;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
;;;; Name:          sql-classes.lisp
;;;; Purpose:       Routines for reading UMLS objects from SQL database
;;;; Programmer:    Kevin M. Rosenberg
;;;; Date Started:  Apr 2000
;;;;
;;;; $Id: sql-classes.lisp,v 1.9 2002/11/11 14:19:26 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)))


(defvar *current-srl* nil)
(defun current-srl ()
  *current-srl*)
(defun current-srl! (srl)
  (setq *current-srl* srl))


;;; Accessors (read on demand)

;; defines a slot-unbound method for class and slot-name, fills
;; the slot by calling reader function with the slot values of
;; the instance's reader-keys
(defmacro def-lazy-reader (class slot-name reader &rest reader-keys)
  (let* ((the-slot-name (gensym))
	 (the-class (gensym))
	 (the-instance (gensym))
	 (keys '()))
    (dolist (key reader-keys)
      (push (list 'slot-value the-instance (list 'quote key)) keys))
    (setq keys (nreverse keys))
    `(defmethod slot-unbound (,the-class (,the-instance ,class)
					 (,the-slot-name (eql ',slot-name)))
       (declare (ignore ,the-class))
       (setf (slot-value ,the-instance ,the-slot-name)
	   (,reader ,@keys)))))

(def-lazy-reader ucon s#term find-uterm-cui cui)
(def-lazy-reader ucon s#def find-udef-cui cui)
(def-lazy-reader ucon s#sty find-usty-cui cui)
(def-lazy-reader ucon s#rel find-urel-cui cui)
(def-lazy-reader ucon s#coc find-ucoc-cui cui)
(def-lazy-reader ucon s#lo find-ulo-cui cui)
(def-lazy-reader ucon s#atx find-uatx-cui cui)
(def-lazy-reader ucon s#sat find-usat-ui cui)

;; For uterms
(def-lazy-reader uterm s#str find-ustr-cuilui cui lui)
(def-lazy-reader uterm s#sat find-usat-ui cui lui)

;; For ustrs
(def-lazy-reader ustr s#sat find-usat-ui cui lui sui)
(def-lazy-reader ustr s#cxt find-ucxt-cuisui cui sui)
(def-lazy-reader ustr s#so find-uso-cuisui cui sui)

;;; Object lookups

;;; Lookup functions for uterms,ustr in ucons

(defun find-uterm-in-ucon (ucon lui)
  (find lui (s#term ucon) :key #'lui :test 'equal))

(defun find-ustr-in-uterm (uterm sui)
  (find sui (s#str uterm) :key #'sui :test 'equal))

(defun find-ustr-in-ucon (ucon sui)
  (let ((found-ustr nil))
    (dolist (uterm (s#term ucon))
      (unless found-ustr
	(dolist (ustr (s#str uterm))
	  (unless found-ustr
	    (when (string-equal sui (sui ustr))
	      (setq found-ustr ustr))))))
    found-ustr))


(defun find-ucon-cui (cui &key (srl *current-srl*))
  "Find ucon for a cui"
  (if (stringp cui)
      (setq cui (parse-cui cui)))
  (if cui
      (let ((ls (format nil "select KPFSTR,KCUILRL from MRCON where CUI=~d"
			cui)))
	(if srl
	    (string-append ls (format nil " and KCUILRL <= ~d limit 1" srl))
	  (string-append ls " limit 1"))
	(kmrcl:awhen (car (mutex-sql-query ls))
		  (make-instance 'ucon :cui cui :pfstr (car kmrcl::it) 
				 :lrl (ensure-integer (cadr kmrcl::it)))))
    nil))

(defun find-ucon-lui (lui &key (srl *current-srl*))
  "Find list of ucon for lui"
  (if (stringp lui)
      (setq lui (parse-lui lui)))
  (if lui
      (let ((ucons '())
	    (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where LUI=~d" lui)))
	(if srl
	    (string-append ls (format nil " and KCUILRL <= ~d" srl)))
	(dolist (tuple (mutex-sql-query ls))
	  (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
			       :pfstr (nth 1 tuple)
			       :lrl (ensure-integer (nth 2 tuple)))
		ucons))
	(nreverse ucons))
    nil))

(defun find-ucon-sui (sui &key (srl *current-srl*))
  "Find list of ucon for sui"
  (if (stringp sui)
      (setq sui (parse-sui sui)))
  (if sui
      (let ((ucons '())
	    (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where SUI=~d" sui)))
	(when srl
	    (string-append ls (format nil " and KCUILRL <= ~d" srl)))
	(let ((tuples (mutex-sql-query ls)))
	  (dolist (tuple tuples)
	    (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple)) 
				 :pfstr (nth 1 tuple)
				 :lrl (ensure-integer (nth 2 tuple)))
		  ucons)))
    (nreverse ucons))
  nil))

(defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
  "Find ucon for cui/sui"
  (if (stringp cui)
      (setq cui (parse-cui cui)))
  (if (stringp sui)
      (setq sui (parse-sui sui)))
  (if (and cui sui)
      (let ((ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where KCUISUI=~d"
			(make-cuisui cui sui))))
	(when srl
	    (string-append ls (format nil " and KCUILRL <= ~d" srl)))
	(kmrcl:aif (car (mutex-sql-query ls))
	     (make-instance 'ucon :cui (ensure-integer (nth 0 kmrcl::it)) 
			    :pfstr (nth 1 kmrcl::it)
			    :lrl (ensure-integer (nth 2 kmrcl::it)))
	     nil))
    nil))

(defun find-ucon-str (str &key (srl *current-srl*))
  "Find ucon that are exact match for str"
  (if str
      (let ((ucons '())
	    (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where STR='~a'" str)))
	(when srl
	    (string-append ls " and KCUILRL <= ~d" srl))
	(dolist (tuple (mutex-sql-query ls))
	  (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple)) 
			       :pfstr (nth 1 tuple)
			       :lrl (ensure-integer (nth 2 tuple))) ucons))
	(nreverse ucons))
    nil))

(defun find-ucon-all (&key (srl *current-srl*))
  "Return list of all ucon's"
  (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
    (when srl
      (string-append ls (format nil " where KCUILRL <= ~d" srl)))
    (string-append ls " order by CUI asc")
    (with-sql-connection (db)
      (clsql:map-query 
       'list
       #'(lambda (cui pfstr cuilrl)
	   (make-instance 'ucon :cui (ensure-integer cui)
			  :pfstr pfstr
			  :lrl (ensure-integer cuilrl)))
       ls
       :database db))))

(defun map-ucon-all (fn &key (srl *current-srl*))
  "Return list of all ucon's"
  (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
    (when srl
      (string-append ls (format nil " where KCUILRL <= ~d" srl)))
    (string-append ls " order by CUI asc")
    (with-sql-connection (db)
      (clsql:map-query 
       nil
       #'(lambda (cui pfstr cuilrl)
	   (funcall fn
		    (make-instance 'ucon :cui (ensure-integer cui)
				   :pfstr pfstr
				   :lrl (ensure-integer cuilrl))))
       ls
       :database db))))


(defun find-udef-cui (cui &key (srl *current-srl*))
  "Return a list of udefs for cui"
  (let ((udefs '())
	(ls (format nil "select SAB,DEF from MRDEF where CUI=~d" cui)))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'udef :sab (car tuple) :def (cadr tuple)) udefs))
    (nreverse udefs)))

(defun find-usty-cui (cui &key (srl *current-srl*))
  "Return a list of usty for cui"
  (let ((ustys '())
	(ls (format nil "select TUI,STY from MRSTY where CUI=~d" cui)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
    ustys))

(defun find-usty-word (word &key (srl *current-srl*))
  "Return a list of usty that match word"
  (let ((ustys '())
	(ls (format nil "select distinct TUI,STY from MRSTY where STY like '%~a%'" word)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
    ustys))

(defun find-urel-cui (cui &key (srl *current-srl*))
  "Return a list of urel for cui"
  (let ((urels '())
	(ls (format nil "select REL,CUI2,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI1=~d" cui)))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'urel 
	      :cui1 cui
	      :rel (nth 0 tuple) 
	      :cui2 (ensure-integer (nth 1 tuple))
	      :rela (nth 2 tuple)
	      :sab (nth 3 tuple)
	      :sl (nth 4 tuple)
	      :mg (nth 5 tuple)
	      :pfstr2 (nth 6 tuple))
	    urels))
    (nreverse urels)))

(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
  "Return a list of urel for cui2"
  (let ((urels '())
	(ls (format nil "select REL,CUI1,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI2=~d" cui2)))
    (when srl
	(string-append ls (format nil " and SRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'urel 
	      :cui2 cui2
	      :rel (nth 0 tuple) 
	      :cui1 (ensure-integer (nth 1 tuple))
	      :rela (nth 2 tuple)
	      :sab (nth 3 tuple)
	      :sl (nth 4 tuple)
	      :mg (nth 5 tuple)
	      :pfstr2 (nth 6 tuple))
	    urels))
    (nreverse urels)))

(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
  (mapcar 
   #'(lambda (cui) (find-ucon-cui cui :srl srl))
   (remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))))

(defun find-ucoc-cui (cui &key (srl *current-srl*))
  "Return a list of ucoc for cui"
  (let ((ucocs '())
	(ls (format nil "select CUI2,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI1=~d" cui)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by COF asc")
    (dolist (tuple (mutex-sql-query ls))
      (let ((cui2 (ensure-integer (nth 0 tuple))))
	(when (zerop cui2)
	  (setq cui2 nil))
	(push (make-instance 'ucoc :cui1 cui
			     :cui2 cui2
			     :soc (nth 1 tuple)
			     :cot (nth 2 tuple)
			     :cof (ensure-integer (nth 3 tuple))
			     :coa (nth 4 tuple)
			     :pfstr2 (nth 5 tuple))
	      ucocs)))
    ucocs)) ;; akready ordered by SQL select

(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
  "Return a list of ucoc for cui2"
  (let ((ucocs '())
	(ls (format nil "select CUI1,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI2=~d" cui2)))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (string-append ls " order by COF asc")
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'ucoc :cui1 (ensure-integer (nth 0 tuple))
			   :cui2 cui2
			   :soc (nth 1 tuple)
			   :cot (nth 2 tuple)
			   :cof (ensure-integer (nth 3 tuple))
			   :coa (nth 4 tuple)
			   :pfstr2 (nth 5 tuple))
	    ucocs))
    ucocs)) ;; already ordered by SQL select

(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
  "List of ucon with co-occurance cui2"
  (mapcar 
   #'(lambda (cui) (find-ucon-cui cui :srl srl))
   (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))

(defun find-ulo-cui (cui &key (srl *current-srl*))
  "Return a list of ulo for cui"
  (let ((ulos '())
	(ls (format nil "select ISN,FR,UN,SUI,SNA,SOUI from MRLO where CUI=~d" cui)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'ulo :isn (nth 0 tuple) 
			   :fr (ensure-integer (nth 1 tuple))
			   :un (nth 2 tuple)
			   :sui (ensure-integer (nth 3 tuple))
			   :sna (nth 4 tuple)
			   :soui (nth 5 tuple))
	    ulos))
    (nreverse ulos)))

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

(defun find-uatx-cui (cui &key (srl *current-srl*))
  "Return a list of uatx for cui"
  (let ((uatxs '())
	(ls (format nil "select SAB,REL,ATX from MRATX where CUI=~d" cui)))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'uatx :sab (nth 0 tuple) 
			   :rel (nth 1 tuple)
			   :atx (nth 2 tuple))
	    uatxs))
    (nreverse uatxs)))


(defun find-uterm-cui (cui &key (srl *current-srl*))
  "Return a list of uterm for cui"
  (let ((uterms '())
	(ls (format nil "select distinct LUI,LAT,TS,KLUILRL from MRCON where CUI=~d" cui)))
    (when srl
	(string-append ls (format nil " and KLUILRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'uterm :lui (ensure-integer (nth 0 tuple))
			   :cui cui
			   :lat (nth 1 tuple)
			   :ts (nth 2 tuple)
			   :lrl (ensure-integer (nth 3 tuple)))
	uterms))
    (nreverse uterms)))

(defun find-uterm-lui (lui &key (srl *current-srl*))
  "Return a list of uterm for lui"
  (if (stringp lui)
      (setq lui (parse-lui lui)))
  (let ((uterms '())
	(ls (format nil "select distinct CUI,LAT,TS,KLUILRL from MRCON where LUI=~d" lui)))
    (when srl
	(string-append ls (format nil " and KLUILRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'uterm :cui (ensure-integer (nth 0 tuple))
			   :lui lui
			   :lat (nth 1 tuple)
			   :ts (nth 2 tuple)
			   :lrl (ensure-integer (nth 3 tuple)))
	    uterms))
    (nreverse uterms)))

(defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
  "Return single uterm for cui/lui"
  (let ((ls (format nil "select LAT,TS,KLUILRL from MRCON where KCUILUI=~d limit 1" (make-cuilui cui lui))))
    (when srl
	(string-append ls (format nil " and KLUILRL <= ~d" srl)))
    (kmrcl:aif (car (mutex-sql-query ls))
	 (make-instance 'uterm :cui cui
			:lui lui
			:lat (nth 0 kmrcl::it)
		       :ts (nth 1 kmrcl::it)
		       :lrl (ensure-integer (nth 2 kmrcl::it)))
	 nil)))

(defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
  "Return a list of ustr for cui/lui"
  (declare (fixnum cui lui))
  (let ((ustrs '())
	(ls (format nil "select SUI,STT,STR,LRL from MRCON where KCUILUI=~d" (make-cuilui cui lui))))
    (when srl
	(string-append ls (format nil " and LRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (let* ((sui (ensure-integer (car tuple)))
	     (ustr (make-instance 'ustr :sui sui
				  :cui cui
				  :cuisui (make-cuisui cui sui)
				  :lui lui
				  :stt (nth 1 tuple)
				  :str (nth 2 tuple)
				  :lrl (ensure-integer (nth 3 tuple)))))
	(push ustr ustrs)))
    (nreverse ustrs)))

(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
  "Return the single ustr for cuisui"
  (let ((ls (format nil "select LUI,STT,STR,LRL from MRCON where KCUISUI=~d"
		    (make-cuisui cui sui))))
    (when srl
	(string-append ls (format nil " and LRL <= ~d" srl)))
    (kmrcl:aif (car (mutex-sql-query ls))
	 (make-instance 'ustr :sui sui 
			:cui cui
			:cuisui (make-cuisui cui sui)
			:lui (ensure-integer (nth 0 kmrcl::it))
			:stt (nth 1 kmrcl::it)
			:str (nth 2 kmrcl::it)
			:lrl (ensure-integer (nth 3 kmrcl::it)))
	 nil)))

(defun find-ustr-sui (sui &key (srl *current-srl*))
  "Return the list of ustr for sui"
  (if (stringp sui)
      (setq sui (parse-sui sui)))
  (let ((ustrs '())
	(ls (format nil "select CUI,LUI,STT,STR,LRL from MRCON where SUI=~d" sui)))
    (when srl
	(string-append ls (format nil " and LRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (let ((cui (ensure-integer (car tuple))))
	(push (make-instance 'ustr :sui sui 
			     :cui cui
			     :cuisui (make-cuisui cui sui)
			     :lui (ensure-integer (nth 1 tuple))
			     :stt (nth 2 tuple)
			     :str (nth 3 tuple)
			     :lrl (ensure-integer (nth 4 tuple)))
	ustrs)))
    (nreverse ustrs)))
      
(defun find-ustr-sab (sab &key (srl *current-srl*))
  "Return the list of ustr for sab"
  (let ((ustrs '())
	(ls (format nil "select KCUISUI from MRSO where SAB='~a'" sab)))
    (when srl
	(string-append ls (format nil " and SRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (let ((cuisui (ensure-integer (car tuple))))
	(push (apply #'find-ustr-cuisui 
		     (append
		      (multiple-value-list (decompose-cuisui cuisui))
		      (list :srl srl)))
	      ustrs)))
    (nreverse ustrs)))

(defun find-ustr-all (&key (srl *current-srl*))
  "Return list of all ustr's"
  (let ((ls "select distinct CUI,LUI,SUI,STT,LRL,KPFSTR from MRCON"))
    (when srl
      (string-append ls (format nil " where LRL <= ~d" srl)))
    (string-append ls " order by SUI asc")
    (with-sql-connection (db)
      (clsql:map-query 
       'list
       #'(lambda (cui lui sui stt lrl pfstr)
	   (setq cui (ensure-integer cui))
	   (setq lui (ensure-integer lui))
	   (setq sui (ensure-integer sui))	
	   (setq lrl (ensure-integer lrl))
	   (make-instance 'ustr :cui cui
			  :lui lui
			  :sui sui
			  :cuisui (make-cuisui cui sui)
			  :stt stt
			  :lrl lrl
			  :str pfstr))
       ls
       :database db))))

(defun find-string-sui (sui &key (srl *current-srl*))
  "Return the string associated with sui"
  (let ((ls (format nil "select STR from MRCON where SUI=~d" sui)))
    (when srl
      (string-append ls (format nil " and LRL <= ~d" srl)))
    (string-append ls " limit 1")
    (caar (mutex-sql-query ls))))

(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
  (declare (fixnum cui sui))
  (let ((usos '())
	(ls (format nil "select SAB,CODE,SRL,TTY from MRSO where KCUISUI=~d"
		    (make-cuisui cui sui))))
    (when srl
	(string-append ls (format nil " and SRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'uso :sab (nth 0 tuple) :code (nth 1 tuple) 
			   :srl (nth 2 tuple) :tty (nth 3 tuple))
	    usos))
    (nreverse usos)))

(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
  (declare (fixnum cui sui))
  (let ((ucxts '())
	(ls (format nil "select SAB,CODE,CXN,CXL,RNK,CXS,CUI2,HCD,RELA,XC from MRCXT where KCUISUI=~d" 
		    (make-cuisui cui sui))))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (dolist (tuple (mutex-sql-query ls))
      (push (make-instance 'ucxt :sab (nth 0 tuple) 
			   :code (nth 1 tuple) 
			   :cxn (ensure-integer (nth 2 tuple))
			   :cxl (nth 3 tuple)
			   :rnk (ensure-integer (nth 4 tuple))
			   :cxs (nth 5 tuple)
			   :cui2 (ensure-integer (nth 6 tuple))
			   :hcd (nth 7 tuple)
			   :rela (nth 8 tuple)
			   :xc (nth 9 tuple))
	    ucxts))
    (nreverse ucxts)))

(defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
  (let ((ls (format nil "select CODE,ATN,SAB,ATV from MRSAT where ")))
    (cond
     (sui (string-append ls (format nil "KCUISUI=~d" (make-cuisui cui sui))))
     (lui (string-append ls (format nil "KCUILUI=~d and sui=0" (make-cuilui cui lui))))
     (t (string-append ls (format nil "cui=~d and lui=0 and sui=0" cui))))
    (when srl
	(string-append ls (format nil " and KSRL <= ~d" srl)))
    (let ((usats '()))
      (dolist (tuple (mutex-sql-query ls))
	(push (make-instance 'usat :code (nth 0 tuple)
			     :atn (nth 1 tuple)
			     :sab (nth 2 tuple)
			     :atv (nth 3 tuple))
	      usats))
      (nreverse usats))))


(defun find-pfstr-cui (cui)
  (caar (mutex-sql-query (format nil "select KPFSTR from MRCON where CUI=~d limit 1" cui))))

(defun find-usty-tui (tui)
  "Find usty for tui"
  (setq tui (parse-tui tui)) 
    (kmrcl:aif (car (mutex-sql-query 
	       (format nil "select STY from MRSTY where TUI=~d limit 1" tui)))
	 (make-instance 'usty :tui tui :sty (nth 0 kmrcl::it))
	 nil))

(defun find-usty-sty (sty)
  "Find usty for a sty"
  (kmrcl:aif (car (mutex-sql-query 
		(format nil "select TUI from MRSTY where STY='~a' limit 1" sty)))
	  (make-instance 'usty :tui (ensure-integer (nth 0 kmrcl::it)) :sty sty)
	  nil))

(defun find-usty-all ()
  "Return list of usty's for all semantic types"
  (let ((ustys '()))
    (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
      (push (find-usty-tui (nth 0 tuple)) ustys))
    (nreverse ustys)))


(defun find-usab-rsab (rsab)
  "Find usab for rsab"
  (aif (car (mutex-sql-query 
	     (format nil "select VCUI,RCUI,VSAB,RSAB,SON,SF,SVER,MSTART,MEND,IMETA,RMETA,SLC,SCC,SRL,TFR,CFR,CXTY,TTYL,ATNL,LAT,CENC,CURVER,SABIN from MRSAB where RSAB='~A'" rsab)))
       (destructuring-bind
	   (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) it
	 (make-instance 'usab :vcui (ensure-integer vcui) 
			:rcui (ensure-integer rcui)
			:vsab vsab :rsab rsab :son son :sf sf :sver sver :mstart mstart
			:mend mend :imeta imeta :rmeta rmeta :slc slc :scc scc
			:srl (ensure-integer srl) 
			:tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
			:cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
			:curver curver :sabin sabin))))

(defun find-cui-max ()
  (let ((cui (caar (mutex-sql-query "select max(CUI) from MRCON"))))
    (ensure-integer cui)))

;;;; Cross table find functions

(defun find-ucon-tui (tui &key (srl *current-srl*))
  "Find list of ucon for tui"
  (when (stringp tui)
      (setq tui (parse-tui tui)))
  (let ((ucons '())
	(ls (format nil "select CUI from MRSTY where TUI=~d" tui)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by cui desc")
    (dolist (tuple (mutex-sql-query ls))
      (push (find-ucon-cui (ensure-integer (car tuple)) :srl srl) ucons))
    ucons))
  
(defun find-ucon-word (word &key (srl *current-srl*) (like nil))
  "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
  (let ((ucons '())
	(ls (format nil "select distinct cui from MRXW_ENG where wd~A'~A'" 
		    (if like " LIKE " "=") 
		    word)))
    (when srl
      (string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by cui desc")
    (dolist (tuple (mutex-sql-query ls))
      (push (find-ucon-cui (car tuple) :srl srl) ucons))
    ucons))

(defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
  "Return list of ucons that match word, optionally use SQL's LIKE syntax"
  (let ((ucons '())
	(ls (format nil "select distinct cui from MRXNW_ENG where nwd~A'~A'" 
		    (if like " LIKE " "=")
		    word)))
    (when srl
      (string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by cui desc")
    (dolist (tuple (mutex-sql-query ls))
      (push (find-ucon-cui (car tuple) :srl srl) ucons))
    ucons))

(defun find-ustr-word (word &key (srl *current-srl*))
  "Return list of ustrs that match word"
  (let ((ustrs '())
	(ls (format nil "select cui,sui from MRXW_ENG where wd='~a'" word)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by cui desc,sui desc")
    (dolist (tuple (mutex-sql-query ls))
      (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
	    ustrs))
    ustrs))

(defun find-ustr-normalized-word (word &key (srl *current-srl*))
  "Return list of ustrs that match word"
  (let ((ustrs '())
	(ls (format nil "select cui,sui from MRXNW_ENG where nwd='~a'" word)))
    (when srl
	(string-append ls (format nil " and KLRL <= ~d" srl)))
    (string-append ls " order by cui desc,sui desc")
    (dolist (tuple (mutex-sql-query ls))
      (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
	    ustrs))
    ustrs))

;; Special tables

(defun find-usrl-all ()
  (let ((usrls '())
	(tuples (mutex-sql-query "select SAB,SRL from USRL order by SAB desc")))
    (dolist (tuple tuples)
      (push (make-instance 'usrl :sab (nth 0 tuple)
			   :srl (ensure-integer (nth 1 tuple))) usrls))
    usrls))

;;; Multiword lookup and score functions

(defun find-ucon-multiword (str &key (srl *current-srl*))
  "Return sorted list of ucon's that match a multiword string"
  (let* ((words (delimited-string-to-list str #\space))
	 (ucons '()))
    (dolist (word words)
      (setq ucons (append ucons (find-ucon-word word :srl srl))))
    (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))

(defun find-ustr-multiword (str &key (srl *current-srl*))
  "Return sorted list of ustr's that match a multiword string"
  (let* ((words (delimited-string-to-list str #\space))
	 (ustrs '()))
    (dolist (word words)
      (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
    (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'cui))))
	
(defun sort-score-ucon-str (str ucons)
  "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
  (sort-score-umlsclass-str ucons str #'pfstr))

(defun sort-score-ustr-str (str ustrs)
  "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
  (sort-score-umlsclass-str ustrs str #'str))

(defun sort-score-umlsclass-str (objs str lookup-func)
  "Sort a list of objects based on scoring to a string"
  (let ((scored '()))
    (dolist (obj objs)
      (push 
       (list obj 
	     (score-multiword-match str (funcall lookup-func obj))) 
       scored))
    (mapcar #'car (sort scored #'> :key #'cadr))))

(defun score-multiword-match (s1 s2)
  "Score a match between two strings with s1 being reference string"
  (let* ((word-list-1 (delimited-string-to-list s1 #\space))
	 (word-list-2 (delimited-string-to-list s2 #\space))
	 (n1 (length word-list-1))
	 (n2 (length word-list-2))
	 (unmatched n1)
	 (score 0)
	 (nlong 0)
	 (nshort 0)
	 short-list long-list)
    (declare (fixnum n1 n2 nshort nlong score unmatched))
    (if (> n1 n2)
	(progn
	  (setq nlong n1)
	  (setq nshort n2)
	  (setq long-list word-list-1)
	  (setq short-list word-list-2))
      (progn
	(setq nlong n2)
	(setq nshort n1)
	(setq long-list word-list-2)
	(setq short-list word-list-1)))
    (decf score (- nlong nshort)) ;; reduce score for extra words
    (dotimes (iword nshort)
      (declare (fixnum iword))
      (kmrcl:aif (position (nth iword short-list) long-list :test #'string-equal)
	   (progn
	     (incf score (- 10 (abs (- kmrcl::it iword))))
	     (decf unmatched))))
    (decf score (* 2 unmatched))
    score))


;;; LEX SQL functions

(defun find-lexterm-eui (eui)
  (kmrcl:awhen (car (mutex-sql-query
		  (format nil "select WRD from LRWD where EUI=~d" eui)))
	    (make-instance 'lexterm :eui eui :wrd (nth 0 kmrcl:it))))

(defun find-lexterm-word (wrd)
  (kmrcl:awhen (mutex-sql-query
	     (format nil "select EUI from LRWD where WRD='~a'" wrd))
	    (let ((terms '()))
	      (dolist (tuple kmrcl:it)
		(let ((eui (ensure-integer (nth 0 tuple))))
		  (push
		   (make-instance 'lexterm :eui eui :wrd (copy-seq wrd))
		   terms)))
	      (nreverse terms))))

;; LEXTERM accessors, read on demand
	      
(def-lazy-reader lexterm s#abr find-labr-eui eui)
(def-lazy-reader lexterm s#agr find-lagr-eui eui)
(def-lazy-reader lexterm s#cmp find-lcmp-eui eui)
(def-lazy-reader lexterm s#mod find-lmod-eui eui)
(def-lazy-reader lexterm s#nom find-lnom-eui eui)
(def-lazy-reader lexterm s#prn find-lprn-eui eui)
(def-lazy-reader lexterm s#prp find-lprp-eui eui)
(def-lazy-reader lexterm s#spl find-lspl-eui eui)
(def-lazy-reader lexterm s#trm find-ltrm-eui eui)
(def-lazy-reader lexterm s#typ find-ltyp-eui eui)

;; LEX SQL Read functions

(defun find-labr-eui (eui)
    (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,ABR,EUI2,BAS2 from LRABR where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'labr :eui eui 
				  :bas (nth 0 tuple) 
				  :abr (nth 1 tuple)
				  :eui2 (ensure-integer (nth 2 tuple))
				  :bas2 (nth 3 tuple))
		   results))
		(nreverse results))))

(defun find-labr-bas (bas)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select EUI,ABR,EUI2,BAS2 from LRABR where BAS='~a'" bas))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'labr :eui (ensure-integer (nth 0 tuple))
				  :bas (copy-seq bas)
				  :abr (nth 1 tuple)
				  :eui2 (ensure-integer (nth 2 tuple))
				  :bas2 (nth 3 tuple))
		   results))
		(nreverse results))))

(defun find-lagr-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select STR,SCA,AGR,CIT,BAS from LRAGR where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lagr 
				  :eui eui
				  :str (nth 0 tuple)
				  :sca (nth 1 tuple)
				  :agr (nth 2 tuple)
				  :cit (nth 3 tuple)
				  :bas (nth 4 tuple))
		   results))
		(nreverse results))))

(defun find-lcmp-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,SCA,COM from LRCMP where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lcmp
				  :eui eui
				  :bas (nth 0 tuple)
				  :sca (nth 1 tuple)
				  :com (nth 2 tuple))
		   results))
		(nreverse results))))

(defun find-lmod-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,SCA,PSN_MOD,FEA from LRMOD where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lmod
				  :eui eui
				  :bas (nth 0 tuple)
				  :sca (nth 1 tuple)
				  :psnmod (nth 2 tuple)
				  :fea (nth 3 tuple))
		   results))
		(nreverse results))))

(defun find-lnom-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,SCA,EUI2,BAS2,SCA2 from LRNOM where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lnom
				  :eui eui
				  :bas (nth 0 tuple)
				  :sca (nth 1 tuple)
				  :eui2 (ensure-integer (nth 2 tuple))
				  :bas2 (nth 3 tuple)
				  :sca2 (nth 4 tuple))
		   results))
		(nreverse results))))

(defun find-lprn-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,NUM,GND,CAS,POS,QNT,FEA from LRPRN where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lprn
				  :eui eui
				  :bas (nth 0 tuple)
				  :num (nth 1 tuple)
				  :gnd (nth 2 tuple)
				  :cas (nth 3 tuple)
				  :pos (nth 4 tuple)
				  :qnt (nth 5 tuple)
				  :fea (nth 6 tuple))
		   results))
		(nreverse results))))

(defun find-lprp-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,STR,SCA,FEA from LRPRP where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lprp
				  :eui eui
				  :bas (nth 0 tuple)
				  :str (nth 1 tuple)
				  :sca (nth 2 tuple)
				  :fea (nth 3 tuple))
		   results))
		(nreverse results))))

(defun find-lspl-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select SPV,BAS from LRSPL where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'lspl
				  :eui eui
				  :spv (nth 0 tuple)
				  :bas (nth 1 tuple))
		   results))
		(nreverse results))))


(defun find-ltrm-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,GEN from LRTRM where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'ltrm
				  :eui eui
				  :bas (nth 0 tuple)
				  :gen (nth 1 tuple))
		   results))
		(nreverse results))))

(defun find-ltyp-eui (eui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select BAS,SCA,TYP from LRTYP where EUI=~d" eui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'ltyp
				  :eui eui
				  :bas (nth 0 tuple)
				  :sca (nth 1 tuple)
				  :typ (nth 2 tuple))
		   results))
		(nreverse results))))

(defun find-lwd-wrd (wrd)
  (kmrcl:awhen (mutex-sql-query 
	     (format nil "select EUI from LRWD where WRD='~a'" wrd))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push (ensure-integer (nth 0 tuple)) results))
		(make-instance 'lwd :wrd wrd
			       :euilist (nreverse results)))))

;;; Semantic Network SQL access functions
 
(defun find-sdef-ui (ui)
  (kmrcl:awhen (car (mutex-sql-query 
		  (format nil "select RT,STY_RL,STN_RTN,DEF,EX,UN,RH,ABR,RIN from SRDEF where UI=~d" ui)))
	    (make-instance 'sdef :rt (nth 0 kmrcl::it)
			   :ui ui
			   :styrl (nth 1 kmrcl::it)
			   :stnrtn (nth 2 kmrcl::it)
			   :def (nth 3 kmrcl::it)
			   :ex (nth 4 kmrcl::it)
			   :un (nth 5 kmrcl::it)
			   :rh (nth 6 kmrcl::it)
			   :abr (nth 7 kmrcl::it)
			   :rin (nth 8 kmrcl::it))))

(defun find-sstre1-ui (ui)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select UI2,UI3 from SRSTRE1 where UI=~d" ui))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'sstre1 :ui ui
				  :ui2 (ensure-integer (nth 0 tuple))
				  :ui3 (ensure-integer (nth 1 tuple)))
		   results))
		(nreverse results))))

(defun find-sstre1-ui2 (ui2)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select UI,UI3 from SRSTRE1 where UI2=~d" ui2))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'sstre1 :ui (ensure-integer (nth 0 tuple))
				  :ui2 ui2
				  :ui3 (ensure-integer (nth 1 tuple)))
		   results))
		(nreverse results))))

(defun find-sstr-rl (rl)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select STY_RL,STY_RL2,LS from SRSTRE where RL='~a'" rl))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'sstr 
				  :rl rl
				  :styrl (nth 0 tuple)
				  :styrl2 (nth 1 tuple)
				  :ls (nth 2 tuple))
		   results))
		(nreverse results))))


(defun find-sstre2-sty (sty)
  (kmrcl:awhen (mutex-sql-query 
	     (format nil "select RL,STY2 from SRSTRE2 where STY='~a'" sty))
	    (let ((results '()))
	      (dolist (tuple kmrcl::it)
		(push
		 (make-instance 'sstre2
				:sty (copy-seq sty)
				:rl (nth 0 tuple)
				:sty2 (nth 1 tuple))
				results))
		(nreverse results))))

(defun find-sstr-styrl (styrl)
  (kmrcl:awhen (mutex-sql-query 
	       (format nil "select RL,STY_RL2,LS from SRSTR where RL='~a'" styrl))
	      (let ((results '()))
		(dolist (tuple kmrcl::it)
		  (push
		   (make-instance 'sstr :styrl styrl
				  :rl (nth 0 tuple)
				  :styrl2 (nth 1 tuple)
				  :ls (nth 2 tuple))
		   results))
		(nreverse results))))