;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
;;;; Name:          composite.lisp
;;;; Purpose:       Composite Classes for UMLisp
;;;; Programmer:    Kevin M. Rosenberg
;;;; Date Started:  Apr 2000
;;;;
;;;; $Id: composite.lisp,v 1.6 2002/10/16 16:05:23 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;;    Copyright (c) 2000-2002 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)
(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))


;;; Semantic type constants

(defun find-tui-word (words)
  (kmrcl:aif (car (find-usty-word words))
       (tui kmrcl::it)
       nil))
(kmrcl:memoize 'find-tui-word)

(defun tui-disease-or-syndrome ()
  (find-tui-word "disease or syndrome"))
(defun tui-sign-or-symptom () 
  (find-tui-word "sign or symptom"))
(defun tui-finding ()
  (find-tui-word "finding"))


;;;; Related concepts with specific tui lookup functions

(defun ucon-is-tui? (ucon tui)
  "Returns t if ucon has a semantic type of tui"
  (find tui (s#sty ucon) :key #'tui))

(defun find-ucon2-tui (ucon tui cui2-func related-con-func)
  "Returns a list of related ucons that have specific tui"
  (remove-duplicates 
   (filter
    #'(lambda (c) 
	(kmrcl:aif (funcall cui2-func c)
	     (let ((ucon2 (find-ucon-cui kmrcl::it)))
 	       (when (ucon-is-tui? ucon2 tui)
		 ucon2))
	     nil))
    (funcall related-con-func ucon))
   :key #'cui))

(defun find-ucon2-coc-tui (ucon tui)
  "Return list of ucon's that have co-occuring concepts of semantic type tui"
  (find-ucon2-tui ucon tui #'cui2 #'s#coc))
  
(defun find-ucon2-rel-tui (ucon tui)
  "Return list of ucon's that have related concepts to ucon and semantic type tui"
  (find-ucon2-tui ucon tui #'cui2 #'s#rel))

;;; Composite Objects

(defclass ucon_freq (umlsclass)
  ((ucon :type ucon :initarg :ucon :reader ucon)
   (freq :type fixnum :initarg :freq :accessor freq))
  (:metaclass kmrcl:ml-class)
  (:default-initargs :cui nil :pfstr nil :freq nil)
  (:title "Concept and Count")
  (:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
  (:ref-fields (cui find-ucon-cui))
  (:documentation "Composite object of ucon/freq"))

(defun ucon_freq-cui (c)
  (cui (ucon c)))

(defun ucon_freq-pfstr (c)
  (pfstr (ucon c)))

(defclass ustr_freq (umlsclass)
  ((ustr :type ustr :initarg :ustr :reader ustr)
   (freq :type fixnum :initarg :freq :accessor freq))
  (:metaclass kmrcl:ml-class)
  (:default-initargs :cui nil :pfstr nil :freq nil)
  (:title "String and Count")
  (:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
  (:ref-fields (sui find-ustr-sui))
  (:documentation "Composite object of ustr/freq"))

(defun ustr_freq-sui (s)
  (sui (ustr s)))

(defun ustr_freq-str (s)
  (str (ustr s)))

(defun ustr_freq-lrl (s)
  (lrl (ustr s)))

(defun ustr_freq-stt (s)
  (stt (ustr s)))

(defclass usty_freq (umlsclass)
  ((usty :type usty :initarg :usty :reader usty)
   (freq :type fixnum :initarg :freq :accessor freq))
  (:metaclass kmrcl:ml-class)
  (:default-initargs :usty nil :freq nil)
  (:title "Semantic Type and Count")
  (:ref-fields (tui find-ucon-tui "subobjects=no"))
  (:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
  (:documentation "Composite object of usty/freq"))

(defmethod tui ((s usty_freq))
  (usty-tui (usty_freq-usty s)))

(defmethod sty ((s usty_freq))
  (usty-sty (usty_freq-usty s)))


(defun find-usty_freq-all ()
  (let ((usty_freqs '()))
    (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
      (let* ((tui (car tuple))
	     (freq (ensure-integer 
		     (caar (mutex-sql-query 
			    (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
	(push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
    (sort usty_freqs #'> :key #'freq)))


(defclass usrl_freq (umlsclass)
  ((usrl :type usrl :initarg :usrl :reader usrl)
   (freq :type fixnum :initarg :freq :accessor freq))
  (:metaclass kmrcl:ml-class)
  (:default-initargs :usrl nil :freq nil)
  (:title "Source and Count")
  (:ref-fields (sab find-ustr-sab))
  (:fields (sab :string) (freq :commainteger) (srl :fixnum))
  (:documentation "Composite object of usrl/freq"))

(defmethod sab ((s usrl_freq))
  (sab (usrl s)))
 
(defmethod srl ((s usrl_freq))
  (srl (usrl s)))


;; Frequency finding functions

(defun find-usrl_freq-all ()
  (let ((freqs '()))
    (dolist (usrl (find-usrl-all))
      (let ((freq (ensure-integer 
		   (caar (mutex-sql-query 
			  (format nil "select count(*) from MRSO where SAB='~a'" 
				  (sab usrl)))))))
	(push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
    (sort freqs #'> :key #'usrl_freq-freq)))

(defun find-ucon2_freq-coc-tui (ucon tui)
"Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui" 
  (let ((ucon_freqs '())) 
    (dolist (ucoc (s#coc ucon)) 
      (kmrcl:aif (cui2 ucoc) 
           (let ((ucon2 (find-ucon-cui kmrcl::it))) 
             (when (ucon-is-tui? ucon2 tui)
	       (push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc)) 
		     ucon_freqs)))))
    (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
    (sort ucon_freqs #'> :key #'freq)))
 
(defun find-ucon2-str&sty (str sty lookup-func)
  "Call lookup-func for ucon and usty for given str and sty"
  (let ((ucon (car (find-ucon-str str)))
	(usty (car (find-usty-word sty))))
    (if (and ucon usty)
	(funcall lookup-func ucon (tui usty))
      nil)))
  
(defun find-ucon2-coc-str&sty (str sty)
  "Find all ucons that are a co-occuring concept for concept named str
   and that have semantic type of sty"
  (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))

(defun find-ucon2-rel-str&sty (str sty)
  "Find all ucons that are a relationship to concept named str
   and that have semantic type of sty"
  (find-ucon2-str&sty str sty #'find-ucon2-rel-tui))

;;; Most common relationships, co-occurances

(defun find-ucon2_freq-tui-all (tui ucon2-tui-func)
  "Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui"
  (let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
    (dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
      (dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
	(kmrcl:aif (aref ucon_freqs (cui ucon2))
	     (setf (freq kmrcl::it) (1+ (freq kmrcl::it)))
	     (setf (aref ucon_freqs (cui ucon2)) 
	       (make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
    (let ((ucon_freq-list '()))
      (dotimes (i (find-cui-max))
	(declare (fixnum i))
	(kmrcl:awhen (aref ucon_freqs i)
	     (push kmrcl::it ucon_freq-list)))
      (sort ucon_freq-list #'> :key #'freq))))

(defun find-ucon2_freq-rel-tui-all (tui)
  "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
  (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))

(defun find-ucon2_freq-coc-tui-all (tui)
  (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))

#+cmu
(dolist (c '(ucon_freq ustr_freq usty_freq usrl_freq))
  (let ((cl #+cmu (pcl:find-class c)
	    #+sbcl (sb-pcl:find-class c)))
    #+cmu (pcl:finalize-inheritance cl)
    #+sbcl (sb-pcl:finalize-inheritance cl)))