;;; $Id: classes.lisp,v 1.1 2002/10/08 22:08:56 kevin Exp $
;;;
;;; UMLS object defintions and printing routines

(in-package :umlisp)
(declaim (optimize (speed 3) (safety 1)))

(defclass umlsclass ()
  ()
  (:metaclass ml-class)
  (:documentation "Parent class of all UMLS objects"))


(defmethod print-object ((obj umlsclass) (s stream))
  (print-unreadable-object (obj s :type t :identity t)
    (let ((fmt (make-instance 'gu.ml::textformat)))
      (apply #'format 
	     s (funcall (gu.ml::obj-data-fmtstr fmt) obj)
	     (multiple-value-list 
	      (funcall (funcall (gu.ml::obj-data-value-func fmt) obj) obj))))))



  
(defclass urank (umlsclass)
  ((rank :type fixnum :initarg :rank :reader rank)
   (sab :type string :initarg :sab :reader sab)
   (tty :type string :initarg :tty :reader tty)
   (supres :type string :initarg :supres :reader supres))
  (:metaclass ml-class)
  (:default-initargs :rank nil :sab nil :tty nil :supres nil)
  (:title "Rank")
  (:fields (rank :fixnum) (sab :string) (tty :string) (supres :string)))

(defclass udef (umlsclass)
  ((def :type string :initarg :def :reader def)
   (sab :type string :initarg :sab :reader sab))
  (:metaclass ml-class)
  (:default-initargs :def nil :sab nil)
  (:title "Definition")
  (:ref-fields (sab find-bsab-sab))
  (:fields (sab :string) (def :cdata)))

(defclass usat (umlsclass)
  ((sab :type string :initarg :sab :reader sab)
   (code :type string :initarg :code :reader code)
   (atn :type string :initarg :atn :reader atn)
   (atv :type string :initarg :atv :reader atv))
  (:metaclass ml-class)
  (:default-initargs :sab nil :code nil :atn nil :atv nil)
  (:title "Simple Attribute")
  (:ref-fields (sab find-bsab-sab))
  (:fields (sab :string) (code :string) (atn :string) (atv :cdata)))

(defclass uso (umlsclass)
  ((sab :type string :initarg :sab :reader sab)
   (code :type string :initarg :code :reader code)
   (tty :type string :initarg :tty :reader tty)
   (srl :type fixnum :initarg :srl :reader srl))
  (:metaclass ml-class)
  (:default-initargs :sab nil :code nil :tty nil :srl nil)
  (:title "Source")
  (:ref-fields (sab find-bsab-sab) (tty find-btty-tty))
  (:fields (sab :string) (code :string) (tty :string) (srl :fixnum)))

(defclass ucxt (umlsclass)
  ((sab :type string :initarg :sab :reader sab)
   (code :type string :initarg :code :reader code)
   (rnk :type fixnum :initarg :rnk :reader rnk)
   (cxn :type fixnum :initarg :cxn :reader cxn)
   (cxl :type string :initarg :cxl :reader cxl)
   (cxs :type string :initarg :cxs :reader cxs)
   (cui2 :type fixnum :initarg :cui2 :reader cui2)
   (hcd :type string :initarg :hcd :reader hcd)
   (rela :type string :initarg :rela :reader rela)
   (xc :type string  :initarg :xc :reader xc))
  (:metaclass ml-class)
  (:default-initargs :sab nil :code nil :rnk nil :cxn nil :cxl nil :cxs nil
		     :cui2 nil :hcd nil :rela nil :xc nil)
  (:title "Context")
  (:ref-fields (sab find-bsab-sab) (cui2 find-ucon-cui))
  (:fields 
   (sab :string) (code :string) (rnk :fixnum) (cxn :fixnum) (cxl :string)
   (hcd :string) (rela :string) (xc :string) (cui2 :string fmt-cui) 
   (cxs :cdata)))

(defclass ustr (umlsclass)
  ((sui :type fixnum :initarg :sui :reader sui)
   (cui :type fixnum :initarg :cui :reader cui)
   (lui :type fixnum :initarg :lui :reader lui)
   (cuisui :type integer :initarg :cuisui :reader cuisui )
   (str :type string :initarg :str :reader str)
   (lrl :type fixnum :initarg :lrl :reader lrl)
   (stt :type string :initarg :stt :reader stt)
   (s#sat :reader s#sat)
   (s#so :reader s#so)
   (s#cxt :reader s#cxt))
  (:metaclass ml-class)
  (:default-initargs 
   :sui nil :cui nil :lui nil :cuisui nil :str nil :lrl nil :stt nil)
  (:title "String")
  (:subobjects-lists (s#sat usat) (s#so uso) (s#cxt ucxt))
  (:fields (sui :string fmt-sui) (stt :string) (lrl :fixnum) (str :cdata))
  (:ref-fields (sui find-ustr-sui)))

(defclass ulo (umlsclass)
  ((isn :type string :initarg :isn :reader isn)
   (fr :type fixnum :initarg :fr :reader fr)
   (un :type string :initarg :un :reader un)
   (sui :type fixnum :initarg :sui :reader sui)
   (sna :type string :initarg :sna :reader sna)
   (soui :type string :initarg :soui :reader soui))
  (:metaclass ml-class)
  (:default-initargs :isn nil :fr nil :un nil :sui nil :sna nil :soui nil)
  (:title "Locator")
  (:fields (isn :string) (fr :fixnum) (un :string) (sna :string)
	   (soui :string) (sui :string fmt-sui) (suistr :string)))

(defclass uterm (umlsclass)
  ((lui :type fixnum :initarg :lui :reader lui)
   (cui :type fixnum :initarg :cui :reader cui)
   (lat :type string :initarg :lat :reader lat)
   (ts :type string  :initarg :ts :reader ts)
   (lrl :type fixnum :initarg :lrl :reader lrl)
   (s#str :reader s#str)
   (s#sat :reader s#sat))
  (:metaclass ml-class)
  (:default-initargs :lui nil :cui nil :lat nil :ts nil :lrl nil)
  (:title "Term")
  (:subobjects-lists (s#sat usat) (s#str ustr))
  (:fields (lui :string fmt-lui) (lat :string) (ts :string) (lrl :fixnum))
  (:ref-fields (lui find-uterm-lui)))

(defclass usty (umlsclass)
  ((tui :type fixnum :initarg :tui :reader tui)
   (sty :type string :initarg :sty :reader sty))
  (:metaclass ml-class)
  (:default-initargs :tui nil :sty nil)
  (:title "Semantic Type")
  (:ref-fields (tui find-ucon-tui (("subobjects" "no"))))
  (:fields (tui :string fmt-tui) (sty :string)))

(defclass urel (umlsclass)
  ((rel :type string :initarg :rel :reader rel)
   (cui1 :type fixnum :initarg :cui1 :reader cui1)
   (cui2 :type fixnum :initarg :cui2 :reader cui2)
   (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
   (rela :type string :initarg :rela :reader rela)
   (sab :type string :initarg :sab :reader sab)
   (sl :type string  :initarg :sl :reader sl)
   (mg :type string  :initarg :mg :reader mg))
  (:metaclass ml-class)
  (:default-initargs 
   :rel nil :cui1 nil :cui2 nil :pfstr2 nil :rela nil :sab nil :sl nil :mg nil)
  (:title "Relationship")
  (:ref-fields (rel find-brel-rel) (sab find-bsab-sab) (cui2 find-ucon-cui))
  (:fields (rel :string) (rela :string) (sab :string) (sl :string) 
	   (mg :string) (cui2 :string fmt-cui) (pfstr2 :cdata)))
	
(defclass ucoc (umlsclass)
  ((cui1 :type fixnum :initarg :cui1 :reader cui1)
   (cui2 :type fixnum :initarg :cui2 :reader cui2)
   (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
   (soc :type string :initarg :soc :reader soc)
   (cot :type string :initarg :cot :reader cot)
   (cof :type fixnum :initarg :cof :reader cof)
   (coa :type string :initarg :coa :reader coa))
  (:metaclass ml-class)
  (:default-initargs 
   :cui1 nil :cui2 nil :pfstr2 nil :soc nil :cot nil :cof nil :coa nil)
  (:title "Co-occuring Concept")
  (:ref-fields (cui2 find-ucon-cui))
  (:fields (soc :string) (cot :string) (cof :fixnum) (coa :cdata)
	   (cui2 :string fmt-cui) (pfstr2 :cdata)))

	
(defclass uatx (umlsclass)
  ((sab :type string :initarg :sab :reader sab)
   (rel :type string :initarg :rel :reader rel)
   (atx :type string :initarg :atx :reader atx))
  (:metaclass ml-class)
  (:default-initargs :sab nil :rel nil :atx nil)
  (:title "Associated Expression")
  (:fields (sab :string) (rel :string) (atx :cdata)))

(defclass ucon (umlsclass)
  ((cui :type fixnum :initarg :cui :reader cui )
   (pfstr :initarg :pfstr :reader pfstr)
   (lrl :initarg :lrl :reader lrl)
   (s#term :reader s#term)
   (s#def :reader s#def)
   (s#lo :reader s#lo)
   (s#rel :reader s#rel)
   (s#coc :reader s#coc)
   (s#sat :reader s#sat)
   (s#atx :reader s#atx)
   (s#sty :reader s#sty))
  (:metaclass ml-class)
  (:default-initargs :cui nil :pfstr nil :lrl nil)
  (:title "Concept")
  (:subobjects-lists 
   (s#def udef) (s#sty usty) (s#lo ulo) (s#atx uatx) (s#sat usat) (s#rel urel) 
   (s#coc ucoc) (s#term uterm))
  (:fields (cui :string fmt-cui) (lrl :fixum) (pfstr :cdata))
  (:ref-fields (cui find-ucon-cui)))

(defclass uxw (umlsclass)
  ((wd :type string :initarg :wd :reader wd)
   (cui :type fixnum :initform nil :initarg :cui :reader cui)
   (lui :type fixnum :initform nil :initarg :lui :reader lui)
   (sui :type fixnum :initform nil :initarg :sui :reader sui))
  (:metaclass ml-class)
  (:default-initargs :wd nil :cui nil :lui nil :sui nil)
  (:title "XW Index")
  (:fields (wd :string) (cui :string fmt-cui) (lui :string fmt-lui) 
	   (sui :string fmt-sui)))

(defclass uxnw (umlsclass)
  ((lat :type string :initarg :lat :reader lat)
   (nwd :type string :initarg :nwd :reader nwd)
  (cuilist :type list :initarg :cuilist :reader uxnw-cuilist))
  (:metaclass ml-class)
  (:default-initargs :lat nil :nwd nil :cuilist nil)
  (:title "XNW Index")
  (:fields (lat :string) (nwd :string) (cuilist :string)))

(defclass uxns (umlsclass)
  ((lat :type string :initarg :lat :reader lat)
   (nstr :type string :initarg :nstr :reader nstr)
   (cuilist :type list :initarg :cuilist :reader cuilist))
  (:metaclass ml-class)
  (:default-initargs :lat nil :nstr nil :cuilist nil)
  (:title "XNS Index")
  (:fields (lat :string) (nstr :string) (cuilist :string)))


;;; LEX objects

(defclass lexterm (umlsclass)
  ((eui :type fixnum :initarg :eui :reader eui)
   (wrd :type string :initarg :wrd :reader wrd)
   (s#abr :reader s#abr)
   (s#agr :reader s#agr)
   (s#cmp :reader s#cmp)
   (s#mod :reader s#mod)
   (s#nom :reader s#nom)
   (s#prn :reader s#prn)
   (s#prp :reader s#prp)
   (s#spl :reader s#spl)
   (s#trm :reader s#trm)
   (s#typ :reader s#typ))
  (:metaclass ml-class)
  (:default-initargs :eui nil :wrd nil)
  (:title "Lexical Term")
  (:subobjects-lists 
   (s#abr labr) (s#agr lagr) (s#cmp lcmp) (s#mod lmod) (s#nom unom) 
   (s#prn lprn) (s#prp lprp) (s#spl lspl) (s#trm ltrm) (s#typ ltyp))
  (:fields (eui :string fmt-eui) (wrd :string))
  (:ref-fields (eui find-lexterm-eui)))


(defclass labr  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (abr :type string :initarg :abr :reader abr)
   (eui2 :type integer :initarg :eui2 :reader eui2)
   (bas2 :type string :initarg :bas2 :reader bas2))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :abr nil :eui2 nil :bas2 nil)
  (:title "Abbreviations and Acronyms")
  (:fields (eui :string fmt-eui) (bas :string) (abr :string) 
	   (eui2 :string fmt-eui) (bas2 :string )))

(defclass lagr  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (str :type string :initarg :str :reader str)
   (sca :type string :initarg :sca :reader sca)
   (agr :type string :initarg :agr :reader agr)
   (cit :type string :initarg :cit :reader cit)
   (bas :type string :initarg :bas :reader bas))
  (:metaclass ml-class)
  (:default-initargs :eui nil :str nil :sca nil :agr nil :cit nil :bas nil)
  (:title "Agreement and Inflection")
  (:fields (eui :string fmt-eui) (str :string) (sca :string) (agr :string)
	   (cit :string) (bas :string)))

(defclass lcmp  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (sca :type string :initarg :sca :reader sca)
   (com :type string :initarg :com :reader com))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :sca nil :com nil)
  (:title "Complementation")
  (:fields (eui :string fmt-eui) (bas :string) (sca :string) (com :string)))

(defclass lmod  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (sca :type string :initarg :sca :reader sca)
   (psnmod :type string :initarg :psnmod :reader psnmod)
   (fea :type string :initarg :fea :reader fea))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :sca nil :psnmod nil :fea nil)
  (:title "Modifiers")
  (:fields (eui :string fmt-eui) (bas :string) (sca :string) (psnmod :string) 
	   (fea :string)))

(defclass lnom  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (sca :type string :initarg :sca :reader sca)
   (eui2 :type integer :initarg :eui2 :reader eui2)
   (bas2 :type string :initarg :bas2 :reader bas2)
   (sca2 :type string :initarg :sca2 :reader sca2))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :sca nil :eui2 nil :bas2 nil :sca2 nil)
  (:title "Nominalizations")
  (:fields (eui :string fmt-eui) (bas :string) (sca :string) 
	   (eui2 :string fmt-eui) (bas2 :string) (sca2 :string)))

(defclass lprn  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (num :type string :initarg :num :reader num)
   (gnd :type string :initarg :gnd :reader gnd)
   (cas :type string :initarg :cas :reader cas)
   (pos :type string :initarg :pos :reader pos)
   (qnt :type string :initarg :qnt :reader qnt)
   (fea :type string :initarg :fea :reader fea))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :num nil :gnd nil :cas nil
		     :pos nil :qnt nil :fea nil)
  (:title "Pronouns")
  (:fields (eui :string fmt-eui) (bas :string) (num :string) (gnd :string)
	   (cas :string) (pos :string) (qnt :string) (fea :string)))

(defclass lprp  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (str :type string :initarg :str :reader str)
   (sca :type string :initarg :sca :reader sca)
   (fea :type string :initarg :fea :reader fea))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :str nil :sca nil :fea nil)
  (:title "Properties")
  (:fields (eui :string fmt-eui) (bas :string) (str :string) (sca :string) 
	   (fea :string)))


(defclass lspl  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (spv :type string :initarg :spv :reader spv)
   (bas :type string :initarg :bas :reader bas))
  (:metaclass ml-class)
  (:default-initargs :eui nil :spv nil :bas nil)
  (:title "Spelling Variants")
  (:fields (eui :string fmt-eui) (spv :string) (bas :string)))



(defclass ltrm  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (gen :type string :initarg :gen :reader gen))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :gen nil)
  (:title "Trade Marks")
  (:fields (eui :string fmt-eui) (bas :string) (gen :string)))

(defclass ltyp  (umlsclass)
  ((eui :type integer :initarg :eui :reader eui)
   (bas :type string :initarg :bas :reader bas)
   (sca :type string :initarg :sca :reader sca)
   (typ :type string :initarg :typ :reader typ))
  (:metaclass ml-class)
  (:default-initargs :eui nil :bas nil :sca nil :typ nil)
  (:title "Inflection Type")
  (:fields (eui :string fmt-eui) (bas :string) (sca :string) (typ :string)))

(defclass lwd (umlsclass)
  ((wrd :type string :initarg :wrd :reader wrd)
   (euilist :type list :initarg :euilist :reader euilist))
  (:metaclass ml-class)
  (:default-initargs :wrd nil :euilist nil)
  (:title "Lexical Word Index")
  (:fields (wrd :string) (euilist :string)))

;;; Semantic NET objects

(defclass sdef (umlsclass)
  ((rt :type string :initarg :rt :reader rt)
   (ui :type integer :initarg :ui :reader ui)
   (styrl :type string :initarg :styrl :reader styrl)
   (stnrtn :type string :initarg :stnrtn :reader stnrtn)
   (def :type string :initarg :def :reader def)
   (ex :type string :initarg :ex :reader ex)
   (un :type string :initarg :un :reader un)
   (rh :type string :initarg :rh :reader rh)
   (abr :type string :initarg :abr :reader abr)
   (rin :type string :initarg :rin :reader rin))
  (:metaclass ml-class)
  (:default-initargs 
   :rt nil :ui nil :styrl nil :stnrtn nil :def nil :ex nil :un nil :rh nil 
   :abr nil :rin nil)
  (:title "Basic information about Semantic Types and Relations")
  (:fields 
   (rt :string) (ui :string fmt-tui) (styrl :string) (stnrtn :string-tui) 
   (def :string) (ex :string) (un :string) (rh :string) (abr :string) 
   (rin :string)))

(defclass sstr (umlsclass)
  ((styrl :type string :initarg :styrl :reader styrl)
   (rl :type string :initarg :rl :reader rl)
   (styrl2 :type string :initarg :styrl2 :reader styrl2)
   (ls :type string :initarg :ls :reader ls))
  (:metaclass ml-class)
  (:default-initargs :styrl nil :rl nil :styrl2 nil :ls nil)
  (:title "Structure of the Network")
  (:fields (styrl :string) (rl :string) (styrl2 :string) (ls :string)))

(defclass sstre1 (umlsclass)
  ((ui :type integer :initarg :ui :reader ui)
   (ui2 :type integer :initarg :ui2 :reader ui2)
   (ui3 :type integer :initarg :ui3 :reader ui3))
  (:metaclass ml-class)
  (:default-initargs :ui nil :ui2 nil :ui3 nil)
  (:title "Fully Inherited Set of Releatons (TUI's)")
  (:fields (ui :string fmt-tui) (ui2 :string fmt-tui) (ui3 :string fmt-tui)))

(defclass sstre2 (umlsclass)
  ((sty :type string :initarg :ui :reader sty)
   (rl :type string :initarg :ui2 :reader rl)
   (sty2 :type string :initarg :ui3 :reader sty2))
  (:metaclass ml-class)
  (:default-initargs :sty nil :rl nil :sty2 nil)
  (:title "Fully Inherited Set of Releatons (strings)")
  (:fields (sty :string) (rl :string) (sty2 :string)))

;;; Formatting routines

(defmethod fmt-cui ((c ucon))
  (format nil "C~7,'0d" (cui c)))

(defmethod fmt-cui ((c fixnum))
  (format nil "C~7,'0d" c))

(defmethod fmt-cui ((c string))
  (if (eql (aref c 0) #\C)
      c
    (format nil "C~7,'0d" (parse-integer c))))

(defmethod fmt-cui ((c null))
  (format nil "nil"))

(defmethod fmt-lui ((l uterm))
  (format nil "L~7,'0d" (lui l)))

(defmethod fmt-lui ((l fixnum))
  (format nil "L~7,'0d" l))

(defmethod fmt-lui ((l string))
  (if (eql (aref l 0) #\L)
      l
  (format nil "L~7,'0d" (parse-integer l))))

(defmethod fmt-sui ((s ustr))
  (format nil "S~7,'0d" (sui s)))

(defmethod fmt-sui ((s fixnum))
  (format nil "S~7,'0d" s))

(defmethod fmt-sui ((s string))
  (if (eql (aref s 0) #\S)
      s
  (format nil "S~7,'0d" (parse-integer s))))

(defmethod fmt-tui ((s fixnum))
  (format nil "T~3,'0d" s))

(defmethod fmt-tui ((s string))
  (if (eql (aref s 0) #\T)
      s
  (format nil "T~3,'0d" (parse-integer s))))

(defmethod fmt-eui ((e fixnum))
  (format nil "E~7,'0d" e))

(defmethod fmt-eui ((e string))
  (if (eql (aref e 0) #\E)
      e
    (format nil "E~7,'0d" (parse-integer e))))

(defmethod fmt-eui ((e null))
  (format nil "nil"))

;;; Generic display functions

(eval-when (:compile-toplevel :load-toplevel :execute)
(defun english-term-p (obj)
  (and (eq (class-name (class-of obj)) 'uterm)
       (string-equal (lat obj) "ENG"))))

(defun display-umls-obj 
  (obj &key (os *standard-output*) (format :text) (label nil) 
       (file-wrapper t) (english-only nil) (subobjects nil)
       (refvars nil))
  (display-ml-class 
   obj :os os :format format :label label :subobjects subobjects
   :file-wrapper file-wrapper
   :english-only-function (if english-only #'english-term-p nil)
   :refvars refvars))
		     
(defmacro defludisp-ml-class (newfuncname lookup-func)
  "Defines functions for looking up and displaying objects"
  `(defun ,newfuncname 
     (keyval &key (os *standard-output*) (format :text) (label nil)
	     (file-wrapper t) (english-only nil) (subobjects nil))
     (let ((obj (funcall ,lookup-func keyval)))
       (display-umls-obj obj :os os :format format :label label 
			 :file-wrapper file-wrapper :english-only english-only
			 :subobjects subobjects))))

(defludisp-ml-class disp-con #'find-ucon-cui)
(defludisp-ml-class disp-term #'find-uterm-lui)
(defludisp-ml-class disp-str #'find-ustr-sui)