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) 2000-2006 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 limit
31 (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
32 (if distinct "DISTINCT " "") fields table))
33 (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}"
36 (%%lrl (format nil " AND ~:@(~A~)<=" lrl))
37 (%%where (when where-name
38 (format nil " where ~:@(~A~)~A" where-name
39 (if like " like " ""))))
40 (%filter (gensym "FILTER-"))
41 (%single (gensym "SINGLE-"))
42 (%limit (gensym "LIMIT-")))
43 `(let ((,%limit ,limit)
49 ,@(when %%where (list %%where))
51 `((typecase ,where-value
54 (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
56 (concatenate 'string "='" (write-to-string ,where-value) "'"))
60 (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
61 (if ,%filter (concatenate 'string
62 ,(if %%where " AND " " WHERE ")
64 (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
65 ,@(when %%order (list %%order))
67 ((and ,%single ,%limit)
68 (error "Can't set single and limit"))
72 (format nil " LIMIT ~D" ,%limit))
76 (defun query-string-eval (table fields &optional srl where-name where-value
77 &key (lrl "KCUILRL") single distinct order like limit filter)
78 (when single (setq limit 1))
81 (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
82 (if distinct "distinct " "") fields table)
83 (if where-name (format nil " where ~:@(~A~)" where-name) "")
90 (if like " like '%~A%""='~A'")))
93 (if filter (concatenate 'string " AND " filter) nil)
94 (if srl (format nil " and ~:@(~A~)<=~D" lrl srl) "")
95 (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) "")
96 (if limit (format nil " limit ~D" limit) "")))
99 (defmacro umlisp-query (table fields srl where-name where-value
100 &key (lrl "KCUILRL") single distinct order like
101 limit filter (query-cmd 'mutex-sql-query))
102 "Query the UMLisp database. Return a list of umlisp objects whose name
103 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
105 (query-string ,table ,fields ,srl ,where-name ,where-value
106 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
107 :filter ,filter :limit ,limit)))
109 (defmacro umlisp-query-eval (table fields srl where-name where-value
110 &key (lrl "KCUILRL") single distinct order like
112 "Query the UMLisp database. Return a list of umlisp objects whose name
113 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
115 (query-string-eval ,table ,fields ,srl ,where-name ,where-value
116 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
117 :filter ,filter :limit ,limit)))
119 ;; only WHERE-VALUE and SRL are evaluated
120 (defmacro collect-umlisp-query ((table fields srl where-name where-value
121 &key (lrl "KCUILRL") distinct single
122 order like (query-cmd 'mutex-sql-query)
125 (let ((value (gensym))
128 (if (and limit (> limit 1))
129 (error "Can't set limit along with single.")
130 `(let* ((,value ,where-value)
131 (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
132 :lrl ,lrl :single ,single
133 :distinct ,distinct :order ,order
134 :like ,like :filter ,filter
135 :query-cmd ,query-cmd))))
136 ,@(unless where-name `((declare (ignore ,value))))
138 (destructuring-bind ,fields tuple
140 `(let ((,value ,where-value))
141 ,@(unless where-name `((declare (ignore ,value))))
143 (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
144 :lrl ,lrl :single ,single :distinct ,distinct
145 :order ,order :filter ,filter :like ,like
147 (push (destructuring-bind ,fields tuple ,@body) ,r))
151 (umlisp-query ,table ,fields ,srl ,where-name ,value
152 :lrl ,lrl :single ,single :distinct ,distinct
153 :order ,order :like ,like :filter ,filter :limit ,limit)
154 collect (destructuring-bind ,fields tuple ,@body))))))
156 (defmacro collect-umlisp-query-eval ((table fields srl where-name where-value
157 &key (lrl "KCUILRL") distinct single
158 order like filter limit)
160 (let ((value (gensym))
162 (eval-fields (cadr fields)))
164 `(let* ((,value ,where-value)
165 (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
166 :lrl ,lrl :single ,single
167 :distinct ,distinct :order ,order
168 :like ,like :filter ,filter
171 (destructuring-bind ,eval-fields tuple
173 `(let ((,value ,where-value)
175 (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
176 :lrl ,lrl :single ,single :distinct ,distinct
177 :order ,order :like ,like
178 :filter ,filter :limit ,limit))
179 (push (destructuring-bind ,eval-fields tuple ,@body) ,r))
183 (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
184 :lrl ,lrl :single ,single :distinct ,distinct
185 :order ,order :like ,like :filter ,filter
187 collect (destructuring-bind ,eval-fields tuple ,@body))))))
190 ;;; Read from SQL database
192 (defmacro ensure-cui-integer (cui)
194 (setq ,cui (parse-cui ,cui))
197 (defmacro ensure-lui-integer (lui)
199 (setq ,lui (parse-lui ,lui))
202 (defmacro ensure-sui-integer (sui)
204 (setq ,sui (parse-sui ,sui))
207 (defmacro ensure-aui-integer (aui)
209 (setq ,aui (parse-aui ,aui))
212 (defmacro ensure-rui-integer (rui)
214 (setq ,rui (parse-rui ,rui))
217 (defmacro ensure-tui-integer (tui)
219 (setq ,tui (parse-tui ,tui))
222 (defmacro ensure-eui-integer (eui)
224 (setq ,eui (parse-eui ,eui))
227 (defun find-ucon-cui (cui &key (srl *current-srl*))
228 "Find ucon for a cui"
229 (ensure-cui-integer cui)
230 (unless cui (return-from find-ucon-cui nil))
232 (let ((tuple (car (mutex-sql-query
234 "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A"
235 cui (if srl (format nil " AND SRL<=~D" srl) ""))))))
237 (setq tuple (car (mutex-sql-query
239 "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D"
240 cui (if srl (format nil " AND SRL<=~D" srl) nil))))))
242 (return-from find-ucon-cui nil))
243 (make-instance 'ucon :cui cui :pfstr (second tuple)
244 :lrl (ensure-integer (first tuple)))))
246 (defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*))
247 "Find ucon for a cui"
248 (ensure-cui-integer cui)
249 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
250 (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
253 (defun find-pfstr-cui (cui &key (srl *current-srl*))
254 "Find preferred string for a cui"
255 (ensure-cui-integer cui)
257 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
258 :filter " KPFENG=1" :single t)
260 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
264 (defun find-ucon-lui (lui &key (srl *current-srl*))
265 "Find list of ucon for lui"
266 (ensure-lui-integer lui)
267 (unless lui (return-from find-ucon-lui nil))
269 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
270 :filter " KPFENG=1" :single t)
271 (make-instance 'ucon :cui (ensure-integer cui)
272 :pfstr str :lrl (ensure-integer kcuilrl)))
273 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
275 (make-instance 'ucon :cui (ensure-integer cui)
276 :pfstr str :lrl (ensure-integer kcuilrl)))))
278 (defun find-ucon-sui (sui &key (srl *current-srl*))
279 "Find list of ucon for sui"
280 (ensure-sui-integer sui)
281 (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t)
282 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
283 :lrl (ensure-integer kcuilrl))))
285 (defun find-ucon-aui (aui &key (srl *current-srl*))
286 "Find list of ucon for aui"
287 (ensure-aui-integer aui)
288 (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
289 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
290 :lrl (ensure-integer kcuilrl))))
292 (defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
293 "Find ucon for cui/sui"
294 (ensure-cui-integer cui)
295 (ensure-sui-integer sui)
297 (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui
298 (make-cuisui cui sui))
299 (make-instance 'ucon :cui cui
300 :pfstr (find-pfstr-cui cui)
301 :lrl (ensure-integer kcuilrl)))))
303 (defun find-ucon-str (str &key (srl *current-srl*))
304 "Find ucon that are exact match for str"
305 (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t)
306 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
307 :lrl (ensure-integer kcuilrl))))
309 (defun find-ucon-all (&key (srl *current-srl*))
310 "Return list of all ucon's"
311 (with-sql-connection (db)
315 (destructuring-bind (cui cuilrl) tuple
316 (make-instance 'ucon :cui (ensure-integer cui)
317 :pfstr (find-pfstr-cui cui)
318 :lrl (ensure-integer cuilrl))))
319 (query-string mrconso (cui kcuilrl) srl nil nil
320 :order (cui asc) :distinct t)
323 (defun find-ucon-all2 (&key (srl *current-srl*))
324 "Return list of all ucon's"
325 (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
327 (make-instance 'ucon :cui (ensure-integer cui)
328 :pfstr (find-pfstr-cui cui)
329 :lrl (ensure-integer kcuilrl))))
331 (defun find-cui-ucon-all (&key (srl *current-srl*))
332 "Return list of CUIs for all ucons"
333 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
337 (defun map-ucon-all (fn &key (srl *current-srl*))
338 "Map a function over all ucon's"
339 (with-sql-connection (db)
343 (destructuring-bind (cui cuilrl) tuple
344 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
345 :pfstr (find-pfstr-cui cui)
346 :lrl (ensure-integer cuilrl)))))
347 (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
352 (defun find-udef-cui (cui &key (srl *current-srl*))
353 "Return a list of udefs for cui"
354 (ensure-cui-integer cui)
355 (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
356 (make-instance 'udef :sab sab :def def :suppress suppress)))
358 (defun find-udoc-key (key)
359 "Return list of abbreviation documentation for a key"
360 (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
361 (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
363 (defun find-udoc-value (value)
364 "Return abbreviation documentation"
365 (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
366 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
368 (defun find-udoc-key-value (dockey value)
369 (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value))
370 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
372 (defun find-udoc-all ()
373 "Return all abbreviation documentation"
374 (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
375 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
377 (defun find-usty-cui (cui &key (srl *current-srl*))
378 "Return a list of usty for cui"
379 (ensure-cui-integer cui)
380 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
381 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
383 (defun find-usty-word (word &key (srl *current-srl*))
384 "Return a list of usty that match word"
385 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
387 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
389 (defun find-urel-cui (cui &key (srl *current-srl*))
390 "Return a list of urel for cui"
391 (ensure-cui-integer cui)
392 (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
393 srl cui1 cui :lrl "KSRL")
394 (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
395 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
396 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
397 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
399 (defun find-urel-rui (rui &key (srl *current-srl*))
400 "Return the urel for a rui"
401 (ensure-rui-integer rui)
402 (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
403 srl rui rui :lrl "KSRL" :single t)
404 (make-instance 'urel :cui1 cui1 :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
405 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
406 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
407 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
409 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
410 "Return a list of urel for cui"
411 (ensure-cui-integer cui)
412 (collect-umlisp-query (mrrel (cui2) srl cui1
416 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
417 "Return a list of urel for cui2"
418 (ensure-cui-integer cui2)
419 (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
420 srl cui2 cui2 :lrl "KSRL")
421 (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
422 :stype2 stype2 :rui (ensure-integer rui) :srui srui
423 :stype1 stype1 :cui1 (ensure-integer cui1)
424 :aui1 (ensure-integer aui1)
425 :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
426 :pfstr2 (find-pfstr-cui cui2))))
428 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
429 (ensure-cui-integer cui2)
430 (loop for cui in (remove-duplicates
431 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
432 collect (find-ucon-cui cui :srl srl)))
434 (defun find-ucoc-cui (cui &key (srl *current-srl*))
435 "Return a list of ucoc for cui"
436 (ensure-cui-integer cui)
437 (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
438 cui :lrl klrl :order (cof asc))
439 (setq cui2 (ensure-integer cui2))
440 (when (eql 0 cui2) (setq cui2 nil))
441 (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1)
442 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2)
443 :cot cot :cof (ensure-integer cof) :coa coa :sab sab
444 :pfstr2 (find-pfstr-cui cui2))))
446 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
447 "Return a list of ucoc for cui2"
448 (ensure-cui-integer cui2)
449 (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
450 cui2 :lrl klrl :order (cof asc))
451 (when (zerop cui2) (setq cui2 nil))
452 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
453 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2)
454 :sab sab :cot cot :cof (ensure-integer cof) :coa coa
455 :pfstr2 (find-pfstr-cui cui2))))
457 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
458 "List of ucon with co-occurance cui2"
459 (ensure-cui-integer cui2)
461 #'(lambda (cui) (find-ucon-cui cui :srl srl))
462 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
465 (defun find-uterm-cui (cui &key (srl *current-srl*))
466 "Return a list of uterm for cui"
467 (ensure-cui-integer cui)
468 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
469 :lrl kluilrl :distinct t)
470 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
471 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
473 (defun find-uterm-lui (lui &key (srl *current-srl*))
474 "Return a list of uterm for lui"
475 (ensure-lui-integer lui)
476 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
477 :lrl kluilrl :distinct t)
478 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
479 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
481 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
482 "Return single uterm for cui/lui"
483 (ensure-cui-integer cui)
484 (ensure-lui-integer lui)
485 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
486 (make-cuilui cui lui)
487 :lrl kluilrl :single t)
488 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
489 :lrl (ensure-integer kluilrl))))
491 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
492 "Return a list of ustr for cui/lui"
493 (ensure-cui-integer cui)
494 (ensure-lui-integer lui)
495 (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
496 (make-cuilui cui lui) :lrl ksuilrl)
497 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
498 :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
499 :lrl (ensure-integer ksuilrl))))
501 (defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
502 "Return the single ustr for cuisui"
503 (ensure-cui-integer cui)
504 (ensure-sui-integer sui)
505 (collect-umlisp-query (mrconso (lui stt str suppress ksuilrl) srl kcuisui
506 (make-cuisui cui sui) :lrl lsuilrl :single t)
507 (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
508 :lui (ensure-integer lui) :stt stt :str str :suppress suppress
509 :lrl (ensure-integer ksuilrl))))
511 (defun find-ustr-sui (sui &key (srl *current-srl*))
512 "Return the list of ustr for sui"
513 (ensure-sui-integer sui)
514 (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
516 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
517 :cuisui (make-cuisui (ensure-integer cui) sui)
519 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
521 (defun find-ustr-sab (sab &key (srl *current-srl*))
522 "Return the list of ustr for sab"
523 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
524 (let ((cuisui (ensure-integer kcuisui)))
525 (apply #'find-ustr-cuisui
527 (multiple-value-list (decompose-cuisui cuisui))
530 (defun find-ustr-all (&key (srl *current-srl*))
531 "Return list of all ustr's"
532 (with-sql-connection (db)
536 (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple
537 (make-instance 'ustr :cui (ensure-integer cui)
538 :lui (ensure-integer lui) :sui (ensure-integer sui)
539 :stt stt :str (find-pfstr-cui cui)
540 :cuisui (make-cuisui (ensure-integer cui)
541 (ensure-integer sui))
543 :lrl (ensure-integer ksuilrl))))
544 (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
549 (defun find-string-sui (sui &key (srl *current-srl*))
550 "Return the string associated with sui"
551 (ensure-sui-integer sui)
552 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
555 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
556 (ensure-sui-integer sui)
557 (ensure-cui-integer cui)
558 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str)
559 srl kcuisui (make-cuisui cui sui) :lrl srl)
560 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
561 :cui cui :sui sui :saui saui :sdui sdui :scui scui
564 (defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
565 (ensure-cui-integer cui)
566 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui)
567 srl cui cui :lrl srl :limit limit
568 :filter (when english-only "LAT='ENG'"))
569 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
570 :cui cui :sui sui :saui saui :sdui sdui :scui scui
573 (defun find-uso-aui (aui &key (srl *current-srl*))
574 (ensure-sui-integer aui)
575 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat str) srl aui
576 aui :lrl srl :single t)
577 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
578 :sui sui :saui saui :sdui sdui :scui scui
581 (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
582 (ensure-cui-integer cui)
583 (ensure-sui-integer sui)
584 (collect-umlisp-query (mrcxt (sab rank code cxn cxl cxs cui2 hcd rela xc)
585 srl kcuisui (make-cuisui cui sui) :lrl ksrl)
586 (make-instance 'ucxt :sab sab :code code
588 :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd
590 :cui2 (ensure-integer cui2))))
592 (defun find-uhier-cui (cui &key (srl *current-srl*))
593 (ensure-cui-integer cui)
594 (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
595 srl cui cui :lrl ksrl)
596 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
597 :cxn (ensure-integer cxn)
598 :paui (ensure-integer paui)
599 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
601 (defun find-uhier-all (&key (srl *current-srl*))
602 (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
603 srl nil nil :lrl ksrl)
604 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
605 :cxn (ensure-integer cxn)
606 :paui (ensure-integer paui)
607 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
609 (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
610 (ensure-cui-integer cui)
611 (ensure-lui-integer lui)
612 (ensure-sui-integer sui)
613 (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
615 (sui (string-append ls "KCUISUI='"
616 (integer-string (make-cuisui cui sui) 14)
618 (lui (string-append ls "KCUILUI='"
619 (integer-string (make-cuilui cui lui) 14)
621 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
622 "' and lui='0' and sui='0'")))
624 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
625 (loop for tuple in (mutex-sql-query ls) collect
626 (destructuring-bind (code atn sab atv) tuple
627 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
629 (defun find-usty-tui (tui)
631 (ensure-tui-integer tui)
632 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
633 (make-instance 'usty :tui tui :sty sty)))
635 (defun find-usty-sty (sty)
636 "Find usty for a sty"
637 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
638 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
640 (defun find-usty-all ()
641 "Return list of usty's for all semantic types"
642 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
643 (find-usty-tui tui)))
645 (defun find-usab-all ()
646 "Return all usab objects"
647 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
648 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
649 cenc curver sabin ssn scit) nil nil nil)
650 (make-instance 'usab :vcui (ensure-integer vcui)
651 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
652 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
653 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
654 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
655 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
656 :curver curver :sabin sabin :ssn ssn :scit scit)))
658 (defun find-usab-by-key (key-name key)
659 "Find usab for a key"
660 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
661 vend imeta rmeta slc scc srl tfr cfr cxty
662 ttyl atnl lat cenc curver sabin
664 nil key-name key :single t)
665 (make-instance 'usab :vcui (ensure-integer vcui)
666 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
667 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
668 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
669 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
670 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
671 :curver curver :sabin sabin
672 :ssn ssn :scit scit)))
674 (defun find-usab-rsab (rsab)
676 (find-usab-by-key 'rsab rsab))
678 (defun find-usab-vsab (vsab)
680 (find-usab-by-key 'vsab vsab))
682 (defun find-cui-max ()
683 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
685 (defun find-umap-cui (cui)
686 (ensure-cui-integer cui)
687 (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr
688 fromtype fromrule fromres rel rela toid tosid
689 toexpr totype torule tores maprule maptype
692 (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid
693 :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid
694 :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres
695 :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype
696 :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn
697 :mapatv mapatv :cvf cvf)))
699 ;;;; Cross table find functions
701 (defun find-ucon-tui (tui &key (srl *current-srl*))
702 "Find list of ucon for tui"
703 (ensure-tui-integer tui)
704 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
705 (find-ucon-cui (ensure-integer cui) :srl srl)))
707 (defun find-ucon-word (word &key (srl *current-srl*) (like nil))
708 "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
709 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
710 :lrl 'klrl :order '(cui asc))
711 (find-ucon-cui cui :srl srl)))
713 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
714 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
715 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
716 :lrl 'klrl :order '(cui asc))
717 (find-ucon-cui cui :srl srl)))
719 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
720 "Return list of cui that match word, optionally use SQL's LIKE syntax"
721 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
722 :lrl 'klrl :order '(cui asc))
725 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
726 "Return list of cui that match word, optionally use SQL's LIKE syntax"
727 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
728 :lrl 'klrl :order '(cui asc))
731 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
732 "Return list of cui that match word, optionally use SQL's LIKE syntax"
733 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
734 :lrl 'klrl :order '(cui asc))
737 (defun find-ustr-word (word &key (srl *current-srl*))
738 "Return list of ustrs that match word"
739 (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
740 :order (cui asc sui asc))
741 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
743 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
744 "Return list of ustrs that match word"
745 (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl
746 :order (cui asc sui asc))
747 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
749 (defun find-uterm-word (word &key (srl *current-srl*))
750 "Return list of uterms that match word"
751 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
752 :order (cui asc lui asc))
753 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
755 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
756 "Return list of uterms that match word"
757 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
758 :order (cui asc lui asc))
759 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
761 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
762 "Return list of ucons that match non-english word"
763 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
764 :distinct t :lrl 'klrl :order '(cui asc))
765 (find-ucon-cui cui :srl srl)))
767 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
768 "Return list of ustrs that match non-english word"
769 (collect-umlisp-query (mrxw_noneng (cui sui) srl wd word :lrl klrl
770 :order (cui asc sui asc))
771 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
775 (defun find-usrl-all ()
776 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
777 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
779 ;;; Multiword lookup and score functions
781 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
782 only-exact-if-match limit)
784 (dolist (word (delimited-string-to-list str #\space))
785 (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl))))
787 (funcall sort-fun str
788 (delete-duplicates uobjs :test #'= :key key))))
789 (let ((len (length sorted)))
792 (return-from find-uobj-multiword nil))
793 ((and only-exact-if-match (multiword-match str (pfstr (first sorted))))
796 (if (and (plusp limit) (> len limit))
797 (subseq sorted 0 limit)
802 (defun find-ucon-multiword (str &key (srl *current-srl*)
803 (only-exact-if-match t)
805 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
806 #'cui srl only-exact-if-match limit))
808 (defun find-uterm-multiword (str &key (srl *current-srl*)
809 (only-exact-if-match t)
811 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
812 #'lui srl only-exact-if-match limit))
814 (defun find-ustr-multiword (str &key (srl *current-srl*)
815 (only-exact-if-match t)
817 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
818 #'sui srl only-exact-if-match limit))
820 (defun sort-score-pfstr-str (str uobjs)
821 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
822 (sort-score-umlsclass-str uobjs str #'pfstr))
824 (defun sort-score-ustr-str (str ustrs)
825 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
826 (sort-score-umlsclass-str ustrs str #'str))
828 (defun sort-score-umlsclass-str (objs str lookup-func)
829 "Sort a list of objects based on scoring to a string"
832 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
834 (mapcar #'car (sort scored #'> :key #'cadr))))
837 ;;; LEX SQL functions
839 (defun find-lexterm-eui (eui)
840 (ensure-eui-integer eui)
841 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
842 (make-instance 'lexterm :eui eui :wrd wrd)))
844 (defun find-lexterm-word (wrd)
845 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
846 (make-instance 'lexterm :eui (ensure-integer eui)
847 :wrd (copy-seq wrd))))
849 ;; LEX SQL Read functions
851 (defun find-labr-eui (eui)
852 (ensure-eui-integer eui)
853 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
854 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
855 :eui2 (ensure-integer eui2))))
857 (defun find-labr-bas (bas)
858 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
859 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
860 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
862 (defun find-lagr-eui (eui)
863 (ensure-eui-integer eui)
864 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
865 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
868 (defun find-lcmp-eui (eui)
869 (ensure-eui-integer eui)
870 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
871 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
873 (defun find-lmod-eui (eui)
874 (ensure-eui-integer eui)
875 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
876 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
878 (defun find-lnom-eui (eui)
879 (ensure-eui-integer eui)
880 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
881 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
882 :eui2 (ensure-integer eui2))))
884 (defun find-lprn-eui (eui)
885 (ensure-eui-integer eui)
886 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
887 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
888 :cas cas :pos pos :qnt qnt :fea fea)))
890 (defun find-lprp-eui (eui)
891 (ensure-eui-integer eui)
892 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
893 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
895 (defun find-lspl-eui (eui)
896 (ensure-eui-integer eui)
897 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
898 (make-instance 'lspl :eui eui :spv spv :bas bas)))
900 (defun find-ltrm-eui (eui)
901 (ensure-eui-integer eui)
902 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
903 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
905 (defun find-ltyp-eui (eui)
906 (ensure-eui-integer eui)
907 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
908 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
910 (defun find-lwd-wrd (wrd)
911 (make-instance 'lwd :wrd wrd
912 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
913 (ensure-integer eui))))
915 ;;; Semantic Network SQL access functions
917 (defun find-sdef-ui (ui)
918 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
920 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
921 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
923 (defun find-sstre1-ui (ui)
924 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
925 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
926 :ui3 (ensure-integer ui3))))
928 (defun find-sstre1-ui2 (ui2)
929 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
930 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
931 :ui3 (ensure-integer ui3))))
933 (defun find-sstr-rl (rl)
934 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
935 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
937 (defun find-sstre2-sty (sty)
938 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
939 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
941 (defun find-sstr-styrl (styrl)
942 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
943 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
946 ;;; **************************
948 ;;; **************************
951 (defun make-ustats ()
952 (with-sql-connection (conn)
953 (ignore-errors (sql-execute "drop table USTATS" conn))
954 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
957 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
958 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
959 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
960 (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
961 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
962 (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
963 (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
964 (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
965 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
966 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
967 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
968 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
969 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
970 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
971 (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
972 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
973 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
974 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
975 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
978 (defun insert-ustats-count (conn name table count-variable srl-control srl)
979 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
981 (defun find-count-table (conn table srl count-variable srl-control)
983 ((stringp srl-control)
985 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
986 count-variable table srl-control srl)
990 (caar (sql-query (format nil "select count(~a) from ~a"
991 count-variable table )
994 (error "Unknown srl-control")
997 (defun insert-ustats (conn name count srl)
998 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
999 name count (if srl srl 3))
1002 (defun find-ustats-all (&key (srl *current-srl*))
1004 (collect-umlisp-query (ustats (name count srl) nil srl srl
1006 (make-instance 'ustats :name name
1007 :hits (ensure-integer count)
1008 :srl (ensure-integer srl)))
1009 (collect-umlisp-query (ustats (name count srl) nil nil nil
1011 (make-instance 'ustats :name name
1012 :hits (ensure-integer count)
1013 :srl (ensure-integer srl)))))
1015 (defun find-ustats-srl (srl)
1016 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
1017 (make-instance 'ustats :name name :hits (ensure-integer count))))
1021 (defun find-bsab-sab (sab)
1022 (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t)
1023 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
1025 (defun find-bsab-all ()
1026 (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc))
1027 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
1029 (defun find-btty-tty (tty)
1030 (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t)
1031 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
1033 (defun find-btty-all ()
1034 (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc))
1035 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
1037 (defun find-brel-rel (rel)
1038 (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel)
1039 (make-instance 'brel :sab sab :sl sl :rel rel :rela rela
1040 :hits (ensure-integer count))))