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 " LINK '%~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 make-ucon-cui (cui)
228 (ensure-cui-integer cui)
230 (make-instance 'ucon :cui cui)))
232 (defun find-ucon-cui (cui &key (srl *current-srl*) without-pfstr)
233 "Find ucon for a cui"
234 (ensure-cui-integer cui)
235 (unless cui (return-from find-ucon-cui nil))
238 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
239 (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
242 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t :filter "KPFENG=1")
243 (make-instance 'ucon :cui cui :pfstr str
245 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t)
246 (make-instance 'ucon :cui cui :pfstr str
249 (defun find-pfstr-cui (cui &key (srl *current-srl*))
250 "Find preferred string for a cui"
251 (ensure-cui-integer cui)
253 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
254 :filter " KPFENG=1" :single t)
256 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
260 (defun find-lrl-cui (cui &key (srl *current-srl*))
262 (ensure-cui-integer cui)
263 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :distinct t :single t)
264 (ensure-integer kcuilrl)))
266 (defun find-ucon-lui (lui &key (srl *current-srl*))
267 "Find list of ucon for lui"
268 (ensure-lui-integer lui)
269 (unless lui (return-from find-ucon-lui nil))
271 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
272 :filter " KPFENG=1" :single t)
273 (make-instance 'ucon :cui (ensure-integer cui)
274 :pfstr str :lrl (ensure-integer kcuilrl)))
275 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
277 (make-instance 'ucon :cui (ensure-integer cui)
278 :pfstr str :lrl (ensure-integer kcuilrl)))))
280 (defun find-ucon-sui (sui &key (srl *current-srl*))
281 "Find list of ucon for sui"
282 (ensure-sui-integer sui)
283 (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t)
284 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
285 :lrl (ensure-integer kcuilrl))))
287 (defun find-ucon-aui (aui &key (srl *current-srl*))
288 "Find list of ucon for aui"
289 (ensure-aui-integer aui)
290 (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
291 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
292 :lrl (ensure-integer kcuilrl))))
294 (defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
295 "Find ucon for cui/sui"
296 (ensure-cui-integer cui)
297 (ensure-sui-integer sui)
299 (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui
300 (make-cuisui cui sui))
301 (make-instance 'ucon :cui cui
302 :pfstr (find-pfstr-cui cui)
303 :lrl (ensure-integer kcuilrl)))))
305 (defun find-ucon-str (str &key (srl *current-srl*))
306 "Find ucon that are exact match for str"
307 (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t)
308 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
309 :lrl (ensure-integer kcuilrl))))
311 (defun find-ucon-all (&key (srl *current-srl*))
312 "Return list of all ucon's"
313 (with-sql-connection (db)
317 (destructuring-bind (cui cuilrl) tuple
318 (make-instance 'ucon :cui (ensure-integer cui)
319 :pfstr (find-pfstr-cui cui)
320 :lrl (ensure-integer cuilrl))))
321 (query-string mrconso (cui kcuilrl) srl nil nil
322 :order (cui asc) :distinct t)
325 (defun find-ucon-all2 (&key (srl *current-srl*))
326 "Return list of all ucon's"
327 (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
329 (make-instance 'ucon :cui (ensure-integer cui)
330 :pfstr (find-pfstr-cui cui)
331 :lrl (ensure-integer kcuilrl))))
333 (defun find-cui-ucon-all (&key (srl *current-srl*))
334 "Return list of CUIs for all ucons"
335 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
339 (defun map-ucon-all (fn &key (srl *current-srl*))
340 "Map a function over all ucon's"
341 (with-sql-connection (db)
345 (destructuring-bind (cui cuilrl) tuple
346 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
347 :pfstr (find-pfstr-cui cui)
348 :lrl (ensure-integer cuilrl)))))
349 (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
354 (defun find-udef-cui (cui &key (srl *current-srl*))
355 "Return a list of udefs for cui"
356 (ensure-cui-integer cui)
357 (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
358 (make-instance 'udef :sab sab :def def :suppress suppress)))
360 (defun find-udoc-key (key)
361 "Return list of abbreviation documentation for a key"
362 (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
363 (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
365 (defun find-udoc-value (value)
366 "Return abbreviation documentation"
367 (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
368 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
370 (defun find-udoc-key-value (dockey value)
371 (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value))
372 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
374 (defun find-udoc-all ()
375 "Return all abbreviation documentation"
376 (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
377 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
379 (defun find-usty-cui (cui &key (srl *current-srl*))
380 "Return a list of usty for cui"
381 (ensure-cui-integer cui)
382 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
383 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
385 (defun find-usty-word (word &key (srl *current-srl*))
386 "Return a list of usty that match word"
387 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
389 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
391 (defun find-urel-cui (cui &key (srl *current-srl*) filter without-pfstr2)
392 "Return a list of urel for cui"
393 (ensure-cui-integer cui)
394 (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
395 srl cui1 cui :lrl "KSRL" :filter filter)
397 (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
398 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
399 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
400 :suppress suppress :cvf cvf)))
401 (unless without-pfstr2
402 (setf (slot-value rel 'pfstr2) (find-pfstr-cui cui2)))
405 (defun find-urel-rui (rui &key (srl *current-srl*))
406 "Return the urel for a rui"
407 (ensure-rui-integer rui)
408 (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
409 srl rui rui :lrl "KSRL" :single t)
410 (make-instance 'urel :cui1 cui1 :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
411 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
412 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
413 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
415 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
416 "Return a list of urel for cui"
417 (ensure-cui-integer cui)
418 (collect-umlisp-query (mrrel (cui2) srl cui1
422 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
423 "Return a list of urel for cui2"
424 (ensure-cui-integer cui2)
425 (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
426 srl cui2 cui2 :lrl "KSRL")
427 (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
428 :stype2 stype2 :rui (ensure-integer rui) :srui srui
429 :stype1 stype1 :cui1 (ensure-integer cui1)
430 :aui1 (ensure-integer aui1)
431 :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
432 :pfstr2 (find-pfstr-cui cui2))))
434 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
435 (ensure-cui-integer cui2)
436 (loop for cui in (remove-duplicates
437 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
438 collect (find-ucon-cui cui :srl srl)))
440 (defun find-ucoc-cui (cui &key (srl *current-srl*))
441 "Return a list of ucoc for cui"
442 (ensure-cui-integer cui)
443 (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
444 cui :lrl klrl :order (cof asc))
445 (setq cui2 (ensure-integer cui2))
446 (when (eql 0 cui2) (setq cui2 nil))
447 (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1)
448 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2)
449 :cot cot :cof (ensure-integer cof) :coa coa :sab sab
450 :pfstr2 (find-pfstr-cui cui2))))
452 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
453 "Return a list of ucoc for cui2"
454 (ensure-cui-integer cui2)
455 (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
456 cui2 :lrl klrl :order (cof asc))
457 (when (zerop cui2) (setq cui2 nil))
458 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
459 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2)
460 :sab sab :cot cot :cof (ensure-integer cof) :coa coa
461 :pfstr2 (find-pfstr-cui cui2))))
463 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
464 "List of ucon with co-occurance cui2"
465 (ensure-cui-integer cui2)
467 #'(lambda (cui) (find-ucon-cui cui :srl srl))
468 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
471 (defun find-uterm-cui (cui &key (srl *current-srl*))
472 "Return a list of uterm for cui"
473 (ensure-cui-integer cui)
474 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
475 :lrl kluilrl :distinct t)
476 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
477 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
479 (defun find-uterm-lui (lui &key (srl *current-srl*))
480 "Return a list of uterm for lui"
481 (ensure-lui-integer lui)
482 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
483 :lrl kluilrl :distinct t)
484 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
485 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
487 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
488 "Return single uterm for cui/lui"
489 (ensure-cui-integer cui)
490 (ensure-lui-integer lui)
491 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
492 (make-cuilui cui lui)
493 :lrl kluilrl :single t)
494 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
495 :lrl (ensure-integer kluilrl))))
497 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
498 "Return a list of ustr for cui/lui"
499 (ensure-cui-integer cui)
500 (ensure-lui-integer lui)
501 (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
502 (make-cuilui cui lui) :lrl ksuilrl)
503 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
504 :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
505 :lrl (ensure-integer ksuilrl))))
507 (defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
508 "Return the single ustr for cuisui"
509 (ensure-cui-integer cui)
510 (ensure-sui-integer sui)
511 (collect-umlisp-query (mrconso (lui stt str suppress ksuilrl) srl kcuisui
512 (make-cuisui cui sui) :lrl lsuilrl :single t)
513 (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
514 :lui (ensure-integer lui) :stt stt :str str :suppress suppress
515 :lrl (ensure-integer ksuilrl))))
517 (defun find-ustr-sui (sui &key (srl *current-srl*))
518 "Return the list of ustr for sui"
519 (ensure-sui-integer sui)
520 (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
522 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
523 :cuisui (make-cuisui (ensure-integer cui) sui)
525 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
527 (defun find-ustr-sab (sab &key (srl *current-srl*))
528 "Return the list of ustr for sab"
529 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
530 (let ((cuisui (ensure-integer kcuisui)))
531 (apply #'find-ustr-cuisui
533 (multiple-value-list (decompose-cuisui cuisui))
536 (defun find-ustr-all (&key (srl *current-srl*))
537 "Return list of all ustr's"
538 (with-sql-connection (db)
542 (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple
543 (make-instance 'ustr :cui (ensure-integer cui)
544 :lui (ensure-integer lui) :sui (ensure-integer sui)
545 :stt stt :str (find-pfstr-cui cui)
546 :cuisui (make-cuisui (ensure-integer cui)
547 (ensure-integer sui))
549 :lrl (ensure-integer ksuilrl))))
550 (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
555 (defun find-string-sui (sui &key (srl *current-srl*))
556 "Return the string associated with sui"
557 (ensure-sui-integer sui)
558 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
561 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
562 (ensure-sui-integer sui)
563 (ensure-cui-integer cui)
564 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str)
565 srl kcuisui (make-cuisui cui sui) :lrl srl)
566 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
567 :cui cui :sui sui :saui saui :sdui sdui :scui scui
570 (defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
571 (ensure-cui-integer cui)
572 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui)
573 srl cui cui :lrl srl :limit limit
574 :filter (when english-only "LAT='ENG'"))
575 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
576 :cui cui :sui sui :saui saui :sdui sdui :scui scui
579 (defun find-uso-aui (aui &key (srl *current-srl*))
580 (ensure-sui-integer aui)
581 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat
582 str) srl aui aui :lrl srl :single t)
583 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
584 :sui sui :saui saui :sdui sdui :scui scui :lat lat
587 (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
588 (ensure-cui-integer cui)
589 (ensure-sui-integer sui)
590 (collect-umlisp-query (mrcxt (sab rank code cxn cxl cxs cui2 hcd rela xc)
591 srl kcuisui (make-cuisui cui sui) :lrl ksrl)
592 (make-instance 'ucxt :sab sab :code code
594 :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd
596 :cui2 (ensure-integer cui2))))
598 (defun find-uhier-cui (cui &key (srl *current-srl*))
599 (ensure-cui-integer cui)
600 (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
601 srl cui cui :lrl ksrl)
602 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
603 :cxn (ensure-integer cxn)
604 :paui (ensure-integer paui)
605 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
607 (defun find-uhier-all (&key (srl *current-srl*))
608 (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
609 srl nil nil :lrl ksrl)
610 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
611 :cxn (ensure-integer cxn)
612 :paui (ensure-integer paui)
613 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
615 (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
616 (ensure-cui-integer cui)
617 (ensure-lui-integer lui)
618 (ensure-sui-integer sui)
619 (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE "))
621 (sui (string-append ls "KCUISUI='"
622 (integer-string (make-cuisui cui sui) 14)
624 (lui (string-append ls "KCUILUI='"
625 (integer-string (make-cuilui cui lui) 14)
627 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
628 "' and lui='0' and sui='0'")))
630 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
631 (loop for tuple in (mutex-sql-query ls) collect
632 (destructuring-bind (code atn sab atv) tuple
633 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
635 (defun find-usty-tui (tui)
637 (ensure-tui-integer tui)
638 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
639 (make-instance 'usty :tui tui :sty sty)))
641 (defun find-usty-sty (sty)
642 "Find usty for a sty"
643 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
644 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
646 (defun find-usty-all ()
647 "Return list of usty's for all semantic types"
648 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
649 (find-usty-tui tui)))
651 (defun find-usab-all ()
652 "Return all usab objects"
653 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
654 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
655 cenc curver sabin ssn scit) nil nil nil)
656 (make-instance 'usab :vcui (ensure-integer vcui)
657 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
658 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
659 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
660 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
661 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
662 :curver curver :sabin sabin :ssn ssn :scit scit)))
664 (defun find-usab-by-key (key-name key)
665 "Find usab for a key"
666 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
667 vend imeta rmeta slc scc srl tfr cfr cxty
668 ttyl atnl lat cenc curver sabin
670 nil key-name key :single t)
671 (make-instance 'usab :vcui (ensure-integer vcui)
672 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
673 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
674 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
675 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
676 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
677 :curver curver :sabin sabin
678 :ssn ssn :scit scit)))
680 (defun find-usab-rsab (rsab)
682 (find-usab-by-key 'rsab rsab))
684 (defun find-usab-vsab (vsab)
686 (find-usab-by-key 'vsab vsab))
688 (defun find-cui-max ()
689 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
691 (defun find-umap-cui (cui)
692 (ensure-cui-integer cui)
693 (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr
694 fromtype fromrule fromres rel rela toid tosid
695 toexpr totype torule tores maprule maptype
698 (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid
699 :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid
700 :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres
701 :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype
702 :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn
703 :mapatv mapatv :cvf cvf)))
705 (defun find-usmap-cui (cui)
706 (ensure-cui-integer cui)
707 (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf)
709 (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab
710 :fromexpr fromexpr :fromtype fromtype
711 :rel rel :rela rela :toexpr toexpr :totype totype
714 ;;;; Cross table find functions
716 (defun find-ucon-tui (tui &key (srl *current-srl*))
717 "Find list of ucon for tui"
718 (ensure-tui-integer tui)
719 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
720 (find-ucon-cui (ensure-integer cui) :srl srl)))
722 (defun find-ucon-word (word &key (srl *current-srl*) (like nil))
723 "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
724 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
725 :lrl 'klrl :order '(cui asc))
726 (find-ucon-cui cui :srl srl)))
728 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
729 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
730 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
731 :lrl 'klrl :order '(cui asc))
732 (find-ucon-cui cui :srl srl)))
734 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
735 "Return list of cui that match word, optionally use SQL's LIKE syntax"
736 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
737 :lrl 'klrl :order '(cui asc))
740 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
741 "Return list of cui that match word, optionally use SQL's LIKE syntax"
742 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
743 :lrl 'klrl :order '(cui asc))
746 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
747 "Return list of cui that match word, optionally use SQL's LIKE syntax"
748 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
749 :lrl 'klrl :order '(cui asc))
752 (defun find-ustr-word (word &key (srl *current-srl*))
753 "Return list of ustrs that match word"
754 (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
755 :order (cui asc sui asc))
756 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
758 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
759 "Return list of ustrs that match word"
760 (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl
761 :order (cui asc sui asc))
762 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
764 (defun find-uterm-word (word &key (srl *current-srl*))
765 "Return list of uterms that match word"
766 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
767 :order (cui asc lui asc))
768 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
770 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
771 "Return list of uterms that match word"
772 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
773 :order (cui asc lui asc))
774 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
776 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
777 "Return list of ucons that match non-english word"
778 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
779 :distinct t :lrl 'klrl :order '(cui asc))
780 (find-ucon-cui cui :srl srl)))
782 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
783 "Return list of ustrs that match non-english word"
784 (collect-umlisp-query (mrxw_noneng (cui sui) srl wd word :lrl klrl
785 :order (cui asc sui asc))
786 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
790 (defun find-usrl-all ()
791 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
792 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
794 ;;; Multiword lookup and score functions
796 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
797 only-exact-if-match limit)
799 (dolist (word (delimited-string-to-list str #\space))
800 (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl))))
802 (funcall sort-fun str
803 (delete-duplicates uobjs :test #'= :key key))))
804 (let ((len (length sorted)))
807 (return-from find-uobj-multiword nil))
808 ((and only-exact-if-match (multiword-match str (pfstr (first sorted))))
811 (if (and (plusp limit) (> len limit))
812 (subseq sorted 0 limit)
817 (defun find-ucon-multiword (str &key (srl *current-srl*)
818 (only-exact-if-match t)
820 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
821 #'cui srl only-exact-if-match limit))
823 (defun find-uterm-multiword (str &key (srl *current-srl*)
824 (only-exact-if-match t)
826 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
827 #'lui srl only-exact-if-match limit))
829 (defun find-ustr-multiword (str &key (srl *current-srl*)
830 (only-exact-if-match t)
832 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
833 #'sui srl only-exact-if-match limit))
835 (defun sort-score-pfstr-str (str uobjs)
836 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
837 (sort-score-umlsclass-str uobjs str #'pfstr))
839 (defun sort-score-ustr-str (str ustrs)
840 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
841 (sort-score-umlsclass-str ustrs str #'str))
843 (defun sort-score-umlsclass-str (objs str lookup-func)
844 "Sort a list of objects based on scoring to a string"
847 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
849 (mapcar #'car (sort scored #'> :key #'cadr))))
852 ;;; LEX SQL functions
854 (defun find-lexterm-eui (eui)
855 (ensure-eui-integer eui)
856 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
857 (make-instance 'lexterm :eui eui :wrd wrd)))
859 (defun find-lexterm-word (wrd)
860 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
861 (make-instance 'lexterm :eui (ensure-integer eui)
862 :wrd (copy-seq wrd))))
864 ;; LEX SQL Read functions
866 (defun find-labr-eui (eui)
867 (ensure-eui-integer eui)
868 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
869 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
870 :eui2 (ensure-integer eui2))))
872 (defun find-labr-bas (bas)
873 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
874 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
875 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
877 (defun find-lagr-eui (eui)
878 (ensure-eui-integer eui)
879 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
880 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
883 (defun find-lcmp-eui (eui)
884 (ensure-eui-integer eui)
885 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
886 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
888 (defun find-lmod-eui (eui)
889 (ensure-eui-integer eui)
890 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
891 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
893 (defun find-lnom-eui (eui)
894 (ensure-eui-integer eui)
895 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
896 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
897 :eui2 (ensure-integer eui2))))
899 (defun find-lprn-eui (eui)
900 (ensure-eui-integer eui)
901 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
902 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
903 :cas cas :pos pos :qnt qnt :fea fea)))
905 (defun find-lprp-eui (eui)
906 (ensure-eui-integer eui)
907 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
908 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
910 (defun find-lspl-eui (eui)
911 (ensure-eui-integer eui)
912 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
913 (make-instance 'lspl :eui eui :spv spv :bas bas)))
915 (defun find-ltrm-eui (eui)
916 (ensure-eui-integer eui)
917 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
918 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
920 (defun find-ltyp-eui (eui)
921 (ensure-eui-integer eui)
922 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
923 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
925 (defun find-lwd-wrd (wrd)
926 (make-instance 'lwd :wrd wrd
927 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
928 (ensure-integer eui))))
930 ;;; Semantic Network SQL access functions
932 (defun find-sdef-ui (ui)
933 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
935 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
936 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
938 (defun find-sstre1-ui (ui)
939 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
940 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
941 :ui3 (ensure-integer ui3))))
943 (defun find-sstre1-ui2 (ui2)
944 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
945 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
946 :ui3 (ensure-integer ui3))))
948 (defun find-sstr-rl (rl)
949 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
950 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
952 (defun find-sstre2-sty (sty)
953 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
954 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
956 (defun find-sstr-styrl (styrl)
957 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
958 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
961 ;;; **************************
963 ;;; **************************
966 (defun make-ustats ()
967 (with-sql-connection (conn)
968 (ignore-errors (sql-execute "drop table USTATS" conn))
969 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
972 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
973 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
974 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
975 (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
976 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
977 (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
978 (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
979 (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
980 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
981 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
982 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
983 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
984 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
985 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
986 (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
987 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
988 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
989 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
990 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
993 (defun insert-ustats-count (conn name table count-variable srl-control srl)
994 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
996 (defun find-count-table (conn table srl count-variable srl-control)
998 ((stringp srl-control)
1000 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
1001 count-variable table srl-control srl)
1005 (caar (sql-query (format nil "select count(~a) from ~a"
1006 count-variable table )
1009 (error "Unknown srl-control")
1012 (defun insert-ustats (conn name count srl)
1013 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
1014 name count (if srl srl 3))
1017 (defun find-ustats-all (&key (srl *current-srl*))
1019 (collect-umlisp-query (ustats (name count srl) nil srl srl
1021 (make-instance 'ustats :name name
1022 :hits (ensure-integer count)
1023 :srl (ensure-integer srl)))
1024 (collect-umlisp-query (ustats (name count srl) nil nil nil
1026 (make-instance 'ustats :name name
1027 :hits (ensure-integer count)
1028 :srl (ensure-integer srl)))))
1030 (defun find-ustats-srl (srl)
1031 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
1032 (make-instance 'ustats :name name :hits (ensure-integer count))))
1036 (defun find-bsab-sab (sab)
1037 (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t)
1038 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
1040 (defun find-bsab-all ()
1041 (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc))
1042 (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
1044 (defun find-btty-tty (tty)
1045 (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t)
1046 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
1048 (defun find-btty-all ()
1049 (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc))
1050 (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
1052 (defun find-brel-rel (rel)
1053 (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel)
1054 (make-instance 'brel :sab sab :sl sl :rel rel :rela rela
1055 :hits (ensure-integer count))))