;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
;;;; Name:     classes-support.lisp
;;;; Purpose:  Support for UMLisp classes
;;;; Author:   Kevin M. Rosenberg
;;;; Created:  Apr 2000
;;;;
;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
;;;;    Copyright (c) 2000-2006 by Kevin M. Rosenberg, M.D.
;;;;
;;;; UMLisp users are granted the rights to distribute and use this software
;;;; as governed by the terms of the GNU General Public License.
;;;; *************************************************************************

(in-package #:umlisp)

;;; Formatting routines

(defgeneric fmt-cui (c))
(defmethod fmt-cui ((c ucon))
  (fmt-cui (cui c)))

(when *has-fixnum-class*
  (defmethod fmt-cui ((c fixnum))
    (prefixed-fixnum-string c #\C 7)))

(defmethod fmt-cui ((c integer))
    (prefixed-integer-string c #\C 7))

(defmethod fmt-cui ((c string))
  (if (eql (aref c 0) #\C)
      c
      (fmt-cui (parse-integer c))))

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

(defgeneric fmt-lui (c))
(defmethod fmt-lui ((l uterm))
  (fmt-lui (lui l)))

(when *has-fixnum-class*
  (defmethod fmt-lui ((l fixnum))
    (prefixed-fixnum-string l #\L 7)))

(defmethod fmt-lui ((l integer))
  (prefixed-integer-string l #\L 7))

(defmethod fmt-lui ((l string))
  (if (eql (aref l 0) #\L)
      l
      (fmt-lui (parse-integer l))))

(defgeneric fmt-sui (s))
(defmethod fmt-sui ((s ustr))
  (fmt-sui (sui s)))

(when *has-fixnum-class*
  (defmethod fmt-sui ((s fixnum))
    (prefixed-fixnum-string s #\S 7)))

(defmethod fmt-sui ((s integer))
  (prefixed-integer-string s #\S 7))

(defmethod fmt-sui ((s string))
  (if (eql (aref s 0) #\S)
      s
      (fmt-sui (parse-integer s))))

(defgeneric fmt-tui (tui))
(when *has-fixnum-class*
  (defmethod fmt-tui ((tui fixnum))
    (prefixed-fixnum-string tui #\T 3)))

(defmethod fmt-tui ((tui integer))
  (prefixed-integer-string tui #\T 3))

(defmethod fmt-tui ((tui string))
  (if (eql (aref tui 0) #\T)
      tui
    (fmt-tui (parse-integer tui))))

(defgeneric fmt-aui (aui))
(when *has-fixnum-class*
  (defmethod fmt-aui ((aui fixnum))
    (if (>= aui 10000000)
      (prefixed-fixnum-string aui #\A 8)
      (prefixed-fixnum-string aui #\A 7))))

(defmethod fmt-aui ((aui integer))
  (if (>= aui 10000000)
    (prefixed-integer-string aui #\A 8)
    (prefixed-integer-string aui #\A 7)))

(defmethod fmt-aui ((aui string))
  (if (eql (aref aui 0) #\A)
      aui
      (fmt-aui (parse-integer aui))))

(defgeneric fmt-rui (rui))
(when *has-fixnum-class*
  (defmethod fmt-rui ((rui fixnum))
    (prefixed-fixnum-string rui #\A 8)))

(defmethod fmt-rui ((rui integer))
  (prefixed-integer-string rui #\A 8))

(defmethod fmt-rui ((rui string))
  (if (eql (aref rui 0) #\R)
      rui
    (fmt-rui (parse-integer rui))))

(defgeneric fmt-eui (e))
(when *has-fixnum-class*
  (defmethod fmt-eui ((e fixnum))
    (prefixed-fixnum-string e #\E 7)))

(defmethod fmt-eui ((e integer))
  (prefixed-integer-string e #\E 7))

(defmethod fmt-eui ((e string))
  (if (eql (aref e 0) #\E)
      e
      (fmt-eui (parse-integer e))))

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

(defun cui-p (ui)
  "Check if a string is a CUI"
  (check-ui ui #\C 7))

(defun lui-p (ui)
  "Check if a string is a LUI"
  (check-ui ui #\L 7))

(defun sui-p (ui)
  "Check if a string is a SUI"
  (check-ui ui #\S 7))

(defun tui-p (ui)
  (check-ui ui #\T 3))

(defun eui-p (ui)
  (check-ui ui #\E 7))

(defun check-ui (ui start-char len)
  (when (and (stringp ui)
	     (= (length ui) (1+ len))
	     (char-equal start-char (schar ui 0))
	     (ignore-errors (parse-integer ui :start 1)))
    t))


;;; Generic display functions

(eval-when (:compile-toplevel :load-toplevel :execute)
(defun english-term-p (obj)
  "Returns two values: T/NIL if term is english and T/NIL if obj is a TERM"
  (if (eq (hyperobject::class-name (hyperobject::class-of obj)) 'uterm)
      (values (string-equal (lat obj) "ENG") t)
    (values nil nil))))

(defun english-term-filter (obj)
  "Retrns NIL if object is a term and not english"
  (multiple-value-bind (is-english is-term) (english-term-p obj)
      (or (not is-term) is-english)))

(defun print-umlsclass (obj &key (stream *standard-output*)
			(vid :compact-text)
			(file-wrapper nil) (english-only t) (subobjects nil)
			(refvars nil) (link-printer nil))
  (view obj :stream stream :vid vid :subobjects subobjects
	:file-wrapper file-wrapper
	:filter (if english-only nil #'english-term-filter)
	:link-printer link-printer
	:refvars refvars))

(defmacro define-lookup-display (newfuncname lookup-func)
  "Defines functions for looking up and displaying objects"
  `(defun ,newfuncname  (keyval &key (stream *standard-output*) (vid :compact-text)
			 (file-wrapper t) (english-only nil) (subobjects nil))
     (let ((obj (funcall ,lookup-func keyval)))
       (print-umlsclass obj :stream stream :vid vid
			:file-wrapper file-wrapper :english-only english-only
			:subobjects subobjects)
       obj)))

(define-lookup-display display-con #'find-ucon-cui)
(define-lookup-display display-term #'find-uterm-lui)
(define-lookup-display display-str #'find-ustr-sui)

(defun ucon-has-tui (ucon tui)
  "Returns T if UCON has a semantic type of TUI."
  (some #'(lambda (usty) (= tui (tui usty))) (s#sty ucon)))

(defgeneric suistr (lo))
(defmethod suistr ((lo ulo))
  "Return the string for a ulo object"
  (find-string-sui (sui lo)))

(defgeneric pf-ustr (obj))
(defmethod pf-ustr ((ucon ucon))
  "Return the preferred ustr for a ucon"
  (pf-ustr
   (find-if (lambda (uterm) (string= "P" (ts uterm))) (s#term ucon))))

(defmethod pf-ustr ((uterm uterm))
  "Return the preferred ustr for a uterm"
  (find-if (lambda (ustr) (string= "PF" (stt ustr))) (s#str uterm)))

(defgeneric mesh-number (obj))
(defmethod mesh-number ((con ucon))
  (mesh-number (pf-ustr con)))

(defmethod mesh-number ((ustr ustr))
  (let ((codes
	 (map-and-remove-nils
	  (lambda (sat)
	    (when (and (string-equal "MSH" (sab sat))
		       (string-equal "MN" (atn sat)))
	      (atv sat)))
	  (s#sat ustr))))
    (if (= 1 (length codes))
	(car codes)
      codes)))

(defun ucon-ustrs (ucon)
  "Return lists of strings for a concept"
  (let (res)
    (dolist (term (s#term ucon) (nreverse res))
      (dolist (str (s#str term))
	(push str res)))))


(defmethod pfstr ((uterm uterm))
  "Return the preferred string for a uterm"
  (dolist (ustr (s#str uterm))
    (when (string= "PF" (stt ustr))
      (return-from pfstr (str ustr)))))

(defmethod pfstr ((ustr ustr))
  "Return the preferred string for a ustr, which is the string itself"
  (str ustr))

(defun remove-non-english-terms (uterms)
  (remove-if-not #'english-term-p uterms))

(defun remove-english-terms (uterms)
  (remove-if #'english-term-p uterms))


(defvar +relationship-abbreviations+
  '(("RB" "Broader" "has a broader relationship")
    ("RN" "Narrower" "has a narrower relationship")
    ("RO" "Other related" "has relationship other than synonymous, narrower, or broader")
    ("RL" "Like" "the two concepts are similar or 'alike'.  In the current edition of the Metathesaurus, most relationships with this attribute are mappings provided by a source")
    ("RQ" "Unspecified" "unspecified source asserted relatedness, possibly synonymous")
    ("SY" "Source Synonymy" "source asserted synonymy")
    ("PAR" "Parent" "has parent relationship in a Metathesaurus source vocabulary")
    ("CHD" "Child" "has child relationship in a Metathesaurus source vocabulary")
    ("SIB" "Sibling" "has sibling relationship in a Metathesaurus source vocabulary")
    ("AQ" "Allowed" "is an allowed qualifier for a concept in a Metathesaurus source vocabulary")
    ("QB" "Qualified" "can be qualified by a concept in a Metathesaurus source vocabulary")))

(defvar *rel-info-table* (make-hash-table :size 30 :test 'equal))
(defvar *is-rel-table-init* nil)
(unless *is-rel-table-init*
  (dolist (relinfo +relationship-abbreviations+)
    (setf (gethash (string-downcase (car relinfo)) *rel-info-table*)
      (cdr relinfo)))
  (setq *is-rel-table-init* t))

(defun rel-abbr-info (rel)
  (nth-value 0 (gethash (string-downcase rel) *rel-info-table*)))

(defun filter-urels-by-rel (urels rel)
  (remove-if-not (lambda (urel) (string-equal rel (rel urel))) urels))


(defvar +language-abbreviations+
    '(("BAQ" . "Basque")
      ("CZE" . "Chech")
      ("DAN" . "Danish")
      ("DUT" . "Dutch")
      ("ENG" . "English")
      ("FIN" . "Finnish")
      ("FRE" . "French")
      ("GER" . "German")
      ("HEB" . "Hebrew")
      ("HUN" . "Hungarian")
      ("ITA" . "Italian")
      ("JPN" . "Japanese")
      ("NOR" . "Norwegian")
      ("POR" . "Portuguese")
      ("RUS" . "Russian")
      ("SPA" . "Spanish")
      ("SWE" . "Swedish")))

(defvar *lat-info-table* (make-hash-table :size 30 :test 'equal))
(defvar *is-lat-table-init* nil)
(unless *is-lat-table-init*
  (dolist (latinfo +language-abbreviations+)
    (setf (gethash (string-downcase (car latinfo)) *lat-info-table*)
      (cdr latinfo)))
  (setq *is-lat-table-init* t))

(defun lat-abbr-info (lat)
  (aif (nth-value 0 (gethash (string-downcase lat) *lat-info-table*))
       it
       lat))



(defun stt-abbr-info (stt)
  (when (string-equal "PF" stt)
    (return-from stt-abbr-info "Preferred"))
  (when (char-equal #\V (schar stt 0))
    (setq stt (subseq stt 1)))
  (loop for c across stt
      collect
	(cond
	 ((char-equal #\C c)
	  "Upper/lower case")
	 ((char-equal #\W c)
	  "Word order")
	 ((char-equal #\S c)
	  "Singular")
	 ((char-equal #\P c)
	  "Plural")
	 ((char-equal #\O c)
	  "Other"))))


(defun ucon-parents (ucon &key sab include-rb)
  (ucon-ancestors ucon :sab sab :include-rb include-rb
                  :ancestors nil))

(defun is-ucon-in-ancestors (ucon ancestors)
  (cond
   ((null ancestors) nil)
   ((atom ancestors) (eql (cui ucon) (cui ancestors)))
   ((listp (car ancestors))
    (or (is-ucon-in-ancestors ucon (car ancestors))
        (is-ucon-in-ancestors ucon (cdr ancestors))))
   (t
    (or (eql (cui ucon) (cui (car ancestors)))
        (is-ucon-in-ancestors ucon (cdr ancestors))))))


(defun sorted-ancestor-cuis (anc)
  (sort (remove-duplicates (map 'list 'cui (flatten anc))) #'<))

(defun shared-cuis (a1 a2)
  (let ((cl1 (sorted-ancestor-cuis a1))
        (cl2 (sorted-ancestor-cuis a2))
        (shared nil))
    (dolist (c1 cl1 (nreverse shared))
      (dolist (c2 cl2)
        (cond
         ((eql c1 c2)
          (push c1 shared))
         ((> c2 c1)
          (return)))))))

(defun cdist-ancestors (anc1 anc2)
  (let ((shareds (shared-cuis anc1 anc2)))
    (let ((min most-positive-fixnum)
          (cui-min nil)
          (path-min nil))
      (declare (fixnum min))
      (dolist (shared shareds)
        (multiple-value-bind (d1 p1) (ancestor-distance shared anc1)
          (multiple-value-bind (d2 p2) (ancestor-distance shared anc2)
            (let ((dtotal (+ d1 d2)))
              (declare (fixnum d1 d2 dtotal))
              (when (< dtotal min)
                (format t "~D ~D ~D ~S ~S~%" d1 d2 dtotal p1 p2)
                (setq min dtotal
                      cui-min shared
                      path-min (append p1 (cdr (reverse p2)))
                      ))))))
      (values min cui-min path-min))))

(defun cdist-metric (c1 c2 &key sab include-rb full-ucon (srl *current-srl*))
  (let* ((anc1 (ucon-ancestors c1 :sab sab :include-rb include-rb :full-ucon full-ucon :srl srl))
         (anc2 (ucon-ancestors c2 :sab sab :include-rb include-rb :full-ucon full-ucon :srl srl)))
    (multiple-value-bind (min cui path)
        (cdist-ancestors (list* c1 anc1) (list* c2 anc2))
      (if cui
          (values min cui (append (list c1) path (unless (eql (cui (car (last path))) (cui c2))
                                                   (list c2))))
        (values nil nil nil)))))
               

(defun ancestor-distance (cui ancestors &key (distance 0) path)
  (cond
   ((null ancestors)
    nil)
   ((atom ancestors)
    (when (eql cui (cui ancestors))
      (values distance (nreverse (list* ancestors path)))))
   ((atom (car ancestors))
    (if (eql cui (cui (car ancestors)))
        (values distance (nreverse (list* (car ancestors) path)))
      (ancestor-distance cui (cdr ancestors) :distance distance :path (list* (car ancestors) path))))
   (t
    (let ((%min most-positive-fixnum)
          %path)
      (dolist (a ancestors)
        (multiple-value-bind (d p) (ancestor-distance cui a :distance (1+ distance) :path path)
          (when (and d (< d %min))
            (setq %min d
                  %path p))))
      (when (< %min most-positive-fixnum)
        (values %min %path))))))

        
(defun ucon-ancestors (ucon &key sab include-rb ancestors full-ucon (srl *current-srl*))
  "Returns a list of ancestor lists for a concept"
  (unless ucon (return-from ucon-ancestors nil))
  (let ((parent-rels (find-urel-cui
                      (cui ucon)
                      :without-pfstr2 t
                      :srl srl
                      :filter (concatenate 'string
                                (if sab (format nil "SAB='~A' AND " sab) "")
                                (if include-rb
                                    "(REL='RB' OR REL='PAR')"
                                  "REL='PAR'"))))
        (parents nil))
    (dolist (rel parent-rels)
      (let ((parent (if full-ucon
                        (find-ucon-cui (cui2 rel))
                      (make-ucon-cui (cui2 rel)))))
        ;; (format t "~S ~S ~S ~S~%" rel ucon parent ancestors)
        (unless (is-ucon-in-ancestors parent ancestors)
          (push
           (list*
            parent
            (ucon-ancestors parent :sab (sab rel) :ancestors (append (list parent) ancestors)
                            :full-ucon full-ucon))
           parents))))
    (nreverse parents)))


(defgeneric cxt-ancestors (obj))
(defmethod cxt-ancestors ((con ucon))
  (loop for term in (s#term con)
      append (cxt-ancestors term)))


(defmethod cxt-ancestors ((term uterm))
  (loop for str in (s#str term)
      append (cxt-ancestors str)))

(defmethod cxt-ancestors ((str ustr))
  "Return the ancestory contexts of a ustr"
  (let* ((anc (remove-if-not
	       (lambda (cxt) (string-equal "ANC" (cxl cxt)))
	       (s#cxt str)))
	 (num-contexts (if anc
			   (apply #'max (mapcar (lambda (cxt) (cxn cxt)) anc))
			 0))
	 (anc-lists '()))
    (dotimes (i num-contexts (nreverse anc-lists))
      (let* ((anc-this-cxn (remove-if-not
			    (lambda (cxt) (= (1+ i) (cxn cxt))) anc)))
	(push
	 (sort anc-this-cxn (lambda (a b) (< (rank a) (rank b))))
	 anc-lists)))))

(defun uso-unique-codes (usos)
  (let ((sab-codes (make-hash-table :test 'equal)))
    (dolist (uso usos)
      (setf (gethash (sab uso) sab-codes) (code uso)))
    (loop for key being the hash-key in sab-codes
        collect (list key (gethash key sab-codes)))))


(defun ucon-has-sab (ucon sab)
  (and (find-if (lambda (uso) (string-equal sab (sab uso))) (s#so ucon)) t))


#+scl
(dolist (c '(urank udef usat uso ucxt ustr ulo uterm usty urel ucoc uatx ucon uxw uxnw uxns lexterm labr lagr lcmp lmod lnom lprn lprp lspl ltrm ltyp lwd sdef sstr sstre1 sstre2 usrl))
    (let ((cl (find-class c)))
      (clos:finalize-inheritance cl)))