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 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 (~S) and limit (~S)" ,%single ,%limit))
72 (format nil " LIMIT ~D" ,%limit))
76 (defun query-string-eval (table fields 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. If set SAB, the without-pfstr is on by default"
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-uconso-cui (cui &key (srl *current-srl*))
250 "Find uconso for a cui."
251 (ensure-cui-integer cui)
252 (unless cui (return-from find-uconso-cui nil))
254 (collect-umlisp-query (mrconso (lat ts lui stt sui ispref aui saui scui sdui sab tty code str
255 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
256 kluilrl ksuilrl) srl cui cui)
257 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
258 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
259 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
260 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
263 (defun find-uconso-cui-sab (cui sab &key (srl *current-srl*))
264 "Find uconso for a cui. If set SAB, the without-pfstr is on by default"
265 (ensure-cui-integer cui)
266 (unless (and cui (stringp sab))
267 (return-from find-uconso-cui-sab nil))
269 (collect-umlisp-query (mrconso (lat ts lui stt sui ispref aui saui scui sdui sab tty code str
270 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
271 kluilrl ksuilrl) srl cui cui
272 :filter (concatenate 'string "SAB='" sab "'"))
273 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
274 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
275 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
276 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
279 (defun find-uconso-sui-sab (sui sab &key (srl *current-srl*))
280 "Find uconso for a sui. If set SAB, the without-pfstr is on by default"
281 (ensure-sui-integer sui)
282 (unless (and sui (stringp sab))
283 (return-from find-uconso-sui-sab nil))
285 (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
286 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
287 kluilrl ksuilrl) srl sui sui
288 :filter (concatenate 'string "SAB='" sab "'"))
289 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
290 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
291 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
292 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
295 (defun find-pfstr-cui (cui &key (srl *current-srl*))
296 "Find preferred string for a cui"
297 (ensure-cui-integer cui)
299 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
300 :filter " KPFENG=1" :single t)
302 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
306 (defun find-lrl-cui (cui &key (srl *current-srl*))
308 (ensure-cui-integer cui)
309 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :distinct t :single t)
310 (ensure-integer kcuilrl)))
312 (defun find-ucon-lui (lui &key (srl *current-srl*))
313 "Find list of ucon for lui"
314 (ensure-lui-integer lui)
315 (unless lui (return-from find-ucon-lui nil))
317 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
318 :filter " KPFENG=1" :single t)
319 (make-instance 'ucon :cui (ensure-integer cui)
320 :pfstr str :lrl (ensure-integer kcuilrl)))
321 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
323 (make-instance 'ucon :cui (ensure-integer cui)
324 :pfstr str :lrl (ensure-integer kcuilrl)))))
326 (defun find-ucon-sui (sui &key (srl *current-srl*))
327 "Find list of ucon for sui"
328 (ensure-sui-integer sui)
329 (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t)
330 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
331 :lrl (ensure-integer kcuilrl))))
333 (defun find-ucon-aui (aui &key (srl *current-srl*))
334 "Find list of ucon for aui"
335 (ensure-aui-integer aui)
336 (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
337 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
338 :lrl (ensure-integer kcuilrl))))
340 (defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
341 "Find ucon for cui/sui"
342 (ensure-cui-integer cui)
343 (ensure-sui-integer sui)
345 (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui
346 (make-cuisui cui sui))
347 (make-instance 'ucon :cui cui
348 :pfstr (find-pfstr-cui cui)
349 :lrl (ensure-integer kcuilrl)))))
351 (defun find-ucon-str (str &key (srl *current-srl*))
352 "Find ucon that are exact match for str"
353 (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t)
354 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
355 :lrl (ensure-integer kcuilrl))))
357 (defun find-ucon-all (&key (srl *current-srl*))
358 "Return list of all ucon's"
359 (with-sql-connection (db)
363 (destructuring-bind (cui cuilrl) tuple
364 (make-instance 'ucon :cui (ensure-integer cui)
365 :pfstr (find-pfstr-cui cui)
366 :lrl (ensure-integer cuilrl))))
367 (query-string mrconso (cui kcuilrl) srl nil nil
368 :order (cui asc) :distinct t)
371 (defun find-ucon-all2 (&key (srl *current-srl*))
372 "Return list of all ucon's"
373 (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
375 (make-instance 'ucon :cui (ensure-integer cui)
376 :pfstr (find-pfstr-cui cui)
377 :lrl (ensure-integer kcuilrl))))
379 (defun find-cui-ucon-all (&key (srl *current-srl*))
380 "Return list of CUIs for all ucons"
381 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
385 (defun map-ucon-all (fn &key (srl *current-srl*))
386 "Map a function over all ucon's"
387 (with-sql-connection (db)
391 (destructuring-bind (cui cuilrl) tuple
392 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
393 :pfstr (find-pfstr-cui cui)
394 :lrl (ensure-integer cuilrl)))))
395 (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
400 (defun find-udef-cui (cui &key (srl *current-srl*))
401 "Return a list of udefs for cui"
402 (ensure-cui-integer cui)
403 (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
404 (make-instance 'udef :sab sab :def def :suppress suppress)))
406 (defun find-udoc-key (key)
407 "Return list of abbreviation documentation for a key"
408 (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
409 (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
411 (defun find-udoc-value (value)
412 "Return abbreviation documentation"
413 (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
414 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
416 (defun find-udoc-key-value (dockey value)
417 (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value))
418 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
420 (defun find-udoc-all ()
421 "Return all abbreviation documentation"
422 (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
423 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
425 (defun find-usty-cui (cui &key (srl *current-srl*))
426 "Return a list of usty for cui"
427 (ensure-cui-integer cui)
428 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
429 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
431 (defun find-usty-word (word &key (srl *current-srl*))
432 "Return a list of usty that match word"
433 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
435 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
437 (defun find-urel-cui (cui &key (srl *current-srl*) filter without-pfstr2)
438 "Return a list of urel for cui"
439 (ensure-cui-integer cui)
440 (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
441 srl cui1 cui :lrl "KSRL" :filter filter)
443 (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
444 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
445 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
446 :suppress suppress :cvf cvf)))
447 (unless without-pfstr2
448 (setf (slot-value rel 'pfstr2) (find-pfstr-cui cui2)))
451 (defun find-urel-rui (rui &key (srl *current-srl*))
452 "Return the urel for a rui"
453 (ensure-rui-integer rui)
454 (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
455 srl rui rui :lrl "KSRL" :single t)
456 (make-instance 'urel :cui1 cui1 :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
457 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
458 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
459 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
461 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
462 "Return a list of urel for cui"
463 (ensure-cui-integer cui)
464 (collect-umlisp-query (mrrel (cui2) srl cui1
468 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
469 "Return a list of urel for cui2"
470 (ensure-cui-integer cui2)
471 (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
472 srl cui2 cui2 :lrl "KSRL")
473 (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
474 :stype2 stype2 :rui (ensure-integer rui) :srui srui
475 :stype1 stype1 :cui1 (ensure-integer cui1)
476 :aui1 (ensure-integer aui1)
477 :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
478 :pfstr2 (find-pfstr-cui cui2))))
480 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
481 (ensure-cui-integer cui2)
482 (loop for cui in (remove-duplicates
483 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
484 collect (find-ucon-cui cui :srl srl)))
486 (defun find-ucoc-cui (cui &key (srl *current-srl*))
487 "Return a list of ucoc for cui"
488 (ensure-cui-integer cui)
489 (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
490 cui :lrl klrl :order (cof asc))
491 (setq cui2 (ensure-integer cui2))
492 (when (eql 0 cui2) (setq cui2 nil))
493 (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1)
494 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2)
495 :cot cot :cof (ensure-integer cof) :coa coa :sab sab
496 :pfstr2 (find-pfstr-cui cui2))))
498 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
499 "Return a list of ucoc for cui2"
500 (ensure-cui-integer cui2)
501 (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
502 cui2 :lrl klrl :order (cof asc))
503 (when (zerop cui2) (setq cui2 nil))
504 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
505 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2)
506 :sab sab :cot cot :cof (ensure-integer cof) :coa coa
507 :pfstr2 (find-pfstr-cui cui2))))
509 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
510 "List of ucon with co-occurance cui2"
511 (ensure-cui-integer cui2)
513 #'(lambda (cui) (find-ucon-cui cui :srl srl))
514 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
517 (defun find-uterm-cui (cui &key (srl *current-srl*))
518 "Return a list of uterm for cui"
519 (ensure-cui-integer cui)
520 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
521 :lrl kluilrl :distinct t)
522 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
523 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
525 (defun find-uterm-lui (lui &key (srl *current-srl*))
526 "Return a list of uterm for lui"
527 (ensure-lui-integer lui)
528 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
529 :lrl kluilrl :distinct t)
530 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
531 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
533 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
534 "Return single uterm for cui/lui"
535 (ensure-cui-integer cui)
536 (ensure-lui-integer lui)
537 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
538 (make-cuilui cui lui)
539 :lrl kluilrl :single t)
540 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
541 :lrl (ensure-integer kluilrl))))
543 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
544 "Return a list of ustr for cui/lui"
545 (ensure-cui-integer cui)
546 (ensure-lui-integer lui)
547 (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
548 (make-cuilui cui lui) :lrl ksuilrl)
549 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
550 :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
551 :lrl (ensure-integer ksuilrl))))
553 (defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
554 "Return the single ustr for cuisui"
555 (ensure-cui-integer cui)
556 (ensure-sui-integer sui)
557 (collect-umlisp-query (mrconso (lui stt str suppress ksuilrl) srl kcuisui
558 (make-cuisui cui sui) :lrl lsuilrl :single t)
559 (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
560 :lui (ensure-integer lui) :stt stt :str str :suppress suppress
561 :lrl (ensure-integer ksuilrl))))
563 (defun find-ustr-sui (sui &key (srl *current-srl*))
564 "Return the list of ustr for sui"
565 (ensure-sui-integer sui)
566 (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
568 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
569 :cuisui (make-cuisui (ensure-integer cui) sui)
571 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
573 (defun find-ustr-sab (sab &key (srl *current-srl*))
574 "Return the list of ustr for sab"
575 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
576 (let ((cuisui (ensure-integer kcuisui)))
577 (apply #'find-ustr-cuisui
579 (multiple-value-list (decompose-cuisui cuisui))
582 (defun find-ustr-all (&key (srl *current-srl*))
583 "Return list of all ustr's"
584 (with-sql-connection (db)
588 (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple
589 (make-instance 'ustr :cui (ensure-integer cui)
590 :lui (ensure-integer lui) :sui (ensure-integer sui)
591 :stt stt :str (find-pfstr-cui cui)
592 :cuisui (make-cuisui (ensure-integer cui)
593 (ensure-integer sui))
595 :lrl (ensure-integer ksuilrl))))
596 (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
601 (defun find-string-sui (sui &key (srl *current-srl*))
602 "Return the string associated with sui"
603 (ensure-sui-integer sui)
604 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
607 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
608 (ensure-sui-integer sui)
609 (ensure-cui-integer cui)
610 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str)
611 srl kcuisui (make-cuisui cui sui) :lrl srl)
612 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
613 :cui cui :sui sui :saui saui :sdui sdui :scui scui
616 (defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
617 (ensure-cui-integer cui)
618 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui)
619 srl cui cui :lrl srl :limit limit
620 :filter (when english-only "LAT='ENG'"))
621 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
622 :cui cui :sui sui :saui saui :sdui sdui :scui scui
625 (defun find-uso-aui (aui &key (srl *current-srl*))
626 (ensure-sui-integer aui)
627 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat
628 str) srl aui aui :lrl srl :single t)
629 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
630 :sui sui :saui saui :sdui sdui :scui scui :lat lat
633 (defun find-uhier-cui (cui &key (srl *current-srl*))
634 (ensure-cui-integer cui)
635 (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
636 srl cui cui :lrl ksrl)
637 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
638 :cxn (ensure-integer cxn)
639 :paui (ensure-integer paui)
640 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
642 (defun find-uhier-all (&key (srl *current-srl*))
643 (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
644 srl nil nil :lrl ksrl)
645 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
646 :cxn (ensure-integer cxn)
647 :paui (ensure-integer paui)
648 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
650 (defun find-usat-ui (cui &key lui sui (srl *current-srl*))
651 (ensure-cui-integer cui)
652 (ensure-lui-integer lui)
653 (ensure-sui-integer sui)
654 (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE "))
656 (sui (string-append ls "KCUISUI='"
657 (integer-string (make-cuisui cui sui) 14)
659 (lui (string-append ls "KCUILUI='"
660 (integer-string (make-cuilui cui lui) 14)
662 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
663 "' and lui='0' and sui='0'")))
665 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
666 (loop for tuple in (mutex-sql-query ls) collect
667 (destructuring-bind (code atn sab atv) tuple
668 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
670 (defun find-usty-tui (tui)
672 (ensure-tui-integer tui)
673 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
674 (make-instance 'usty :tui tui :sty sty)))
676 (defun find-usty-sty (sty)
677 "Find usty for a sty"
678 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
679 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
681 (defun find-usty-all ()
682 "Return list of usty's for all semantic types"
683 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
684 (find-usty-tui tui)))
686 (defun find-usab-all ()
687 "Return all usab objects"
688 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
689 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
690 cenc curver sabin ssn scit) nil nil nil)
691 (make-instance 'usab :vcui (ensure-integer vcui)
692 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
693 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
694 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
695 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
696 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
697 :curver curver :sabin sabin :ssn ssn :scit scit)))
699 (defun find-usab-by-key (key-name key)
700 "Find usab for a key"
701 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
702 vend imeta rmeta slc scc srl tfr cfr cxty
703 ttyl atnl lat cenc curver sabin
705 nil key-name key :single t)
706 (make-instance 'usab :vcui (ensure-integer vcui)
707 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
708 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
709 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
710 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
711 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
712 :curver curver :sabin sabin
713 :ssn ssn :scit scit)))
715 (defun find-usab-rsab (rsab)
717 (find-usab-by-key 'rsab rsab))
719 (defun find-usab-vsab (vsab)
721 (find-usab-by-key 'vsab vsab))
723 (defun find-cui-max ()
724 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
726 (defun find-umap-cui (cui)
727 (ensure-cui-integer cui)
728 (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr
729 fromtype fromrule fromres rel rela toid tosid
730 toexpr totype torule tores maprule maptype
733 (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid
734 :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid
735 :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres
736 :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype
737 :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn
738 :mapatv mapatv :cvf cvf)))
740 (defun find-usmap-cui (cui)
741 (ensure-cui-integer cui)
742 (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf)
744 (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab
745 :fromexpr fromexpr :fromtype fromtype
746 :rel rel :rela rela :toexpr toexpr :totype totype
749 ;;;; Cross table find functions
751 (defun find-ucon-tui (tui &key (srl *current-srl*))
752 "Find list of ucon for tui"
753 (ensure-tui-integer tui)
754 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
755 (find-ucon-cui (ensure-integer cui) :srl srl)))
757 (defun find-ucon-word (word &key (srl *current-srl*) (like nil))
758 "Return list of ucons that match word. Optionally, use SQL's LIKE syntax"
759 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
760 :lrl 'klrl :order '(cui asc))
761 (find-ucon-cui cui :srl srl)))
763 (defun find-uconso-word (word &key (srl *current-srl*) (like nil))
764 "Return list of uconso objects that match word. Optionally, use SQL's LIKE syntax"
765 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
766 :lrl 'klrl :order '(cui asc))
767 (find-uconso-cui cui :srl srl)))
769 (defun mrconso-query-word-cui (word sab srl like)
770 (format nil "SELECT DISTINCT c.cui FROM MRCONSO c,MRXW_ENG x WHERE x.WD ~A '~A' AND x.cui=c.cui AND ~A ~A"
772 (clsql-sys::sql-escape-quotes word)
775 (format nil " c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
777 (format nil " c.sab IN (~{'~A'~^,~})"
778 (mapcar 'clsql-sys::sql-escape-quotes sab)))
780 (error "SAB missing")))
781 (if srl (format nil "AND KCUILRL <= ~A" srl) "")))
783 (defun mrconso-query-word-sui (word sab srl like)
784 (format nil "SELECT DISTINCT c.sui FROM MRCONSO c,MRXW_ENG x WHERE x.WD ~A '~A' AND x.sui=c.sui AND ~A ~A"
786 (clsql-sys::sql-escape-quotes word)
789 (format nil " c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
791 (format nil " c.sab IN (~{'~A'~^,~})"
792 (mapcar 'clsql-sys::sql-escape-quotes sab)))
794 (error "SAB missing")))
795 (if srl (format nil "AND KCUILRL <= ~A" srl) "")))
797 (defun find-uconso-word-sab (word &key sab (srl *current-srl*) (like nil))
798 "Return list of uconso that match word in matching SAB. Optionally, use SQL's LIKE syntax"
799 (let ((sui-query (mrconso-query-word-sui word sab srl like))
801 (dolist (sui (remove-duplicates (sort (mapcar 'car (mutex-sql-query sui-query)) #'<)))
802 (setq uconsos (nconc uconsos (find-uconso-sui-sab sui sab))))
803 (remove-duplicates uconsos :key 'cui)))
805 (defun find-ucon-word-sab (word &key sab (srl *current-srl*) (like nil))
806 "Return list of ucon that match word in matching SAB. Optionally, use SQL's LIKE syntax"
807 (let ((query (mrconso-query-word-cui word sab srl like)))
808 (loop for tuple in (mutex-sql-query query)
809 collect (make-instance 'ucon :cui (first tuple)))))
811 (defun find-ustr-word-sab (word &key sab (srl *current-srl*) (like nil))
812 "Return list of ustr that match word in matching SAB. Optionally, use SQL's LIKE syntax"
813 (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 AND ~A ~A"
815 (clsql-sys::sql-escape-quotes word)
818 (format nil " c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
820 (format nil " c.sab IN (~('~A'~^,~))"
821 (mapcar 'clsql-sys::sql-escape-quotes sab)))
823 (error "SAB missing")))
824 (if srl (format nil "AND KCUILRL <= ~D" srl) ""))))
825 (loop for tuple in (mutex-sql-query query)
826 collect (destructuring-bind (sui cui lui str lrl stt suppress cuisui) tuple
827 (make-instance 'ustr :sui sui :cui cui :lui lui :str str :lrl lrl
828 :stt stt :suppress suppress :cuisui cuisui)))))
831 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
832 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
833 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
834 :lrl 'klrl :order '(cui asc))
835 (find-ucon-cui cui :srl srl)))
837 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
838 "Return list of cui that match word, optionally use SQL's LIKE syntax"
839 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
840 :lrl 'klrl :order '(cui asc))
843 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
844 "Return list of cui that match word, optionally use SQL's LIKE syntax"
845 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
846 :lrl 'klrl :order '(cui asc))
849 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
850 "Return list of cui that match word, optionally use SQL's LIKE syntax"
851 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
852 :lrl 'klrl :order '(cui asc))
855 (defun find-ustr-word (word &key (srl *current-srl*))
856 "Return list of ustrs that match word"
857 (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
858 :order (cui asc sui asc))
859 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
861 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
862 "Return list of ustrs that match word"
863 (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl
864 :order (cui asc sui asc))
865 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
867 (defun find-uterm-word (word &key (srl *current-srl*))
868 "Return list of uterms that match word"
869 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
870 :order (cui asc lui asc))
871 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
873 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
874 "Return list of uterms that match word"
875 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
876 :order (cui asc lui asc))
877 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
879 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
880 "Return list of ucons that match non-english word"
881 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
882 :distinct t :lrl 'klrl :order '(cui asc))
883 (find-ucon-cui cui :srl srl)))
885 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
886 "Return list of ustrs that match non-english word"
887 (collect-umlisp-query (mrxw_noneng (cui sui) srl wd word :lrl klrl
888 :order (cui asc sui asc))
889 (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
893 (defun find-usrl-all ()
894 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
895 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
897 ;;; Multiword lookup and score functions
899 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
900 only-exact-if-match limit &key extra-lookup-args)
902 (dolist (word (delimited-string-to-list str #\space))
903 (setq uobjs (append uobjs (apply obj-lookup-fun word :srl srl extra-lookup-args))))
905 (funcall sort-fun str
906 (delete-duplicates uobjs :test #'= :key key))))
907 (let ((len (length sorted)))
910 (return-from find-uobj-multiword nil))
911 ((and only-exact-if-match (multiword-match str (pfstr (first sorted))))
914 (if (and (plusp limit) (> len limit))
915 (subseq sorted 0 limit)
920 (defun find-ucon-multiword (str &key (srl *current-srl*)
921 (only-exact-if-match t)
925 (find-uobj-multiword str #'find-ucon-word-sab #'sort-score-pfstr-str
926 #'cui srl only-exact-if-match limit
927 :extra-lookup-args (list :sab sab))
928 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
929 #'cui srl only-exact-if-match limit)))
931 (defun find-uconso-multiword (str &key (srl *current-srl*)
932 (only-exact-if-match t)
936 (find-uobj-multiword str #'find-uconso-word-sab #'sort-score-pfstr-str
937 #'cui srl only-exact-if-match limit
938 :extra-lookup-args (list :sab sab))
939 (find-uobj-multiword str #'find-uconso-word #'sort-score-pfstr-str
940 #'cui srl only-exact-if-match limit)))
942 (defun find-uterm-multiword (str &key (srl *current-srl*)
943 (only-exact-if-match t)
945 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
946 #'lui srl only-exact-if-match limit))
948 (defun find-ustr-multiword (str &key (srl *current-srl*)
949 (only-exact-if-match t)
953 (find-uobj-multiword str #'find-ustr-word-sab #'sort-score-ustr-str
954 #'sui srl only-exact-if-match limit
955 :extra-lookup-args (list :sab sab))
956 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
957 #'sui srl only-exact-if-match limit)))
959 (defun sort-score-pfstr-str (str uobjs)
960 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
961 (sort-score-umlsclass-str uobjs str #'pfstr))
963 (defun sort-score-ustr-str (str ustrs)
964 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
965 (sort-score-umlsclass-str ustrs str #'str))
967 (defun sort-score-umlsclass-str (objs str lookup-func)
968 "Sort a list of objects based on scoring to a string"
971 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
973 (mapcar #'car (sort scored #'> :key #'cadr))))
976 ;;; LEX SQL functions
978 (defun find-lexterm-eui (eui)
979 (ensure-eui-integer eui)
980 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
981 (make-instance 'lexterm :eui eui :wrd wrd)))
983 (defun find-lexterm-word (wrd)
984 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
985 (make-instance 'lexterm :eui (ensure-integer eui)
986 :wrd (copy-seq wrd))))
988 ;; LEX SQL Read functions
990 (defun find-labr-eui (eui)
991 (ensure-eui-integer eui)
992 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
993 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
994 :eui2 (ensure-integer eui2))))
996 (defun find-labr-bas (bas)
997 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
998 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
999 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
1001 (defun find-lagr-eui (eui)
1002 (ensure-eui-integer eui)
1003 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
1004 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
1005 :cit cit :bas bas)))
1007 (defun find-lcmp-eui (eui)
1008 (ensure-eui-integer eui)
1009 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
1010 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
1012 (defun find-lmod-eui (eui)
1013 (ensure-eui-integer eui)
1014 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
1015 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
1017 (defun find-lnom-eui (eui)
1018 (ensure-eui-integer eui)
1019 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
1020 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
1021 :eui2 (ensure-integer eui2))))
1023 (defun find-lprn-eui (eui)
1024 (ensure-eui-integer eui)
1025 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
1026 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
1027 :cas cas :pos pos :qnt qnt :fea fea)))
1029 (defun find-lprp-eui (eui)
1030 (ensure-eui-integer eui)
1031 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
1032 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
1034 (defun find-lspl-eui (eui)
1035 (ensure-eui-integer eui)
1036 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
1037 (make-instance 'lspl :eui eui :spv spv :bas bas)))
1039 (defun find-ltrm-eui (eui)
1040 (ensure-eui-integer eui)
1041 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
1042 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
1044 (defun find-ltyp-eui (eui)
1045 (ensure-eui-integer eui)
1046 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
1047 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
1049 (defun find-lwd-wrd (wrd)
1050 (make-instance 'lwd :wrd wrd
1051 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
1052 (ensure-integer eui))))
1054 ;;; Semantic Network SQL access functions
1056 (defun find-sdef-ui (ui)
1057 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
1058 nil ui ui :single t)
1059 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
1060 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
1062 (defun find-sstre1-ui (ui)
1063 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
1064 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
1065 :ui3 (ensure-integer ui3))))
1067 (defun find-sstre1-ui2 (ui2)
1068 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
1069 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
1070 :ui3 (ensure-integer ui3))))
1072 (defun find-sstr-rl (rl)
1073 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
1074 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
1076 (defun find-sstre2-sty (sty)
1077 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
1078 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
1080 (defun find-sstr-styrl (styrl)
1081 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
1082 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
1085 ;;; **************************
1087 ;;; **************************
1090 (defun make-ustats ()
1091 (with-sql-connection (conn)
1092 (ignore-errors (sql-execute "drop table USTATS" conn))
1093 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
1096 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
1097 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
1098 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
1099 (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
1100 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
1101 (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
1102 (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
1103 (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
1104 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
1105 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
1106 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
1107 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
1108 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
1109 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
1110 (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
1111 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
1112 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
1113 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
1114 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
1117 (defun insert-ustats-count (conn name table count-variable srl-control srl)
1118 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
1120 (defun find-count-table (conn table srl count-variable srl-control)
1122 ((stringp srl-control)
1124 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
1125 count-variable table srl-control srl)
1129 (caar (sql-query (format nil "select count(~a) from ~a"
1130 count-variable table )
1133 (error "Unknown srl-control")
1136 (defun insert-ustats (conn name count srl)
1137 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
1138 name count (if srl srl 3))
1141 (defun find-ustats-all (&key (srl *current-srl*))
1143 (collect-umlisp-query (ustats (name count srl) nil srl srl
1145 (make-instance 'ustats :name name
1146 :hits (ensure-integer count)
1147 :srl (ensure-integer srl)))
1148 (collect-umlisp-query (ustats (name count srl) nil nil nil
1150 (make-instance 'ustats :name name
1151 :hits (ensure-integer count)
1152 :srl (ensure-integer srl)))))
1154 (defun find-ustats-srl (srl)
1155 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
1156 (make-instance 'ustats :name name :hits (ensure-integer count))))