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 ;;;; Author: Kevin M. Rosenberg
12 ;;;; This file, part of UMLisp, is
13 ;;;; Copyright (c) 2000-2003 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 ;;;; *************************************************************************
22 (defvar *current-srl* nil)
25 (defun current-srl! (srl)
26 (setq *current-srl* srl))
28 (defmacro query-string (table fields &optional srl where-name where-value
29 &key (lrl "KCUILRL") single distinct order like)
30 (let* ((%%fields (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
31 (if distinct "distinct " "") fields table))
32 (%%order (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}"
35 (%%lrl (format nil " and ~:@(~A~)<=" lrl))
36 (%%where (when where-name
37 (format nil " where ~:@(~A~)~A" where-name
38 (if like " like " "")))))
42 ,@(when %%where (list %%where))
44 `((typecase ,where-value
47 (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
49 (concatenate 'string "='" (write-to-string ,where-value) "'"))
53 (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
54 (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
55 ,@(when %%order (list %%order))
56 ,@(when single (list " limit 1")))))
58 (defun query-string-eval (table fields &optional srl where-name where-value
59 &key (lrl "KCUILRL") single distinct order like)
62 (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
63 (if distinct "distinct " "") fields table)
64 (if where-name (format nil " where ~:@(~A~)" where-name) "")
71 (if like " like '%~A%""='~A'")))
74 (if srl (format nil " and ~:@(~A~)<=~D" lrl srl) "")
75 (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) "")
76 (if single " limit 1" "")))
79 (defmacro umlisp-query (table fields srl where-name where-value
80 &key (lrl "KCUILRL") single distinct order like
81 (query-cmd 'mutex-sql-query))
82 "Query the UMLisp database. Return a list of umlisp objects whose name
83 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
85 (query-string ,table ,fields ,srl ,where-name ,where-value
86 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
88 (defmacro umlisp-query-eval (table fields srl where-name where-value
89 &key (lrl "KCUILRL") single distinct order like)
90 "Query the UMLisp database. Return a list of umlisp objects whose name
91 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
93 (query-string-eval ,table ,fields ,srl ,where-name ,where-value
94 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
96 ;; only WHERE-VALUE and SRL are evaluated
97 (defmacro collect-umlisp-query ((table fields srl where-name where-value
98 &key (lrl "KCUILRL") distinct single
99 order like (query-cmd 'mutex-sql-query))
101 (let ((value (gensym))
104 `(let* ((,value ,where-value)
105 (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
106 :lrl ,lrl :single ,single
107 :distinct ,distinct :order ,order
109 :query-cmd ,query-cmd))))
110 ,@(unless where-name `((declare (ignore ,value))))
112 (destructuring-bind ,fields tuple
114 `(let ((,value ,where-value))
115 ,@(unless where-name `((declare (ignore ,value))))
117 (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
118 :lrl ,lrl :single ,single :distinct ,distinct
119 :order ,order :like ,like))
120 (push (destructuring-bind ,fields tuple ,@body) ,r))
124 (umlisp-query ,table ,fields ,srl ,where-name ,value
125 :lrl ,lrl :single ,single :distinct ,distinct
126 :order ,order :like ,like)
127 collect (destructuring-bind ,fields tuple ,@body))))))
129 (defmacro collect-umlisp-query-eval ((table fields srl where-name where-value
130 &key (lrl "KCUILRL") distinct single
133 (let ((value (gensym))
135 (eval-fields (cadr fields)))
137 `(let* ((,value ,where-value)
138 (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
139 :lrl ,lrl :single ,single
140 :distinct ,distinct :order ,order
143 (destructuring-bind ,eval-fields tuple
145 `(let ((,value ,where-value)
147 (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
148 :lrl ,lrl :single ,single :distinct ,distinct
149 :order ,order :like ,like))
150 (push (destructuring-bind ,eval-fields tuple ,@body) ,r))
154 (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
155 :lrl ,lrl :single ,single :distinct ,distinct
156 :order ,order :like ,like)
157 collect (destructuring-bind ,eval-fields tuple ,@body))))))
160 ;;; Read from SQL database
162 (defmacro ensure-cui-integer (cui)
164 (setq ,cui (parse-cui ,cui))
167 (defmacro ensure-lui-integer (lui)
169 (setq ,lui (parse-lui ,lui))
172 (defmacro ensure-sui-integer (sui)
174 (setq ,sui (parse-sui ,sui))
177 (defmacro ensure-tui-integer (tui)
179 (setq ,tui (parse-tui ,tui))
182 (defmacro ensure-eui-integer (eui)
184 (setq ,eui (parse-eui ,eui))
187 (defun find-ucon-cui (cui &key (srl *current-srl*))
188 "Find ucon for a cui"
189 (ensure-cui-integer cui)
190 (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl cui cui :single t)
191 (make-instance 'ucon :cui cui :pfstr kpfstr
192 :lrl (ensure-integer kcuilrl))))
194 (defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*))
195 "Find ucon for a cui"
196 (ensure-cui-integer cui)
197 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
198 (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
201 (defun find-pfstr-cui (cui &key (srl *current-srl*))
202 "Find preferred string for a cui"
203 (ensure-cui-integer cui)
204 (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t)
208 (defun find-ucon-lui (lui &key (srl *current-srl*))
209 "Find list of ucon for lui"
210 (ensure-lui-integer lui)
211 (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui
213 (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
214 :lrl (ensure-integer kcuilrl))))
216 (defun find-ucon-sui (sui &key (srl *current-srl*))
217 "Find list of ucon for sui"
218 (ensure-sui-integer sui)
219 (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t)
220 (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
221 :lrl (ensure-integer kcuilrl))))
223 (defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
224 "Find ucon for cui/sui"
225 (ensure-cui-integer cui)
226 (ensure-sui-integer sui)
228 (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl kcuisui
229 (make-cuisui cui sui))
230 (make-instance 'ucon :cui cui
232 :lrl (ensure-integer kcuilrl)))))
234 (defun find-ucon-str (str &key (srl *current-srl*))
235 "Find ucon that are exact match for str"
236 (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t)
237 (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
238 :lrl (ensure-integer kcuilrl))))
240 (defun find-ucon-all (&key (srl *current-srl*))
241 "Return list of all ucon's"
242 (with-sql-connection (db)
246 (destructuring-bind (cui pfstr cuilrl) tuple
247 (make-instance 'ucon :cui (ensure-integer cui)
249 :lrl (ensure-integer cuilrl))))
250 (query-string mrconso (cui kpfstr kcuilrl) srl nil nil
251 :order (cui asc) :distinct t)
254 (defun find-ucon-all2 (&key (srl *current-srl*))
255 "Return list of all ucon's"
256 (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
258 (make-instance 'ucon :cui (ensure-integer cui)
260 :lrl (ensure-integer kcuilrl))))
262 (defun find-cui-ucon-all (&key (srl *current-srl*))
263 "Return list of CUIs for all ucons"
264 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
268 (defun map-ucon-all (fn &key (srl *current-srl*))
269 "Map a function over all ucon's"
270 (with-sql-connection (db)
274 (destructuring-bind (cui pfstr cuilrl) tuple
275 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
277 :lrl (ensure-integer cuilrl)))))
278 (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
283 (defun find-udef-cui (cui &key (srl *current-srl*))
284 "Return a list of udefs for cui"
285 (ensure-cui-integer cui)
286 (collect-umlisp-query (mrdef (sab def) srl cui cui :lrl "KSRL")
287 (make-instance 'udef :sab sab :def def)))
289 (defun find-usty-cui (cui &key (srl *current-srl*))
290 "Return a list of usty for cui"
291 (ensure-cui-integer cui)
292 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
293 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
295 (defun find-usty-word (word &key (srl *current-srl*))
296 "Return a list of usty that match word"
297 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
299 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
301 (defun find-urel-cui (cui &key (srl *current-srl*))
302 "Return a list of urel for cui"
303 (ensure-cui-integer cui)
304 (collect-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1
306 (make-instance 'urel :cui1 cui :rel rel
307 :cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl
308 :mg mg :pfstr2 kpfstr2)))
310 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
311 "Return a list of urel for cui"
312 (ensure-cui-integer cui)
313 (collect-umlisp-query (mrrel (cui2) srl cui1
317 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
318 "Return a list of urel for cui2"
319 (ensure-cui-integer cui2)
320 (collect-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2
322 (make-instance 'urel :cui2 cui2 :rel rel
323 :cui1 (ensure-integer cui1) :rela rela :sab sab :sl sl
324 :mg mg :pfstr2 kpfstr2)))
326 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
327 (ensure-cui-integer cui2)
328 (loop for cui in (remove-duplicates
329 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
330 collect (find-ucon-cui cui :srl srl)))
332 (defun find-ucoc-cui (cui &key (srl *current-srl*))
333 "Return a list of ucoc for cui"
334 (ensure-cui-integer cui)
335 (collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1
336 cui :lrl klrl :order (cof asc))
337 (setq cui2 (ensure-integer cui2))
338 (when (eql 0 cui2) (setq cui2 nil))
339 (make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2)
340 :soc soc :cot cot :cof (ensure-integer cof) :coa coa
343 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
344 "Return a list of ucoc for cui2"
345 (ensure-cui-integer cui2)
346 (collect-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2
347 cui2 :lrl klrl :order (cof asc))
348 (when (zerop cui2) (setq cui2 nil))
349 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
350 :soc soc :cot cot :cof (ensure-integer cof) :coa coa
353 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
354 "List of ucon with co-occurance cui2"
355 (ensure-cui-integer cui2)
357 #'(lambda (cui) (find-ucon-cui cui :srl srl))
358 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
360 (defun find-ulo-cui (cui &key (srl *current-srl*))
361 "Return a list of ulo for cui"
362 (ensure-cui-integer cui)
363 (collect-umlisp-query (mrlo (isn fr un sui sna soui) srl cui cui
365 (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un
366 :sui (ensure-integer sui) :sna sna :soui soui)))
369 (defun find-uterm-cui (cui &key (srl *current-srl*))
370 "Return a list of uterm for cui"
371 (ensure-cui-integer cui)
372 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
373 :lrl kluilrl :distinct t)
374 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
375 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
377 (defun find-uterm-lui (lui &key (srl *current-srl*))
378 "Return a list of uterm for lui"
379 (ensure-lui-integer lui)
380 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
381 :lrl kluilrl :distinct t)
382 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
383 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
385 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
386 "Return single uterm for cui/lui"
387 (ensure-cui-integer cui)
388 (ensure-lui-integer lui)
389 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
390 (make-cuilui cui lui)
391 :lrl kluilrl :single t)
392 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
393 :lrl (ensure-integer kluilrl))))
395 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
396 "Return a list of ustr for cui/lui"
397 (ensure-cui-integer cui)
398 (ensure-lui-integer lui)
399 (collect-umlisp-query (mrconso (sui stt str ksuilrl) srl kcuilui
400 (make-cuilui cui lui) :lrl ksuilrl)
401 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
402 :cuisui (make-cuisui cui sui) :stt stt :str str
403 :lrl (ensure-integer ksuilrl))))
405 (defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
406 "Return the single ustr for cuisui"
407 (ensure-cui-integer cui)
408 (ensure-sui-integer sui)
409 (collect-umlisp-query (mrconso (lui stt str ksuilrl) srl kcuisui
410 (make-cuisui cui sui) :lrl lsuilrl :single t)
411 (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
412 :lui (ensure-integer lui) :stt stt :str str
413 :lrl (ensure-integer ksuilrl))))
415 (defun find-ustr-sui (sui &key (srl *current-srl*))
416 "Return the list of ustr for sui"
417 (ensure-sui-integer sui)
418 (collect-umlisp-query (mrconso (cui lui stt str ksuilrl) srl sui sui
420 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
421 :cuisui (make-cuisui (ensure-integer cui) sui)
422 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
424 (defun find-ustr-sab (sab &key (srl *current-srl*))
425 "Return the list of ustr for sab"
426 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
427 (let ((cuisui (ensure-integer kcuisui)))
428 (apply #'find-ustr-cuisui
430 (multiple-value-list (decompose-cuisui cuisui))
433 (defun find-ustr-all (&key (srl *current-srl*))
434 "Return list of all ustr's"
435 (with-sql-connection (db)
439 (destructuring-bind (cui lui sui stt ksuilrl pfstr) tuple
440 (make-instance 'ustr :cui (ensure-integer cui)
441 :lui (ensure-integer lui) :sui (ensure-integer sui)
443 :cuisui (make-cuisui (ensure-integer cui)
444 (ensure-integer sui))
445 :lrl (ensure-integer ksuilrl))))
446 (query-string mrconso (cui lui sui stt ksuilrl kpfstr) srl nil nil :lrl ksuilrl
451 (defun find-string-sui (sui &key (srl *current-srl*))
452 "Return the string associated with sui"
453 (ensure-sui-integer sui)
454 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
457 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
458 (ensure-sui-integer sui)
459 (ensure-cui-integer cui)
460 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui
461 (make-cuisui cui sui) :lrl srl)
462 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
463 :cui cui :sui sui :saui saui :sdui sdui :scui scui)))
465 (defun find-uso-aui (aui &key (srl *current-srl*))
466 (ensure-sui-integer aui)
467 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui) srl aui
468 aui :lrl srl :single t)
469 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
470 :sui sui :saui saui :sdui sdui :scui scui)))
472 (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
473 (ensure-cui-integer cui)
474 (ensure-sui-integer sui)
475 (collect-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc)
476 srl kcuisui (make-cuisui cui sui) :lrl ksrl)
477 (make-instance 'ucxt :sab sab :code code
478 :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd
479 :rela rela :xc xc :rnk (ensure-integer rnk)
480 :cui2 (ensure-integer cui2))))
482 (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
483 (ensure-cui-integer cui)
484 (ensure-lui-integer lui)
485 (ensure-sui-integer sui)
486 (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
488 (sui (string-append ls "KCUISUI='"
489 (integer-string (make-cuisui cui sui) 14)
491 (lui (string-append ls "KCUILUI='"
492 (integer-string (make-cuilui cui lui) 14)
494 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
495 "' and lui='0' and sui='0'")))
497 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
498 (loop for tuple in (mutex-sql-query ls) collect
499 (destructuring-bind (code atn sab atv) tuple
500 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
502 (defun find-usty-tui (tui)
504 (ensure-tui-integer tui)
505 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
506 (make-instance 'usty :tui tui :sty sty)))
508 (defun find-usty-sty (sty)
509 "Find usty for a sty"
510 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
511 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
513 (defun find-usty-all ()
514 "Return list of usty's for all semantic types"
515 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
516 (find-usty-tui tui)))
518 (defun find-usab-all ()
519 "Find usab for a key"
520 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
521 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
522 cenc curver sabin) nil nil nil)
523 (make-instance 'usab :vcui (ensure-integer vcui)
524 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
525 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
526 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
527 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
528 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
529 :curver curver :sabin sabin)))
531 (defun find-usab-by-key (key-name key)
532 "Find usab for a key"
533 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
534 vend imeta rmeta slc scc srl tfr cfr cxty
535 ttyl atnl lat cenc curver sabin)
536 nil key-name key :single t)
537 (make-instance 'usab :vcui (ensure-integer vcui)
538 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
539 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
540 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
541 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
542 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
543 :curver curver :sabin sabin)))
545 (defun find-usab-rsab (rsab)
547 (find-usab-by-key 'rsab rsab))
549 (defun find-usab-vsab (vsab)
551 (find-usab-by-key 'vsab vsab))
553 (defun find-cui-max ()
554 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
556 ;;;; Cross table find functions
558 (defun find-ucon-tui (tui &key (srl *current-srl*))
559 "Find list of ucon for tui"
560 (ensure-tui-integer tui)
561 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
562 (find-ucon-cui (ensure-integer cui) :srl srl)))
564 (defun find-ucon-word (word &key (srl *current-srl*) (like nil))
565 "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
566 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
567 :lrl 'klrl :order '(cui asc))
568 (find-ucon-cui cui :srl srl)))
570 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
571 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
572 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
573 :lrl 'klrl :order '(cui asc))
574 (find-ucon-cui cui :srl srl)))
576 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
577 "Return list of cui that match word, optionally use SQL's LIKE syntax"
578 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
579 :lrl 'klrl :order '(cui asc))
582 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
583 "Return list of cui that match word, optionally use SQL's LIKE syntax"
584 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
585 :lrl 'klrl :order '(cui asc))
588 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
589 "Return list of cui that match word, optionally use SQL's LIKE syntax"
590 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
591 :lrl 'klrl :order '(cui asc))
594 (defun find-ustr-word (word &key (srl *current-srl*))
595 "Return list of ustrs that match word"
596 (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
597 :order (cui asc sui asc))
598 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
600 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
601 "Return list of ustrs that match word"
602 (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl
603 :order (cui asc sui asc))
604 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
606 (defun find-uterm-word (word &key (srl *current-srl*))
607 "Return list of uterms that match word"
608 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
609 :order (cui asc lui asc))
610 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
612 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
613 "Return list of uterms that match word"
614 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
615 :order (cui asc lui asc))
616 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
618 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
619 "Return list of ucons that match non-english word"
620 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
621 :distinct t :lrl 'klrl :order '(cui asc))
622 (find-ucon-cui cui :srl srl)))
624 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
625 "Return list of ustrs that match non-english word"
626 (collect-umlisp-query (mrxw_noneng (cui sui) srl wd word :lrl klrl
627 :order (cui asc sui asc))
628 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
632 (defun find-usrl-all ()
633 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
634 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
636 ;;; Multiword lookup and score functions
638 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
641 (dolist (word (delimited-string-to-list str #\space))
642 (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl))))
644 (funcall sort-fun str
645 (delete-duplicates uobjs :test #'= :key key))))
646 (if (and (plusp (length sorted))
648 (multiword-match str (pfstr (first sorted))))
652 (defun find-ucon-multiword (str &key (srl *current-srl*)
653 (only-exact-if-match t))
654 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
655 #'cui srl only-exact-if-match))
657 (defun find-uterm-multiword (str &key (srl *current-srl*)
658 (only-exact-if-match t))
659 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
660 #'lui srl only-exact-if-match))
662 (defun find-ustr-multiword (str &key (srl *current-srl*)
663 (only-exact-if-match t))
664 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
665 #'sui srl only-exact-if-match))
667 (defun sort-score-pfstr-str (str uobjs)
668 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
669 (sort-score-umlsclass-str uobjs str #'pfstr))
671 (defun sort-score-ustr-str (str ustrs)
672 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
673 (sort-score-umlsclass-str ustrs str #'str))
675 (defun sort-score-umlsclass-str (objs str lookup-func)
676 "Sort a list of objects based on scoring to a string"
679 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
681 (mapcar #'car (sort scored #'> :key #'cadr))))
684 ;;; LEX SQL functions
686 (defun find-lexterm-eui (eui)
687 (ensure-eui-integer eui)
688 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
689 (make-instance 'lexterm :eui eui :wrd wrd)))
691 (defun find-lexterm-word (wrd)
692 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
693 (make-instance 'lexterm :eui (ensure-integer eui)
694 :wrd (copy-seq wrd))))
696 ;; LEX SQL Read functions
698 (defun find-labr-eui (eui)
699 (ensure-eui-integer eui)
700 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
701 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
702 :eui2 (ensure-integer eui2))))
704 (defun find-labr-bas (bas)
705 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
706 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
707 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
709 (defun find-lagr-eui (eui)
710 (ensure-eui-integer eui)
711 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
712 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
715 (defun find-lcmp-eui (eui)
716 (ensure-eui-integer eui)
717 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
718 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
720 (defun find-lmod-eui (eui)
721 (ensure-eui-integer eui)
722 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
723 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
725 (defun find-lnom-eui (eui)
726 (ensure-eui-integer eui)
727 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
728 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
729 :eui2 (ensure-integer eui2))))
731 (defun find-lprn-eui (eui)
732 (ensure-eui-integer eui)
733 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
734 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
735 :cas cas :pos pos :qnt qnt :fea fea)))
737 (defun find-lprp-eui (eui)
738 (ensure-eui-integer eui)
739 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
740 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
742 (defun find-lspl-eui (eui)
743 (ensure-eui-integer eui)
744 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
745 (make-instance 'lspl :eui eui :spv spv :bas bas)))
747 (defun find-ltrm-eui (eui)
748 (ensure-eui-integer eui)
749 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
750 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
752 (defun find-ltyp-eui (eui)
753 (ensure-eui-integer eui)
754 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
755 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
757 (defun find-lwd-wrd (wrd)
758 (make-instance 'lwd :wrd wrd
759 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
760 (ensure-integer eui))))
762 ;;; Semantic Network SQL access functions
764 (defun find-sdef-ui (ui)
765 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
767 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
768 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
770 (defun find-sstre1-ui (ui)
771 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
772 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
773 :ui3 (ensure-integer ui3))))
775 (defun find-sstre1-ui2 (ui2)
776 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
777 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
778 :ui3 (ensure-integer ui3))))
780 (defun find-sstr-rl (rl)
781 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
782 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
784 (defun find-sstre2-sty (sty)
785 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
786 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
788 (defun find-sstr-styrl (styrl)
789 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
790 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
793 ;;; **************************
795 ;;; **************************
798 (defun make-ustats ()
799 (with-sql-connection (conn)
800 (ignore-errors (sql-execute "drop table USTATS" conn))
801 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
804 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
805 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
806 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
807 (insert-ustats-count conn "String Count" "MRCONSO" "*" "LRL" srl)
808 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "LRL" srl)
809 (insert-ustats-count conn "Context Count" "MRCXT" "*" "KSRL" srl)
810 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
811 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
812 (insert-ustats-count conn "Locator Count" "MRLO" "*" "KLRL" srl)
813 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
814 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
815 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
816 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
817 (insert-ustats-count conn "Source Count" "MRSO" "*" "SRL" srl)
818 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
819 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
820 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl)
821 (insert-ustats-count conn "Bonus Attribute Name Count" "BONUS_ATN" "*" nil srl)
822 (insert-ustats-count conn "Bonus Relationship Count" "BONUS_REL" "*" nil srl)
823 (insert-ustats-count conn "Bonus Source Abbreviation Count" "BONUS_SAB" "*" nil srl)
824 (insert-ustats-count conn "Bonus Term Type Count" "BONUS_TTY" "*" nil srl))
825 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
828 (defun insert-ustats-count (conn name table count-variable srl-control srl)
829 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
831 (defun find-count-table (conn table srl count-variable srl-control)
833 ((stringp srl-control)
835 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
836 count-variable table srl-control srl)
840 (caar (sql-query (format nil "select count(~a) from ~a"
841 count-variable table )
844 (error "Unknown srl-control")
847 (defun insert-ustats (conn name count srl)
848 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
849 name count (if srl srl 3))
852 (defun find-ustats-all (&key (srl *current-srl*))
854 (collect-umlisp-query (ustats (name count srl) nil srl srl
856 (make-instance 'ustats :name name
857 :hits (ensure-integer count)
858 :srl (ensure-integer srl)))
859 (collect-umlisp-query (ustats (name count srl) nil nil nil
861 (make-instance 'ustats :name name
862 :hits (ensure-integer count)
863 :srl (ensure-integer srl)))))
865 (defun find-ustats-srl (srl)
866 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
867 (make-instance 'ustats :name name :hits (ensure-integer count))))
871 (defun find-bsab-sab (sab)
872 (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t)
873 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
875 (defun find-bsab-all ()
876 (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc))
877 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
879 (defun find-btty-tty (tty)
880 (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t)
881 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
883 (defun find-btty-all ()
884 (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc))
885 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
887 (defun find-brel-rel (rel)
888 (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel)
889 (make-instance 'brel :sab sab :sl sl :rel rel :rela rela
890 :hits (ensure-integer count))))