which can affect the unachieved slot
[_Situation174] (forall (the subclasses of Change)
(forall2 (the expected-effect of (thelast VirusInvadesCell))
 where (((the checkedValue of It2) /= (the expectedValue of It2)) and
((the affectedSlot of (the affect of (a It))) = (the affectedSlot of It2)))
(:seq It (the subclasses of It))))

((:seq Arrive) (:seq Move Convey Exit Enter PassThroughSeparator))

;; *************************************************
;; 4. NewVirusInvadesCell includes Arrive
;; *************************************************
(global-situation)

(NewVirusInvadesCell has (superclasses (Invade)))

(every NewVirusInvadesCell has 
       (agent ((a Virus)))
       (patient ((a Cell)))

;       (firstevent ((the Enter subevents of (Self))))
       (subevents 
	((a Enter with 
	    (self-contained (t))
	    (patient ((Self agent)))
	    (beneficiary ((Self patient)))
	    (firstevent ((the Penetrate subevents of 
			      (the Enter subevents of Self))))
	    (prereq ((a Penetrate with 
			(self-contained (t))
			(agent ((Self agent)))
			(patient (Self agent))
			(firstevent ((the Endocytosis byMeansOf of 
					  (the Penetrate prereq of (the Enter subevents of Self)))))
			(byMeansOf ((a Endocytosis with 
				       (agent ((Self patient)))
				       (patient ((Self agent)))
				       (source ((a Space with (location-of ((Self agent)))))))))
			(nextevent ((the Deliver enables of (the Enter subevents of Self)))))))
	    (enables
	     ((a Deliver with   ; Deliver = Convey + Release
		 (agent ((Self agent)))     ; coerced to be a Container
		 (patient ((the Dna contains of (Self agent))))
		 (destination ((the inside of ((the Cytoplasm contains of 
						    (Self patient))))))
		 (subevents 
		  ((a Convey with 
		      (patient ((Self agent)))
		      (firstevent ((the Fuse byMeansOf of 
					(the Convey subevents of 
					     (the Deliver subevents of 
						  (the Enter subevents 
						       of Self))))))
;		      (source ((a Space with (location-of ((Self agent))))))
		      (source ((the destination of 
				    (the Endocytosis byMeansOf of 
					 (the Penetrate prereq of 
					      (the Enter subevents of Self))))))
		      (destination ((the destination of 
					 (the Deliver subevents of 
					      (the Enter subevents of Self))
					 )))
		      (byMeansOf 
		       ((a Fuse with 
			   (agent ((oneof (the Lysosome contains of 
					       (the Cytoplasm contains of 
						    (Self patient))) 
					  where (t))))
			   (patient ((the Vesicle creates of 
					  (the Endocytosis byMeansOf
					       of (the Penetrate 
						       prereq of
						       (the Enter subevents of Self)))))))))
		      (nextevent ((the Release subevents of 
				       (the Deliver subevents of 
					    (the Enter subevents of Self)))
				  )))
		   (a Release with   
#| 
                      note: the agent of the Release is
                            set by the Deliver component, to be *virus
|#
; incompleteness in KM! (patient ((the Dna contains of (Self agent))))
			(patient ((the Dna parts of (Self agent))))
		      (destination ((a Space with (location-of ((the CytoplasmFluid contains of
					 (the Cytoplasm contains of 
					      (Self patient))))))))
		      (firstevent ((the Degrade subevents of 
					(the Release subevents of 
					     (the Deliver subevents of 
						  (the Enter subevents 
						       of Self))))))
		      (subevents 
		       ((a Degrade with 
			   (agent ((Self patient)))
			   (patient ((the ProteinCoat 
					  parts of (Self agent))))
			   (nextevent ((the Exit subevents of 
					    (the Release subevents of
						 (the Deliver subevents of
						      (the Enter subevents
							   of Self))))))
			   (instrument 
			    ((the Acid contains of 
				  (the Lysosome agent of 
				       (the Fuse byMeansOf of 
					    (the Convey subevents of
						 (the Deliver
						      subevents of
						      (the Enter 
							   subevents 
							   of Self)))))))))
			(a Exit with	
; incompleteness in KM!    (patient ((the Dna contains of (Self agent))))
			   (patient ((the Dna parts of (Self agent))))
			   (destination ((a Space with (location-of ((the CytoplasmFluid contains of
					      (the Cytoplasm contains of 
						   (Self patient)))))))))
		   ))))))))))))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; User adds Arrive as the first subevent 
(every NewVirusInvadesCell has
     (firstevent ((the Arrive subevents of (Self))))
     (subevents 
      ((a Arrive with (agent ((Self agent)))  
	              (patient ((Self agent)))
		      (source ((the location of ((Self agent)))))
		     ;(destination ((the near of ((Self patient))))) ;; near cell
		      (destination ((Self patient))) ;; near cell
		      (is-possible (t))
		      (nextevent ((the Enter subevents of (Self)))))))
     (expected-effect ((a Affect with
        (affectedThing ((Self agent)))
        (affectedSlot (location)) 
        (checkedValue ((the location of ((Self agent)))))	
        (expectedValue ((the inside of (the contains of ((Self patient)))))))))
)

;; *************************************************
;; 5. define new start-situation & simulate again
;; *************************************************
(*new-new-start-situation has
	(instance-of (Situation)))
(in-situation *new-new-start-situation)

(a NewVirusInvadesCell with
  	 (agent (*virus))
	 (patient (*cell)))

[*new-start-situation] KM> (forall (the actions of (thelast NewVirusInvadesCell))
              where (the is-possible of It) (do-and-next It))
 0: (do-action |_Arrive192| :change-to-next-situation t)
 0: returned |_Situation211|
 0: (do-action |_Endocytosis203| :change-to-next-situation t)
 0: returned |_Situation216|
 0: (do-action |_Fuse206| :change-to-next-situation t)
 0: returned |_Situation243|
 0: (do-action |_Convey204| :change-to-next-situation t)
 0: returned |_Situation246|
 0: (do-action |_Degrade207| :change-to-next-situation t)
 0: returned |_Situation250|
 0: (do-action |_Release205| :change-to-next-situation t)
 0: returned |_Situation252|
 0: (do-action |_Deliver199| :change-to-next-situation t)
 0: returned |_Situation253|
 0: (do-action |_NewVirusInvadesCell190| :change-to-next-situation t)
 0: returned |_Situation254|
(_Situation211 _Situation216 _Situation243 _Situation246 _Situation250
 _Situation252 _Situation253 _Situation254)

;; where is virus?
[_Situation254] KM> (the location of (the Virus))

;;; what sub-action of NewVirusInvadesCell caused location change?
KM> (forall (the affect of 
			 (the actions of (thelast NewVirusInvadesCell))) where (t)
 (forall2 (the expected-effect of (thelast NewVirusInvadesCell))
 where (((the checkedValue of It2) = (the expectedValue of It2)) and
        ((the affectedSlot of It) = (the affectedSlot of It2)) and 
((the affectedThing of It) = (the affectedThing of It2)))
(the affect-of of It)))

(_Arrive192 _Endocytosis203 _Convey204)

;;*******************************************************
;; Questions:
;;  about slot 'fluent-status' (*Fluent,...);?
;;  about slot 'situation-specific'