1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
5 ;;;; Name: sql-classes.lisp
6 ;;;; Purpose: Routines for reading UMLS objects from SQL database
7 ;;;; Programmer: Kevin M. Rosenberg
8 ;;;; Date Started: Apr 2000
10 ;;;; $Id: sql-classes.lisp,v 1.10 2002/11/12 18:05:00 kevin Exp $
12 ;;;; This file, part of UMLisp, is
13 ;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
15 ;;;; UMLisp users are granted the rights to distribute and use this software
16 ;;;; as governed by the terms of the GNU General Public License.
17 ;;;; *************************************************************************
20 (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
23 (defvar *current-srl* nil)
26 (defun current-srl! (srl)
27 (setq *current-srl* srl))
30 ;;; Accessors (read on demand)
32 ;; defines a slot-unbound method for class and slot-name, fills
33 ;; the slot by calling reader function with the slot values of
34 ;; the instance's reader-keys
35 (defmacro def-lazy-reader (class slot-name reader &rest reader-keys)
36 (let* ((the-slot-name (gensym))
38 (the-instance (gensym))
40 (dolist (key reader-keys)
41 (push (list 'slot-value the-instance (list 'quote key)) keys))
42 (setq keys (nreverse keys))
43 `(defmethod slot-unbound (,the-class (,the-instance ,class)
44 (,the-slot-name (eql ',slot-name)))
45 (declare (ignore ,the-class))
46 (setf (slot-value ,the-instance ,the-slot-name)
49 (def-lazy-reader ucon s#term find-uterm-cui cui)
50 (def-lazy-reader ucon s#def find-udef-cui cui)
51 (def-lazy-reader ucon s#sty find-usty-cui cui)
52 (def-lazy-reader ucon s#rel find-urel-cui cui)
53 (def-lazy-reader ucon s#coc find-ucoc-cui cui)
54 (def-lazy-reader ucon s#lo find-ulo-cui cui)
55 (def-lazy-reader ucon s#atx find-uatx-cui cui)
56 (def-lazy-reader ucon s#sat find-usat-ui cui)
59 (def-lazy-reader uterm s#str find-ustr-cuilui cui lui)
60 (def-lazy-reader uterm s#sat find-usat-ui cui lui)
63 (def-lazy-reader ustr s#sat find-usat-ui cui lui sui)
64 (def-lazy-reader ustr s#cxt find-ucxt-cuisui cui sui)
65 (def-lazy-reader ustr s#so find-uso-cuisui cui sui)
69 ;;; Lookup functions for uterms,ustr in ucons
71 (defun find-uterm-in-ucon (ucon lui)
72 (find lui (s#term ucon) :key #'lui :test 'equal))
74 (defun find-ustr-in-uterm (uterm sui)
75 (find sui (s#str uterm) :key #'sui :test 'equal))
77 (defun find-ustr-in-ucon (ucon sui)
78 (let ((found-ustr nil))
79 (dolist (uterm (s#term ucon))
81 (dolist (ustr (s#str uterm))
83 (when (string-equal sui (sui ustr))
84 (setq found-ustr ustr))))))
88 (defun find-ucon-cui (cui &key (srl *current-srl*))
91 (setq cui (parse-cui cui)))
93 (let ((ls (format nil "select KPFSTR,KCUILRL from MRCON where CUI=~d"
96 (string-append ls (format nil " and KCUILRL <= ~d limit 1" srl))
97 (string-append ls " limit 1"))
98 (kmrcl:awhen (car (mutex-sql-query ls))
99 (make-instance 'ucon :cui cui :pfstr (car kmrcl::it)
100 :lrl (ensure-integer (cadr kmrcl::it)))))
103 (defun find-ucon-lui (lui &key (srl *current-srl*))
104 "Find list of ucon for lui"
106 (setq lui (parse-lui lui)))
109 (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where LUI=~d" lui)))
111 (string-append ls (format nil " and KCUILRL <= ~d" srl)))
112 (dolist (tuple (mutex-sql-query ls))
113 (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
115 :lrl (ensure-integer (nth 2 tuple)))
120 (defun find-ucon-sui (sui &key (srl *current-srl*))
121 "Find list of ucon for sui"
123 (setq sui (parse-sui sui)))
126 (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where SUI=~d" sui)))
128 (string-append ls (format nil " and KCUILRL <= ~d" srl)))
129 (let ((tuples (mutex-sql-query ls)))
130 (dolist (tuple tuples)
131 (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
133 :lrl (ensure-integer (nth 2 tuple)))
138 (defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
139 "Find ucon for cui/sui"
141 (setq cui (parse-cui cui)))
143 (setq sui (parse-sui sui)))
145 (let ((ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where KCUISUI=~d"
146 (make-cuisui cui sui))))
148 (string-append ls (format nil " and KCUILRL <= ~d" srl)))
149 (kmrcl:aif (car (mutex-sql-query ls))
150 (make-instance 'ucon :cui (ensure-integer (nth 0 kmrcl::it))
151 :pfstr (nth 1 kmrcl::it)
152 :lrl (ensure-integer (nth 2 kmrcl::it)))
156 (defun find-ucon-str (str &key (srl *current-srl*))
157 "Find ucon that are exact match for str"
160 (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where STR='~a'" str)))
162 (string-append ls " and KCUILRL <= ~d" srl))
163 (dolist (tuple (mutex-sql-query ls))
164 (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
166 :lrl (ensure-integer (nth 2 tuple))) ucons))
170 (defun find-ucon-all (&key (srl *current-srl*))
171 "Return list of all ucon's"
172 (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
174 (string-append ls (format nil " where KCUILRL <= ~d" srl)))
175 (string-append ls " order by CUI asc")
176 (with-sql-connection (db)
179 #'(lambda (cui pfstr cuilrl)
180 (make-instance 'ucon :cui (ensure-integer cui)
182 :lrl (ensure-integer cuilrl)))
186 (defun map-ucon-all (fn &key (srl *current-srl*))
187 "Return list of all ucon's"
188 (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
190 (string-append ls (format nil " where KCUILRL <= ~d" srl)))
191 (string-append ls " order by CUI asc")
192 (with-sql-connection (db)
195 #'(lambda (cui pfstr cuilrl)
197 (make-instance 'ucon :cui (ensure-integer cui)
199 :lrl (ensure-integer cuilrl))))
204 (defun find-udef-cui (cui &key (srl *current-srl*))
205 "Return a list of udefs for cui"
207 (ls (format nil "select SAB,DEF from MRDEF where CUI=~d" cui)))
209 (string-append ls (format nil " and KSRL <= ~d" srl)))
210 (dolist (tuple (mutex-sql-query ls))
211 (push (make-instance 'udef :sab (car tuple) :def (cadr tuple)) udefs))
214 (defun find-usty-cui (cui &key (srl *current-srl*))
215 "Return a list of usty for cui"
217 (ls (format nil "select TUI,STY from MRSTY where CUI=~d" cui)))
219 (string-append ls (format nil " and KLRL <= ~d" srl)))
220 (dolist (tuple (mutex-sql-query ls))
221 (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
224 (defun find-usty-word (word &key (srl *current-srl*))
225 "Return a list of usty that match word"
227 (ls (format nil "select distinct TUI,STY from MRSTY where STY like '%~a%'" word)))
229 (string-append ls (format nil " and KLRL <= ~d" srl)))
230 (dolist (tuple (mutex-sql-query ls))
231 (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
234 (defun find-urel-cui (cui &key (srl *current-srl*))
235 "Return a list of urel for cui"
237 (ls (format nil "select REL,CUI2,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI1=~d" cui)))
239 (string-append ls (format nil " and KSRL <= ~d" srl)))
240 (dolist (tuple (mutex-sql-query ls))
241 (push (make-instance 'urel
244 :cui2 (ensure-integer (nth 1 tuple))
249 :pfstr2 (nth 6 tuple))
253 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
254 "Return a list of urel for cui2"
256 (ls (format nil "select REL,CUI1,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI2=~d" cui2)))
258 (string-append ls (format nil " and SRL <= ~d" srl)))
259 (dolist (tuple (mutex-sql-query ls))
260 (push (make-instance 'urel
263 :cui1 (ensure-integer (nth 1 tuple))
268 :pfstr2 (nth 6 tuple))
272 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
274 #'(lambda (cui) (find-ucon-cui cui :srl srl))
275 (remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))))
277 (defun find-ucoc-cui (cui &key (srl *current-srl*))
278 "Return a list of ucoc for cui"
280 (ls (format nil "select CUI2,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI1=~d" cui)))
282 (string-append ls (format nil " and KLRL <= ~d" srl)))
283 (string-append ls " order by COF asc")
284 (dolist (tuple (mutex-sql-query ls))
285 (let ((cui2 (ensure-integer (nth 0 tuple))))
288 (push (make-instance 'ucoc :cui1 cui
292 :cof (ensure-integer (nth 3 tuple))
294 :pfstr2 (nth 5 tuple))
296 ucocs)) ;; akready ordered by SQL select
298 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
299 "Return a list of ucoc for cui2"
301 (ls (format nil "select CUI1,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI2=~d" cui2)))
303 (string-append ls (format nil " and KSRL <= ~d" srl)))
304 (string-append ls " order by COF asc")
305 (dolist (tuple (mutex-sql-query ls))
306 (push (make-instance 'ucoc :cui1 (ensure-integer (nth 0 tuple))
310 :cof (ensure-integer (nth 3 tuple))
312 :pfstr2 (nth 5 tuple))
314 ucocs)) ;; already ordered by SQL select
316 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
317 "List of ucon with co-occurance cui2"
319 #'(lambda (cui) (find-ucon-cui cui :srl srl))
320 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
322 (defun find-ulo-cui (cui &key (srl *current-srl*))
323 "Return a list of ulo for cui"
325 (ls (format nil "select ISN,FR,UN,SUI,SNA,SOUI from MRLO where CUI=~d" cui)))
327 (string-append ls (format nil " and KLRL <= ~d" srl)))
328 (dolist (tuple (mutex-sql-query ls))
329 (push (make-instance 'ulo :isn (nth 0 tuple)
330 :fr (ensure-integer (nth 1 tuple))
332 :sui (ensure-integer (nth 3 tuple))
338 (defgeneric suistr (lo))
339 (defmethod suistr ((lo ulo))
340 "Return the string for a ulo object"
341 (find-string-sui (sui lo)))
343 (defun find-uatx-cui (cui &key (srl *current-srl*))
344 "Return a list of uatx for cui"
346 (ls (format nil "select SAB,REL,ATX from MRATX where CUI=~d" cui)))
348 (string-append ls (format nil " and KSRL <= ~d" srl)))
349 (dolist (tuple (mutex-sql-query ls))
350 (push (make-instance 'uatx :sab (nth 0 tuple)
357 (defun find-uterm-cui (cui &key (srl *current-srl*))
358 "Return a list of uterm for cui"
360 (ls (format nil "select distinct LUI,LAT,TS,KLUILRL from MRCON where CUI=~d" cui)))
362 (string-append ls (format nil " and KLUILRL <= ~d" srl)))
363 (dolist (tuple (mutex-sql-query ls))
364 (push (make-instance 'uterm :lui (ensure-integer (nth 0 tuple))
368 :lrl (ensure-integer (nth 3 tuple)))
372 (defun find-uterm-lui (lui &key (srl *current-srl*))
373 "Return a list of uterm for lui"
375 (setq lui (parse-lui lui)))
377 (ls (format nil "select distinct CUI,LAT,TS,KLUILRL from MRCON where LUI=~d" lui)))
379 (string-append ls (format nil " and KLUILRL <= ~d" srl)))
380 (dolist (tuple (mutex-sql-query ls))
381 (push (make-instance 'uterm :cui (ensure-integer (nth 0 tuple))
385 :lrl (ensure-integer (nth 3 tuple)))
389 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
390 "Return single uterm for cui/lui"
391 (let ((ls (format nil "select LAT,TS,KLUILRL from MRCON where KCUILUI=~d limit 1" (make-cuilui cui lui))))
393 (string-append ls (format nil " and KLUILRL <= ~d" srl)))
394 (kmrcl:aif (car (mutex-sql-query ls))
395 (make-instance 'uterm :cui cui
397 :lat (nth 0 kmrcl::it)
398 :ts (nth 1 kmrcl::it)
399 :lrl (ensure-integer (nth 2 kmrcl::it)))
402 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
403 "Return a list of ustr for cui/lui"
404 (declare (fixnum cui lui))
406 (ls (format nil "select SUI,STT,STR,LRL from MRCON where KCUILUI=~d" (make-cuilui cui lui))))
408 (string-append ls (format nil " and LRL <= ~d" srl)))
409 (dolist (tuple (mutex-sql-query ls))
410 (let* ((sui (ensure-integer (car tuple)))
411 (ustr (make-instance 'ustr :sui sui
413 :cuisui (make-cuisui cui sui)
417 :lrl (ensure-integer (nth 3 tuple)))))
421 (defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
422 "Return the single ustr for cuisui"
423 (let ((ls (format nil "select LUI,STT,STR,LRL from MRCON where KCUISUI=~d"
424 (make-cuisui cui sui))))
426 (string-append ls (format nil " and LRL <= ~d" srl)))
427 (kmrcl:aif (car (mutex-sql-query ls))
428 (make-instance 'ustr :sui sui
430 :cuisui (make-cuisui cui sui)
431 :lui (ensure-integer (nth 0 kmrcl::it))
432 :stt (nth 1 kmrcl::it)
433 :str (nth 2 kmrcl::it)
434 :lrl (ensure-integer (nth 3 kmrcl::it)))
437 (defun find-ustr-sui (sui &key (srl *current-srl*))
438 "Return the list of ustr for sui"
440 (setq sui (parse-sui sui)))
442 (ls (format nil "select CUI,LUI,STT,STR,LRL from MRCON where SUI=~d" sui)))
444 (string-append ls (format nil " and LRL <= ~d" srl)))
445 (dolist (tuple (mutex-sql-query ls))
446 (let ((cui (ensure-integer (car tuple))))
447 (push (make-instance 'ustr :sui sui
449 :cuisui (make-cuisui cui sui)
450 :lui (ensure-integer (nth 1 tuple))
453 :lrl (ensure-integer (nth 4 tuple)))
457 (defun find-ustr-sab (sab &key (srl *current-srl*))
458 "Return the list of ustr for sab"
460 (ls (format nil "select KCUISUI from MRSO where SAB='~a'" sab)))
462 (string-append ls (format nil " and SRL <= ~d" srl)))
463 (dolist (tuple (mutex-sql-query ls))
464 (let ((cuisui (ensure-integer (car tuple))))
465 (push (apply #'find-ustr-cuisui
467 (multiple-value-list (decompose-cuisui cuisui))
472 (defun find-ustr-all (&key (srl *current-srl*))
473 "Return list of all ustr's"
474 (let ((ls "select distinct CUI,LUI,SUI,STT,LRL,KPFSTR from MRCON"))
476 (string-append ls (format nil " where LRL <= ~d" srl)))
477 (string-append ls " order by SUI asc")
478 (with-sql-connection (db)
481 #'(lambda (cui lui sui stt lrl pfstr)
482 (setq cui (ensure-integer cui))
483 (setq lui (ensure-integer lui))
484 (setq sui (ensure-integer sui))
485 (setq lrl (ensure-integer lrl))
486 (make-instance 'ustr :cui cui
489 :cuisui (make-cuisui cui sui)
496 (defun find-string-sui (sui &key (srl *current-srl*))
497 "Return the string associated with sui"
498 (let ((ls (format nil "select STR from MRCON where SUI=~d" sui)))
500 (string-append ls (format nil " and LRL <= ~d" srl)))
501 (string-append ls " limit 1")
502 (caar (mutex-sql-query ls))))
504 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
505 (declare (fixnum cui sui))
507 (ls (format nil "select SAB,CODE,SRL,TTY from MRSO where KCUISUI=~d"
508 (make-cuisui cui sui))))
510 (string-append ls (format nil " and SRL <= ~d" srl)))
511 (dolist (tuple (mutex-sql-query ls))
512 (push (make-instance 'uso :sab (nth 0 tuple) :code (nth 1 tuple)
513 :srl (nth 2 tuple) :tty (nth 3 tuple))
517 (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
518 (declare (fixnum cui sui))
520 (ls (format nil "select SAB,CODE,CXN,CXL,RNK,CXS,CUI2,HCD,RELA,XC from MRCXT where KCUISUI=~d"
521 (make-cuisui cui sui))))
523 (string-append ls (format nil " and KSRL <= ~d" srl)))
524 (dolist (tuple (mutex-sql-query ls))
525 (push (make-instance 'ucxt :sab (nth 0 tuple)
527 :cxn (ensure-integer (nth 2 tuple))
529 :rnk (ensure-integer (nth 4 tuple))
531 :cui2 (ensure-integer (nth 6 tuple))
538 (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
539 (let ((ls (format nil "select CODE,ATN,SAB,ATV from MRSAT where ")))
541 (sui (string-append ls (format nil "KCUISUI=~d" (make-cuisui cui sui))))
542 (lui (string-append ls (format nil "KCUILUI=~d and sui=0" (make-cuilui cui lui))))
543 (t (string-append ls (format nil "cui=~d and lui=0 and sui=0" cui))))
545 (string-append ls (format nil " and KSRL <= ~d" srl)))
547 (dolist (tuple (mutex-sql-query ls))
548 (push (make-instance 'usat :code (nth 0 tuple)
556 (defun find-pfstr-cui (cui)
557 (caar (mutex-sql-query (format nil "select KPFSTR from MRCON where CUI=~d limit 1" cui))))
559 (defun find-usty-tui (tui)
561 (setq tui (parse-tui tui))
562 (kmrcl:aif (car (mutex-sql-query
563 (format nil "select STY from MRSTY where TUI=~d limit 1" tui)))
564 (make-instance 'usty :tui tui :sty (nth 0 kmrcl::it))
567 (defun find-usty-sty (sty)
568 "Find usty for a sty"
569 (kmrcl:aif (car (mutex-sql-query
570 (format nil "select TUI from MRSTY where STY='~a' limit 1" sty)))
571 (make-instance 'usty :tui (ensure-integer (nth 0 kmrcl::it)) :sty sty)
574 (defun find-usty-all ()
575 "Return list of usty's for all semantic types"
577 (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
578 (push (find-usty-tui (nth 0 tuple)) ustys))
581 (defun find-usab-all ()
582 "Find usab for a key"
584 (dolist (tuple (mutex-sql-query "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"))
586 (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) tuple
588 (make-instance 'usab :vcui (ensure-integer vcui)
589 :rcui (ensure-integer rcui)
590 :vsab vsab :rsab rsab :son son :sf sf :sver sver :mstart mstart
591 :mend mend :imeta imeta :rmeta rmeta :slc slc :scc scc
592 :srl (ensure-integer srl)
593 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
594 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
595 :curver curver :sabin sabin)
599 (defun find-usab-by-key (key-name key)
600 "Find usab for a key"
601 (aif (car (mutex-sql-query
602 (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 ~A='~A'" key-name key)))
604 (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) it
605 (make-instance 'usab :vcui (ensure-integer vcui)
606 :rcui (ensure-integer rcui)
607 :vsab vsab :rsab rsab :son son :sf sf :sver sver :mstart mstart
608 :mend mend :imeta imeta :rmeta rmeta :slc slc :scc scc
609 :srl (ensure-integer srl)
610 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
611 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
612 :curver curver :sabin sabin))))
614 (defun find-usab-rsab (rsab)
616 (find-usab-by-key "RSAB" rsab))
618 (defun find-usab-vsab (vsab)
620 (find-usab-by-key "VSAB" vsab))
622 (defun find-cui-max ()
623 (let ((cui (caar (mutex-sql-query "select max(CUI) from MRCON"))))
624 (ensure-integer cui)))
626 ;;;; Cross table find functions
628 (defun find-ucon-tui (tui &key (srl *current-srl*))
629 "Find list of ucon for tui"
631 (setq tui (parse-tui tui)))
633 (ls (format nil "select CUI from MRSTY where TUI=~d" tui)))
635 (string-append ls (format nil " and KLRL <= ~d" srl)))
636 (string-append ls " order by cui desc")
637 (dolist (tuple (mutex-sql-query ls))
638 (push (find-ucon-cui (ensure-integer (car tuple)) :srl srl) ucons))
641 (defun find-ucon-word (word &key (srl *current-srl*) (like nil))
642 "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
644 (ls (format nil "select distinct cui from MRXW_ENG where wd~A'~A'"
645 (if like " LIKE " "=")
648 (string-append ls (format nil " and KLRL <= ~d" srl)))
649 (string-append ls " order by cui desc")
650 (dolist (tuple (mutex-sql-query ls))
651 (push (find-ucon-cui (car tuple) :srl srl) ucons))
654 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
655 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
657 (ls (format nil "select distinct cui from MRXNW_ENG where nwd~A'~A'"
658 (if like " LIKE " "=")
661 (string-append ls (format nil " and KLRL <= ~d" srl)))
662 (string-append ls " order by cui desc")
663 (dolist (tuple (mutex-sql-query ls))
664 (push (find-ucon-cui (car tuple) :srl srl) ucons))
667 (defun find-ustr-word (word &key (srl *current-srl*))
668 "Return list of ustrs that match word"
670 (ls (format nil "select cui,sui from MRXW_ENG where wd='~a'" word)))
672 (string-append ls (format nil " and KLRL <= ~d" srl)))
673 (string-append ls " order by cui desc,sui desc")
674 (dolist (tuple (mutex-sql-query ls))
675 (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
679 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
680 "Return list of ustrs that match word"
682 (ls (format nil "select cui,sui from MRXNW_ENG where nwd='~a'" word)))
684 (string-append ls (format nil " and KLRL <= ~d" srl)))
685 (string-append ls " order by cui desc,sui desc")
686 (dolist (tuple (mutex-sql-query ls))
687 (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
693 (defun find-usrl-all ()
695 (tuples (mutex-sql-query "select SAB,SRL from USRL order by SAB desc")))
696 (dolist (tuple tuples)
697 (push (make-instance 'usrl :sab (nth 0 tuple)
698 :srl (ensure-integer (nth 1 tuple))) usrls))
701 ;;; Multiword lookup and score functions
703 (defun find-ucon-multiword (str &key (srl *current-srl*))
704 "Return sorted list of ucon's that match a multiword string"
705 (let* ((words (delimited-string-to-list str #\space))
708 (setq ucons (append ucons (find-ucon-word word :srl srl))))
709 (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
711 (defun find-ustr-multiword (str &key (srl *current-srl*))
712 "Return sorted list of ustr's that match a multiword string"
713 (let* ((words (delimited-string-to-list str #\space))
716 (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
717 (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'cui))))
719 (defun sort-score-ucon-str (str ucons)
720 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
721 (sort-score-umlsclass-str ucons str #'pfstr))
723 (defun sort-score-ustr-str (str ustrs)
724 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
725 (sort-score-umlsclass-str ustrs str #'str))
727 (defun sort-score-umlsclass-str (objs str lookup-func)
728 "Sort a list of objects based on scoring to a string"
733 (score-multiword-match str (funcall lookup-func obj)))
735 (mapcar #'car (sort scored #'> :key #'cadr))))
737 (defun score-multiword-match (s1 s2)
738 "Score a match between two strings with s1 being reference string"
739 (let* ((word-list-1 (delimited-string-to-list s1 #\space))
740 (word-list-2 (delimited-string-to-list s2 #\space))
741 (n1 (length word-list-1))
742 (n2 (length word-list-2))
747 short-list long-list)
748 (declare (fixnum n1 n2 nshort nlong score unmatched))
753 (setq long-list word-list-1)
754 (setq short-list word-list-2))
758 (setq long-list word-list-2)
759 (setq short-list word-list-1)))
760 (decf score (- nlong nshort)) ;; reduce score for extra words
761 (dotimes (iword nshort)
762 (declare (fixnum iword))
763 (kmrcl:aif (position (nth iword short-list) long-list :test #'string-equal)
765 (incf score (- 10 (abs (- kmrcl::it iword))))
767 (decf score (* 2 unmatched))
771 ;;; LEX SQL functions
773 (defun find-lexterm-eui (eui)
774 (kmrcl:awhen (car (mutex-sql-query
775 (format nil "select WRD from LRWD where EUI=~d" eui)))
776 (make-instance 'lexterm :eui eui :wrd (nth 0 kmrcl:it))))
778 (defun find-lexterm-word (wrd)
779 (kmrcl:awhen (mutex-sql-query
780 (format nil "select EUI from LRWD where WRD='~a'" wrd))
782 (dolist (tuple kmrcl:it)
783 (let ((eui (ensure-integer (nth 0 tuple))))
785 (make-instance 'lexterm :eui eui :wrd (copy-seq wrd))
789 ;; LEXTERM accessors, read on demand
791 (def-lazy-reader lexterm s#abr find-labr-eui eui)
792 (def-lazy-reader lexterm s#agr find-lagr-eui eui)
793 (def-lazy-reader lexterm s#cmp find-lcmp-eui eui)
794 (def-lazy-reader lexterm s#mod find-lmod-eui eui)
795 (def-lazy-reader lexterm s#nom find-lnom-eui eui)
796 (def-lazy-reader lexterm s#prn find-lprn-eui eui)
797 (def-lazy-reader lexterm s#prp find-lprp-eui eui)
798 (def-lazy-reader lexterm s#spl find-lspl-eui eui)
799 (def-lazy-reader lexterm s#trm find-ltrm-eui eui)
800 (def-lazy-reader lexterm s#typ find-ltyp-eui eui)
802 ;; LEX SQL Read functions
804 (defun find-labr-eui (eui)
805 (kmrcl:awhen (mutex-sql-query
806 (format nil "select BAS,ABR,EUI2,BAS2 from LRABR where EUI=~d" eui))
808 (dolist (tuple kmrcl::it)
810 (make-instance 'labr :eui eui
813 :eui2 (ensure-integer (nth 2 tuple))
816 (nreverse results))))
818 (defun find-labr-bas (bas)
819 (kmrcl:awhen (mutex-sql-query
820 (format nil "select EUI,ABR,EUI2,BAS2 from LRABR where BAS='~a'" bas))
822 (dolist (tuple kmrcl::it)
824 (make-instance 'labr :eui (ensure-integer (nth 0 tuple))
827 :eui2 (ensure-integer (nth 2 tuple))
830 (nreverse results))))
832 (defun find-lagr-eui (eui)
833 (kmrcl:awhen (mutex-sql-query
834 (format nil "select STR,SCA,AGR,CIT,BAS from LRAGR where EUI=~d" eui))
836 (dolist (tuple kmrcl::it)
846 (nreverse results))))
848 (defun find-lcmp-eui (eui)
849 (kmrcl:awhen (mutex-sql-query
850 (format nil "select BAS,SCA,COM from LRCMP where EUI=~d" eui))
852 (dolist (tuple kmrcl::it)
860 (nreverse results))))
862 (defun find-lmod-eui (eui)
863 (kmrcl:awhen (mutex-sql-query
864 (format nil "select BAS,SCA,PSN_MOD,FEA from LRMOD where EUI=~d" eui))
866 (dolist (tuple kmrcl::it)
872 :psnmod (nth 2 tuple)
875 (nreverse results))))
877 (defun find-lnom-eui (eui)
878 (kmrcl:awhen (mutex-sql-query
879 (format nil "select BAS,SCA,EUI2,BAS2,SCA2 from LRNOM where EUI=~d" eui))
881 (dolist (tuple kmrcl::it)
887 :eui2 (ensure-integer (nth 2 tuple))
891 (nreverse results))))
893 (defun find-lprn-eui (eui)
894 (kmrcl:awhen (mutex-sql-query
895 (format nil "select BAS,NUM,GND,CAS,POS,QNT,FEA from LRPRN where EUI=~d" eui))
897 (dolist (tuple kmrcl::it)
909 (nreverse results))))
911 (defun find-lprp-eui (eui)
912 (kmrcl:awhen (mutex-sql-query
913 (format nil "select BAS,STR,SCA,FEA from LRPRP where EUI=~d" eui))
915 (dolist (tuple kmrcl::it)
924 (nreverse results))))
926 (defun find-lspl-eui (eui)
927 (kmrcl:awhen (mutex-sql-query
928 (format nil "select SPV,BAS from LRSPL where EUI=~d" eui))
930 (dolist (tuple kmrcl::it)
937 (nreverse results))))
940 (defun find-ltrm-eui (eui)
941 (kmrcl:awhen (mutex-sql-query
942 (format nil "select BAS,GEN from LRTRM where EUI=~d" eui))
944 (dolist (tuple kmrcl::it)
951 (nreverse results))))
953 (defun find-ltyp-eui (eui)
954 (kmrcl:awhen (mutex-sql-query
955 (format nil "select BAS,SCA,TYP from LRTYP where EUI=~d" eui))
957 (dolist (tuple kmrcl::it)
965 (nreverse results))))
967 (defun find-lwd-wrd (wrd)
968 (kmrcl:awhen (mutex-sql-query
969 (format nil "select EUI from LRWD where WRD='~a'" wrd))
971 (dolist (tuple kmrcl::it)
972 (push (ensure-integer (nth 0 tuple)) results))
973 (make-instance 'lwd :wrd wrd
974 :euilist (nreverse results)))))
976 ;;; Semantic Network SQL access functions
978 (defun find-sdef-ui (ui)
979 (kmrcl:awhen (car (mutex-sql-query
980 (format nil "select RT,STY_RL,STN_RTN,DEF,EX,UN,RH,ABR,RIN from SRDEF where UI=~d" ui)))
981 (make-instance 'sdef :rt (nth 0 kmrcl::it)
983 :styrl (nth 1 kmrcl::it)
984 :stnrtn (nth 2 kmrcl::it)
985 :def (nth 3 kmrcl::it)
986 :ex (nth 4 kmrcl::it)
987 :un (nth 5 kmrcl::it)
988 :rh (nth 6 kmrcl::it)
989 :abr (nth 7 kmrcl::it)
990 :rin (nth 8 kmrcl::it))))
992 (defun find-sstre1-ui (ui)
993 (kmrcl:awhen (mutex-sql-query
994 (format nil "select UI2,UI3 from SRSTRE1 where UI=~d" ui))
996 (dolist (tuple kmrcl::it)
998 (make-instance 'sstre1 :ui ui
999 :ui2 (ensure-integer (nth 0 tuple))
1000 :ui3 (ensure-integer (nth 1 tuple)))
1002 (nreverse results))))
1004 (defun find-sstre1-ui2 (ui2)
1005 (kmrcl:awhen (mutex-sql-query
1006 (format nil "select UI,UI3 from SRSTRE1 where UI2=~d" ui2))
1007 (let ((results '()))
1008 (dolist (tuple kmrcl::it)
1010 (make-instance 'sstre1 :ui (ensure-integer (nth 0 tuple))
1012 :ui3 (ensure-integer (nth 1 tuple)))
1014 (nreverse results))))
1016 (defun find-sstr-rl (rl)
1017 (kmrcl:awhen (mutex-sql-query
1018 (format nil "select STY_RL,STY_RL2,LS from SRSTRE where RL='~a'" rl))
1019 (let ((results '()))
1020 (dolist (tuple kmrcl::it)
1022 (make-instance 'sstr
1024 :styrl (nth 0 tuple)
1025 :styrl2 (nth 1 tuple)
1028 (nreverse results))))
1031 (defun find-sstre2-sty (sty)
1032 (kmrcl:awhen (mutex-sql-query
1033 (format nil "select RL,STY2 from SRSTRE2 where STY='~a'" sty))
1034 (let ((results '()))
1035 (dolist (tuple kmrcl::it)
1037 (make-instance 'sstre2
1040 :sty2 (nth 1 tuple))
1042 (nreverse results))))
1044 (defun find-sstr-styrl (styrl)
1045 (kmrcl:awhen (mutex-sql-query
1046 (format nil "select RL,STY_RL2,LS from SRSTR where RL='~a'" styrl))
1047 (let ((results '()))
1048 (dolist (tuple kmrcl::it)
1050 (make-instance 'sstr :styrl styrl
1052 :styrl2 (nth 1 tuple)
1055 (nreverse results))))