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
10 ;;;; This file, part of UMLisp, is
11 ;;;; Copyright (c) 2000-2010 by Kevin M. Rosenberg, M.D.
13 ;;;; UMLisp users are granted the rights to distribute and use this software
14 ;;;; as governed by the terms of the GNU General Public License.
15 ;;;; *************************************************************************
20 (defvar *current-srl* nil)
23 (defun set-current-srl (srl)
24 (setq *current-srl* srl))
26 (defmacro query-string (table fields srl where-name where-value
27 &key (lrl "KCUILRL") single distinct order like limit
29 (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
30 (if distinct "DISTINCT " "") fields table))
31 (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}"
34 (%%lrl (format nil " AND ~:@(~A~)<=" lrl))
35 (%%where (when where-name
36 (format nil " WHERE ~:@(~A~)~A" where-name
37 (if like " like " ""))))
38 (%filter (gensym "FILTER-"))
39 (%single (gensym "SINGLE-"))
40 (%limit (gensym "LIMIT-")))
41 `(let ((,%limit ,limit)
47 ,@(when %%where (list %%where))
49 `((typecase ,where-value
52 (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
54 (concatenate 'string "='" (write-to-string ,where-value) "'"))
58 (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
59 (if ,%filter (concatenate 'string
60 ,(if %%where " AND " " WHERE ")
62 (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
63 ,@(when %%order (list %%order))
65 ((and ,%single ,%limit)
66 (error "Can't set single (~S) and limit (~S)" ,%single ,%limit))
70 (format nil " LIMIT ~D" ,%limit))
74 (defun query-string-eval (table fields srl where-name where-value
75 &key (lrl "KCUILRL") single distinct order like limit filter)
76 (when single (setq limit 1))
79 (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
80 (if distinct "DISTINCT " "") fields table)
81 (if where-name (format nil " WHERE ~:@(~A~)" where-name) "")
88 (if like " LIKE '%~A%'" "='~A'")))
91 (if filter (concatenate 'string " AND " filter) nil)
92 (if srl (format nil " AND ~:@(~A~)<=~D" lrl srl) "")
93 (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}" order) "")
94 (if limit (format nil " LIMIT ~D" limit) "")))
97 (defmacro umlisp-query (table fields srl where-name where-value
98 &key (lrl "KCUILRL") single distinct order like
99 limit filter (query-cmd 'mutex-sql-query))
100 "Query the UMLisp database. Return a list of umlisp objects whose name
101 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
103 (query-string ,table ,fields ,srl ,where-name ,where-value
104 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
105 :filter ,filter :limit ,limit)))
107 (defmacro umlisp-query-eval (table fields srl where-name where-value
108 &key (lrl "KCUILRL") single distinct order like
110 "Query the UMLisp database. Return a list of umlisp objects whose name
111 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
113 (query-string-eval ,table ,fields ,srl ,where-name ,where-value
114 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
115 :filter ,filter :limit ,limit)))
117 ;; only WHERE-VALUE and SRL are evaluated
118 (defmacro collect-umlisp-query ((table fields srl where-name where-value
119 &key (lrl "KCUILRL") distinct single
120 order like (query-cmd 'mutex-sql-query)
123 (let ((value (gensym))
126 (if (and limit (> limit 1))
127 (error "Can't set limit along with single.")
128 `(let* ((,value ,where-value)
129 (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
130 :lrl ,lrl :single ,single
131 :distinct ,distinct :order ,order
132 :like ,like :filter ,filter
133 :query-cmd ,query-cmd))))
134 ,@(unless where-name `((declare (ignore ,value))))
136 (destructuring-bind ,fields tuple
138 `(let ((,value ,where-value))
139 ,@(unless where-name `((declare (ignore ,value))))
141 (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
142 :lrl ,lrl :single ,single :distinct ,distinct
143 :order ,order :filter ,filter :like ,like
145 (push (destructuring-bind ,fields tuple ,@body) ,r))
149 (umlisp-query ,table ,fields ,srl ,where-name ,value
150 :lrl ,lrl :single ,single :distinct ,distinct
151 :order ,order :like ,like :filter ,filter :limit ,limit)
152 collect (destructuring-bind ,fields tuple ,@body))))))
154 (defmacro collect-umlisp-query-eval ((table fields srl where-name where-value
155 &key (lrl "KCUILRL") distinct single
156 order like filter limit)
158 (let ((value (gensym))
160 (eval-fields (cadr fields)))
162 `(let* ((,value ,where-value)
163 (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
164 :lrl ,lrl :single ,single
165 :distinct ,distinct :order ,order
166 :like ,like :filter ,filter
169 (destructuring-bind ,eval-fields tuple
171 `(let ((,value ,where-value)
173 (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
174 :lrl ,lrl :single ,single :distinct ,distinct
175 :order ,order :like ,like
176 :filter ,filter :limit ,limit))
177 (push (destructuring-bind ,eval-fields tuple ,@body) ,r))
181 (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
182 :lrl ,lrl :single ,single :distinct ,distinct
183 :order ,order :like ,like :filter ,filter
185 collect (destructuring-bind ,eval-fields tuple ,@body))))))
188 ;;; Read from SQL database
190 (defmacro ensure-cui-integer (cui)
192 (setq ,cui (parse-cui ,cui))
195 (defmacro ensure-lui-integer (lui)
197 (setq ,lui (parse-lui ,lui))
200 (defmacro ensure-sui-integer (sui)
202 (setq ,sui (parse-sui ,sui))
205 (defmacro ensure-aui-integer (aui)
207 (setq ,aui (parse-aui ,aui))
210 (defmacro ensure-rui-integer (rui)
212 (setq ,rui (parse-rui ,rui))
215 (defmacro ensure-tui-integer (tui)
217 (setq ,tui (parse-tui ,tui))
220 (defmacro ensure-eui-integer (eui)
222 (setq ,eui (parse-eui ,eui))
225 (defun make-ucon-cui (cui)
226 (ensure-cui-integer cui)
228 (make-instance 'ucon :cui cui)))
230 (defun find-ucon-cui (cui &key (srl *current-srl*) without-pfstr)
231 "Find ucon for a cui. If set SAB, the without-pfstr is on by default"
232 (ensure-cui-integer cui)
233 (unless cui (return-from find-ucon-cui nil))
236 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
237 (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
240 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t :filter "KPFENG=1")
241 (make-instance 'ucon :cui cui :pfstr str
243 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t)
244 (make-instance 'ucon :cui cui :pfstr str
247 (defun find-uconso-cui (cui &key sab (srl *current-srl*))
248 "Find uconso for a cui."
249 (ensure-cui-integer cui)
250 (unless cui (return-from find-uconso-cui nil))
252 (collect-umlisp-query (mrconso (lat ts lui stt sui ispref aui saui scui sdui sab tty code str
253 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
254 kluilrl ksuilrl) srl cui cui
255 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
256 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
257 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
258 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
259 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
262 (defun find-uconso-cuisui (cuisui &key sab (srl *current-srl*))
263 "Find uconso for a cuisui."
264 (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
265 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
266 kluilrl ksuilrl) srl kcuisui cuisui
267 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
268 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
269 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
270 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
271 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
275 (defun find-uconso-code (code &key first sab (srl *current-srl*) (like nil))
276 "Return list of uconso objects that match code. Optional, filter for SAB. Optionally, use SQL's LIKE syntax"
277 (collect-umlisp-query (mrconso (cui sab) srl code code :like like :distinct t
279 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
280 (let ((uconsos (find-uconso-cui cui :sab sab :srl srl)))
285 (defun find-uconso-sui (sui &key sab (srl *current-srl*))
286 "Find uconso for a sui. If set SAB, the without-pfstr is on by default"
287 (ensure-sui-integer sui)
288 ;; (unless (and sui (stringp sab))
290 (return-from find-uconso-sui nil))
292 (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
293 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
294 kluilrl ksuilrl) srl sui sui
296 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
297 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
298 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
299 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
300 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
303 (defun find-pfstr-cui (cui &key (srl *current-srl*))
304 "Find preferred string for a cui"
305 (ensure-cui-integer cui)
307 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
308 :filter " KPFENG=1" :single t)
310 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
314 (defun find-lrl-cui (cui &key (srl *current-srl*))
316 (ensure-cui-integer cui)
317 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :distinct t :single t)
318 (ensure-integer kcuilrl)))
320 (defun find-ucon-lui (lui &key (srl *current-srl*))
321 "Find list of ucon for lui"
322 (ensure-lui-integer lui)
323 (unless lui (return-from find-ucon-lui nil))
325 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
326 :filter " KPFENG=1" :single t)
327 (make-instance 'ucon :cui (ensure-integer cui)
328 :pfstr str :lrl (ensure-integer kcuilrl)))
329 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
331 (make-instance 'ucon :cui (ensure-integer cui)
332 :pfstr str :lrl (ensure-integer kcuilrl)))))
334 (defun find-ucon-sui (sui &key (srl *current-srl*))
335 "Find list of ucon for sui"
336 (ensure-sui-integer sui)
337 (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t)
338 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
339 :lrl (ensure-integer kcuilrl))))
341 (defun find-ucon-aui (aui &key (srl *current-srl*))
342 "Find list of ucon for aui"
343 (ensure-aui-integer aui)
344 (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
345 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
346 :lrl (ensure-integer kcuilrl))))
348 (defun find-ucon-cuisui (cuisui &key (srl *current-srl*))
349 "Find ucon for cui/sui"
350 (collect-umlisp-query (mrconso (cui kcuilrl) srl kcuisui cuisui)
351 (make-instance 'ucon :cui cui
352 :pfstr (find-pfstr-cui cui)
353 :lrl (ensure-integer kcuilrl))))
355 (defun find-ucon-cui-sui (cui sui &key (srl *current-srl*))
356 "Find ucon for cui/sui"
357 (ensure-cui-integer cui)
358 (ensure-sui-integer sui)
360 (find-ucon-cui-sui cui sui :srl srl)))
362 (defun find-ucon-str (str &key (srl *current-srl*))
363 "Find ucon that are exact match for str"
364 (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t)
365 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
366 :lrl (ensure-integer kcuilrl))))
368 (defun find-ucon-all (&key (srl *current-srl*))
369 "Return list of all ucon's"
370 (with-sql-connection (db)
374 (destructuring-bind (cui cuilrl) tuple
375 (make-instance 'ucon :cui (ensure-integer cui)
376 :pfstr (find-pfstr-cui cui)
377 :lrl (ensure-integer cuilrl))))
378 (query-string mrconso (cui kcuilrl) srl nil nil
379 :order (cui asc) :distinct t)
382 (defun find-ucon-all2 (&key (srl *current-srl*))
383 "Return list of all ucon's"
384 (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
386 (make-instance 'ucon :cui (ensure-integer cui)
387 :pfstr (find-pfstr-cui cui)
388 :lrl (ensure-integer kcuilrl))))
390 (defun find-cui-ucon-all (&key (srl *current-srl*))
391 "Return list of CUIs for all ucons"
392 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
396 (defun map-ucon-all (fn &key (srl *current-srl*))
397 "Map a function over all ucon's"
398 (with-sql-connection (db)
402 (destructuring-bind (cui cuilrl) tuple
403 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
404 :pfstr (find-pfstr-cui cui)
405 :lrl (ensure-integer cuilrl)))))
406 (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
411 (defun find-udef-cui (cui &key (srl *current-srl*))
412 "Return a list of udefs for cui"
413 (ensure-cui-integer cui)
414 (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
415 (make-instance 'udef :sab sab :def def :suppress suppress)))
417 (defun find-udoc-key (key)
418 "Return list of abbreviation documentation for a key"
419 (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
420 (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
422 (defun find-udoc-value (value)
423 "Return abbreviation documentation"
424 (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
425 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
427 (defun find-udoc-key-value (dockey value)
428 (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value))
429 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
431 (defun find-udoc-all ()
432 "Return all abbreviation documentation"
433 (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
434 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
436 (defun find-usty-cui (cui &key (srl *current-srl*))
437 "Return a list of usty for cui"
438 (ensure-cui-integer cui)
439 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
440 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
442 (defun find-usty-word (word &key (srl *current-srl*))
443 "Return a list of usty that match word"
444 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
446 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
448 (defun find-urel-cui (cui &key (srl *current-srl*) filter without-pfstr2)
449 "Return a list of urel for cui"
450 (ensure-cui-integer cui)
451 (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
452 srl cui1 cui :lrl "KSRL" :filter filter)
454 (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
455 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
456 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
457 :suppress suppress :cvf cvf)))
458 (unless without-pfstr2
459 (setf (slot-value rel 'pfstr2) (find-pfstr-cui cui2)))
462 (defun find-urel-rui (rui &key (srl *current-srl*))
463 "Return the urel for a rui"
464 (ensure-rui-integer rui)
465 (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
466 srl rui rui :lrl "KSRL" :single t)
467 (make-instance 'urel :cui1 cui1 :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
468 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
469 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
470 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
472 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
473 "Return a list of urel for cui"
474 (ensure-cui-integer cui)
475 (collect-umlisp-query (mrrel (cui2) srl cui1
479 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
480 "Return a list of urel for cui2"
481 (ensure-cui-integer cui2)
482 (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
483 srl cui2 cui2 :lrl "KSRL")
484 (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
485 :stype2 stype2 :rui (ensure-integer rui) :srui srui
486 :stype1 stype1 :cui1 (ensure-integer cui1)
487 :aui1 (ensure-integer aui1)
488 :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
489 :pfstr2 (find-pfstr-cui cui2))))
491 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
492 (ensure-cui-integer cui2)
493 (loop for cui in (remove-duplicates
494 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
495 collect (find-ucon-cui cui :srl srl)))
497 (defun find-ucoc-cui (cui &key (srl *current-srl*))
498 "Return a list of ucoc for cui"
499 (ensure-cui-integer cui)
500 (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
501 cui :lrl klrl :order (cof asc))
502 (setq cui2 (ensure-integer cui2))
503 (when (eql 0 cui2) (setq cui2 nil))
504 (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1)
505 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2)
506 :cot cot :cof (ensure-integer cof) :coa coa :sab sab
507 :pfstr2 (find-pfstr-cui cui2))))
509 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
510 "Return a list of ucoc for cui2"
511 (ensure-cui-integer cui2)
512 (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
513 cui2 :lrl klrl :order (cof asc))
514 (when (zerop cui2) (setq cui2 nil))
515 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
516 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2)
517 :sab sab :cot cot :cof (ensure-integer cof) :coa coa
518 :pfstr2 (find-pfstr-cui cui2))))
520 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
521 "List of ucon with co-occurance cui2"
522 (ensure-cui-integer cui2)
524 #'(lambda (cui) (find-ucon-cui cui :srl srl))
525 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
528 (defun find-uterm-cui (cui &key (srl *current-srl*))
529 "Return a list of uterm for cui"
530 (ensure-cui-integer cui)
531 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
532 :lrl kluilrl :distinct t)
533 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
534 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
536 (defun find-uterm-lui (lui &key (srl *current-srl*))
537 "Return a list of uterm for lui"
538 (ensure-lui-integer lui)
539 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
540 :lrl kluilrl :distinct t)
541 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
542 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
544 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
545 "Return single uterm for cui/lui"
546 (ensure-cui-integer cui)
547 (ensure-lui-integer lui)
548 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
549 (make-cuilui cui lui)
550 :lrl kluilrl :single t)
551 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
552 :lrl (ensure-integer kluilrl))))
554 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
555 "Return a list of ustr for cui/lui"
556 (ensure-cui-integer cui)
557 (ensure-lui-integer lui)
558 (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
559 (make-cuilui cui lui) :lrl ksuilrl :distinct t)
560 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
561 :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
562 :lrl (ensure-integer ksuilrl))))
564 (defun find-ustr-cuisui (cuisui &key (srl *current-srl*))
565 "Return the single ustr for cuisui"
566 (collect-umlisp-query (mrconso (cui lui sui stt str suppress ksuilrl) srl kcuisui
567 cuisui :lrl ksuilrl :single t)
568 (make-instance 'ustr :sui sui :cui cui :cuisui cuisui
569 :lui (ensure-integer lui) :stt stt :str str :suppress suppress
570 :lrl (ensure-integer ksuilrl))))
572 (defun find-ustr-cui-sui (cui sui &key (srl *current-srl*))
573 "Return the single ustr for cuisui"
574 (ensure-cui-integer cui)
575 (ensure-sui-integer sui)
576 (find-ustr-cuisui (make-cuisui cui sui) :srl srl))
578 (defun find-ustr-sui (sui &key (srl *current-srl*))
579 "Return the list of ustr for sui"
580 (ensure-sui-integer sui)
581 (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
582 :lrl ksuilrl :distinct t)
583 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
584 :cuisui (make-cuisui (ensure-integer cui) sui)
586 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
588 (defun find-ustr-sab (sab &key (srl *current-srl*))
589 "Return the list of ustr for sab"
590 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
591 (let ((cuisui (ensure-integer kcuisui)))
592 (find-ustr-cuisui cuisui :srl srl))))
594 (defun find-ustr-all (&key (srl *current-srl*))
595 "Return list of all ustr's"
596 (with-sql-connection (db)
600 (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple
601 (make-instance 'ustr :cui (ensure-integer cui)
602 :lui (ensure-integer lui) :sui (ensure-integer sui)
603 :stt stt :str (find-pfstr-cui cui)
604 :cuisui (make-cuisui (ensure-integer cui)
605 (ensure-integer sui))
607 :lrl (ensure-integer ksuilrl))))
608 (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
613 (defun find-string-sui (sui &key (srl *current-srl*))
614 "Return the string associated with sui"
615 (ensure-sui-integer sui)
616 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
619 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
620 (ensure-sui-integer sui)
621 (ensure-cui-integer cui)
622 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str ts)
623 srl kcuisui (make-cuisui cui sui) :lrl srl)
624 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
625 :cui cui :sui sui :saui saui :sdui sdui :scui scui
626 :lat lat :str str :ts ts)))
628 (defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
629 (ensure-cui-integer cui)
630 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui ts)
631 srl cui cui :lrl srl :limit limit
632 :filter (when english-only "LAT='ENG'"))
633 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
634 :cui cui :sui sui :saui saui :sdui sdui :scui scui
635 :lat lat :str str :ts ts)))
637 (defun find-uso-aui (aui &key (srl *current-srl*))
638 (ensure-sui-integer aui)
639 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat
640 str ts) srl aui aui :lrl srl :single t)
641 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
642 :sui sui :saui saui :sdui sdui :scui scui :lat lat
645 (defun find-uhier-cui (cui &key (srl *current-srl*))
646 (ensure-cui-integer cui)
647 (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
648 srl cui cui :lrl ksrl)
649 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
650 :cxn (ensure-integer cxn)
651 :paui (ensure-integer paui)
652 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
654 (defun find-uhier-all (&key (srl *current-srl*))
655 (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
656 srl nil nil :lrl ksrl)
657 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
658 :cxn (ensure-integer cxn)
659 :paui (ensure-integer paui)
660 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
662 (defun find-usat-ui (cui &optional lui sui &key (srl *current-srl*))
663 (ensure-cui-integer cui)
664 (ensure-lui-integer lui)
665 (ensure-sui-integer sui)
666 (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE "))
668 (sui (string-append ls "KCUISUI='"
669 (integer-string (make-cuisui cui sui) 14)
671 (lui (string-append ls "KCUILUI='"
672 (integer-string (make-cuilui cui lui) 14)
674 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
675 "' and lui='0' and sui='0'")))
677 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
678 (loop for tuple in (mutex-sql-query ls) collect
679 (destructuring-bind (code atn sab atv) tuple
680 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
682 (defun find-usty-tui (tui)
684 (ensure-tui-integer tui)
685 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
686 (make-instance 'usty :tui tui :sty sty)))
688 (defun find-usty-sty (sty)
689 "Find usty for a sty"
690 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
691 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
693 (defun find-usty-all ()
694 "Return list of usty's for all semantic types"
695 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
696 (find-usty-tui tui)))
698 (defun find-usab-all ()
699 "Return all usab objects"
700 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
701 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
702 cenc curver sabin ssn scit) nil nil nil)
703 (make-instance 'usab :vcui (ensure-integer vcui)
704 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
705 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
706 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
707 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
708 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
709 :curver curver :sabin sabin :ssn ssn :scit scit)))
711 (defun find-usab-by-key (key-name key &key current)
712 "Find usab for a key"
713 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
714 vend imeta rmeta slc scc srl tfr cfr cxty
715 ttyl atnl lat cenc curver sabin
717 nil key-name key :single t
718 :filter (when current "RMETA=''"))
719 (make-instance 'usab :vcui (ensure-integer vcui)
720 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
721 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
722 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
723 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
724 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
725 :curver curver :sabin sabin
726 :ssn ssn :scit scit)))
728 (defun find-usab-rsab (rsab &key (current t))
730 (find-usab-by-key 'rsab rsab))
732 (defun find-usab-vsab (vsab &key (current t))
734 (find-usab-by-key 'vsab vsab))
736 (defun find-cui-max ()
737 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
739 (defun find-umap-cui (cui)
740 (ensure-cui-integer cui)
741 (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr
742 fromtype fromrule fromres rel rela toid tosid
743 toexpr totype torule tores maprule maptype
746 (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid
747 :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid
748 :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres
749 :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype
750 :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn
751 :mapatv mapatv :cvf cvf)))
753 (defun find-usmap-cui (cui)
754 (ensure-cui-integer cui)
755 (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf)
757 (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab
758 :fromexpr fromexpr :fromtype fromtype
759 :rel rel :rela rela :toexpr toexpr :totype totype
762 ;;;; Cross table find functions
764 (defun find-ucon-tui (tui &key (srl *current-srl*))
765 "Find list of ucon for tui"
766 (ensure-tui-integer tui)
767 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
768 (find-ucon-cui (ensure-integer cui) :srl srl)))
770 (defun mrconso-query-word-cui (word sab srl like)
771 (format nil "SELECT DISTINCT c.cui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.cui=c.cui~A~A"
772 (if like " LIKE " "=")
773 (clsql-sys::sql-escape-quotes word)
776 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
778 (format nil " AND c.sab IN (~{'~A'~^,~})"
779 (mapcar 'clsql-sys::sql-escape-quotes sab)))
782 (if srl (format nil " AND KCUILRL <= ~A" srl) "")))
784 (defun mrconso-query-word-sui (word sab srl like)
785 (format nil "SELECT DISTINCT c.sui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.sui=c.sui~A~A"
786 (if like " LIKE " "=")
787 (clsql-sys::sql-escape-quotes word)
790 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
792 (format nil " AND c.sab IN (~{'~A'~^,~})"
793 (mapcar 'clsql-sys::sql-escape-quotes sab)))
796 (if srl (format nil " AND KCUILRL <= ~A" srl) "")))
798 (defun find-uconso-word (word &key sab (srl *current-srl*) (like nil))
799 "Return list of uconso that match word. Optionally, matching SAB. Optionally, use SQL's LIKE syntax"
802 (let ((sui-query (mrconso-query-word-sui word sab srl like))
804 (dolist (sui (remove-duplicates (sort (mapcar 'car (mutex-sql-query sui-query)) #'<)))
805 (setq uconsos (nconc uconsos (find-uconso-sui sui :sab sab))))
806 (remove-duplicates uconsos :key 'cui)))
808 (collect-umlisp-query-eval ('mrxw_eng '(kcuisui) srl 'wd word :like like
809 :lrl 'klrl :order '(kcuisui asc))
810 (find-uconso-cuisui kcuisui :srl srl)))))
812 (defun find-ucon-word (word &key sab (srl *current-srl*) (like nil))
813 "Return list of ucon that match word in matching SAB. Optionally, use SQL's LIKE syntax"
816 (let ((query (mrconso-query-word-cui word sab srl like)))
817 (loop for tuple in (mutex-sql-query query)
818 collect (make-instance 'ucon :cui (first tuple)))))
820 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
821 :lrl 'klrl :order '(cui asc))
822 (find-ucon-cui cui :srl srl)))))
824 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
825 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
826 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
827 :lrl 'klrl :order '(cui asc))
828 (find-ucon-cui cui :srl srl)))
830 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
831 "Return list of cui that match word, optionally use SQL's LIKE syntax"
832 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
833 :lrl 'klrl :order '(cui asc))
836 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
837 "Return list of cui that match word, optionally use SQL's LIKE syntax"
838 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
839 :lrl 'klrl :order '(cui asc))
842 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
843 "Return list of cui that match word, optionally use SQL's LIKE syntax"
844 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
845 :lrl 'klrl :order '(cui asc))
848 (defun find-ustr-word (word &key sab (srl *current-srl*) (like nil))
849 "Return list of ustr that match word in matching SAB. Optionally, use SQL's LIKE syntax"
852 (let ((query (format nil "SELECT c.sui,c.cui,c.lui,c.str,c.lrl,c.stt,c.suppress,c.cuisui FROM MRCONSO c,MRXW_ENG x WHERE x.WD ~A '~A' AND x.cui=c.cui AND x.lui=c.lui AND x.sui=c.sui~A~A"
854 (clsql-sys::sql-escape-quotes word)
857 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
859 (format nil " AND c.sab IN (~('~A'~^,~))"
860 (mapcar 'clsql-sys::sql-escape-quotes sab)))
863 (if srl (format nil " AND KCUILRL <= ~D" srl) ""))))
864 (loop for tuple in (mutex-sql-query query)
865 collect (destructuring-bind (sui cui lui str lrl stt suppress cuisui) tuple
866 (make-instance 'ustr :sui sui :cui cui :lui lui :str str :lrl lrl
867 :stt stt :suppress suppress :cuisui cuisui)))))
869 (collect-umlisp-query (mrxw_eng (kcuisui) srl wd word :lrl klrl
870 :order (cui asc sui asc))
871 (find-ustr-cuisui kcuisui :srl srl)))))
873 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
874 "Return list of ustrs that match word"
875 (collect-umlisp-query (mrxnw_eng (kcuisui) srl nwd word :lrl klrl
876 :order (cui asc sui asc))
877 (find-ustr-cuisui kcuisui :srl srl)))
879 (defun find-uterm-word (word &key (srl *current-srl*))
880 "Return list of uterms that match word"
881 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
882 :order (cui asc lui asc))
883 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
885 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
886 "Return list of uterms that match word"
887 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
888 :order (cui asc lui asc))
889 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
891 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
892 "Return list of ucons that match non-english word"
893 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
894 :distinct t :lrl 'klrl :order '(cui asc))
895 (find-ucon-cui cui :srl srl)))
897 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
898 "Return list of ustrs that match non-english word"
899 (collect-umlisp-query (mrxw_noneng (kcuisui) srl wd word :lrl klrl
900 :order (cui asc sui asc))
901 (find-ustr-cuisui kcuisui :srl srl)))
905 (defun find-usrl-all ()
906 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
907 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
909 ;;; Multiword lookup and score functions
911 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
912 only-exact-if-match limit &key extra-lookup-args)
914 (dolist (word (delimited-string-to-list str #\space))
915 (setq uobjs (nconc uobjs
916 (kmrcl:flatten (apply obj-lookup-fun word :srl srl extra-lookup-args)))))
918 (funcall sort-fun str
919 (delete-duplicates uobjs :test #'= :key key))))
920 (let ((len (length sorted)))
923 (return-from find-uobj-multiword nil))
924 ((and only-exact-if-match (multiword-match str (pfstr (first sorted))))
927 (if (and (plusp limit) (> len limit))
928 (subseq sorted 0 limit)
933 (defun find-ucon-multiword (str &key (srl *current-srl*)
934 (only-exact-if-match t)
937 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
938 #'cui srl only-exact-if-match limit
939 :extra-lookup-args (list :sab sab)))
941 (defun find-uconso-multiword (str &key (srl *current-srl*)
942 (only-exact-if-match t)
945 (find-uobj-multiword str #'find-uconso-word #'sort-score-pfstr-str
946 #'cui srl only-exact-if-match limit
947 :extra-lookup-args (list :sab sab)))
949 (defun find-uterm-multiword (str &key (srl *current-srl*)
950 (only-exact-if-match t)
952 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
953 #'lui srl only-exact-if-match limit))
955 (defun find-ustr-multiword (str &key (srl *current-srl*)
956 (only-exact-if-match t)
959 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
960 #'sui srl only-exact-if-match limit
961 :extra-lookup-args (list :sab sab)))
963 (defun sort-score-pfstr-str (str uobjs)
964 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
965 (sort-score-umlsclass-str uobjs str #'pfstr))
967 (defun sort-score-ustr-str (str ustrs)
968 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
969 (sort-score-umlsclass-str ustrs str #'str))
971 (defun sort-score-umlsclass-str (objs str lookup-func)
972 "Sort a list of objects based on scoring to a string"
975 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
977 (mapcar #'car (sort scored #'> :key #'cadr))))
980 ;;; LEX SQL functions
982 (defun find-lexterm-eui (eui)
983 (ensure-eui-integer eui)
984 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
985 (make-instance 'lexterm :eui eui :wrd wrd)))
987 (defun find-lexterm-word (wrd)
988 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
989 (make-instance 'lexterm :eui (ensure-integer eui)
990 :wrd (copy-seq wrd))))
992 ;; LEX SQL Read functions
994 (defun find-labr-eui (eui)
995 (ensure-eui-integer eui)
996 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
997 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
998 :eui2 (ensure-integer eui2))))
1000 (defun find-labr-bas (bas)
1001 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
1002 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
1003 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
1005 (defun find-lagr-eui (eui)
1006 (ensure-eui-integer eui)
1007 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
1008 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
1009 :cit cit :bas bas)))
1011 (defun find-lcmp-eui (eui)
1012 (ensure-eui-integer eui)
1013 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
1014 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
1016 (defun find-lmod-eui (eui)
1017 (ensure-eui-integer eui)
1018 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
1019 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
1021 (defun find-lnom-eui (eui)
1022 (ensure-eui-integer eui)
1023 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
1024 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
1025 :eui2 (ensure-integer eui2))))
1027 (defun find-lprn-eui (eui)
1028 (ensure-eui-integer eui)
1029 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
1030 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
1031 :cas cas :pos pos :qnt qnt :fea fea)))
1033 (defun find-lprp-eui (eui)
1034 (ensure-eui-integer eui)
1035 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
1036 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
1038 (defun find-lspl-eui (eui)
1039 (ensure-eui-integer eui)
1040 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
1041 (make-instance 'lspl :eui eui :spv spv :bas bas)))
1043 (defun find-ltrm-eui (eui)
1044 (ensure-eui-integer eui)
1045 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
1046 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
1048 (defun find-ltyp-eui (eui)
1049 (ensure-eui-integer eui)
1050 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
1051 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
1053 (defun find-lwd-wrd (wrd)
1054 (make-instance 'lwd :wrd wrd
1055 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
1056 (ensure-integer eui))))
1058 ;;; Semantic Network SQL access functions
1060 (defun find-sdef-ui (ui)
1061 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
1062 nil ui ui :single t)
1063 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
1064 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
1066 (defun find-sstre1-ui (ui)
1067 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
1068 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
1069 :ui3 (ensure-integer ui3))))
1071 (defun find-sstre1-ui2 (ui2)
1072 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
1073 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
1074 :ui3 (ensure-integer ui3))))
1076 (defun find-sstr-rl (rl)
1077 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
1078 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
1080 (defun find-sstre2-sty (sty)
1081 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
1082 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
1084 (defun find-sstr-styrl (styrl)
1085 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
1086 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
1089 ;;; **************************
1091 ;;; **************************
1094 (defun make-ustats ()
1095 (with-sql-connection (conn)
1096 (ignore-errors (sql-execute "drop table USTATS" conn))
1097 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
1099 (dolist (srl '(0 1 2 3 4 9))
1100 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
1101 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
1102 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
1103 (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
1104 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
1105 (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
1106 (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
1107 (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
1108 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
1109 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
1110 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
1111 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
1112 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
1113 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
1114 (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
1115 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
1116 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
1117 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
1118 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
1121 (defun insert-ustats-count (conn name table count-variable srl-control srl)
1122 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
1124 (defun find-count-table (conn table srl count-variable srl-control)
1126 ((stringp srl-control)
1128 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
1129 count-variable table srl-control srl)
1133 (caar (sql-query (format nil "select count(~a) from ~a"
1134 count-variable table )
1137 (error "Unknown srl-control")
1140 (defun insert-ustats (conn name count srl)
1141 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
1142 name count (if srl srl 3))
1145 (defun find-ustats-all (&key (srl *current-srl*))
1147 (collect-umlisp-query (ustats (name count srl) nil srl srl
1149 (make-instance 'ustats :name name
1150 :hits (ensure-integer count)
1151 :srl (ensure-integer srl)))
1152 (collect-umlisp-query (ustats (name count srl) nil nil nil
1154 (make-instance 'ustats :name name
1155 :hits (ensure-integer count)
1156 :srl (ensure-integer srl)))))
1158 (defun find-ustats-srl (srl)
1159 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
1160 (make-instance 'ustats :name name :hits (ensure-integer count))))