;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: sql-classes.lisp
-;;;; Purpose: Routines for reading UMLS objects from SQL database
-;;;; Author: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
+;;;; Name: sql-classes.lisp
+;;;; Purpose: Routines for reading UMLS objects from SQL database
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
;;;;
-;;;; $Id: sql-classes.lisp,v 1.86 2003/06/24 00:27:59 kevin Exp $
+;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D.
,%%fields
,@(when %%where (list %%where))
,@(when %%where
- `((typecase ,where-value
- (fixnum
- (prefixed-fixnum-string ,where-value #\= 10))
- (number
- (concatenate 'string "=" (write-to-string ,where-value)))
- (null
- " is null")
- (t
- (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
+ `((typecase ,where-value
+ #+ignore
+ (fixnum
+ (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
+ (number
+ (concatenate 'string "='" (write-to-string ,where-value) "'"))
+ (null
+ " is null")
+ (t
+ (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
(if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
,@(when %%order (list %%order))
,@(when single (list " limit 1")))))
(if where-name
(format nil
(typecase where-value
- (number "=~D")
+ (number "='~D'")
(null " is null")
(t
(if like " like '%~A%""='~A'")))
(defmacro umlisp-query (table fields srl where-name where-value
- &key (lrl "KCUILRL") single distinct order like)
+ &key (lrl "KCUILRL") single distinct order like
+ (query-cmd 'mutex-sql-query))
"Query the UMLisp database. Return a list of umlisp objects whose name
is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
- `(mutex-sql-query
+ `(,query-cmd
(query-string ,table ,fields ,srl ,where-name ,where-value
:lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
;; only WHERE-VALUE and SRL are evaluated
(defmacro collect-umlisp-query ((table fields srl where-name where-value
&key (lrl "KCUILRL") distinct single
- order like)
- &body body)
+ order like (query-cmd 'mutex-sql-query))
+ &body body)
(let ((value (gensym))
(r (gensym)))
(if single
(tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single
:distinct ,distinct :order ,order
- :like ,like))))
+ :like ,like
+ :query-cmd ,query-cmd))))
,@(unless where-name `((declare (ignore ,value))))
(when tuple
(destructuring-bind ,fields tuple
(defun find-ucon-cui (cui &key (srl *current-srl*))
"Find ucon for a cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrcon (kpfstr kcuilrl) srl cui cui :single t)
+ (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl cui cui :single t)
(make-instance 'ucon :cui cui :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*))
"Find ucon for a cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrcon (kcuilrl) srl cui cui :single t)
+ (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
(make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
:pfstr nil)))
(defun find-pfstr-cui (cui &key (srl *current-srl*))
"Find preferred string for a cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrcon (kpfstr) srl cui cui :single t)
+ (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t)
kpfstr))
+
(defun find-ucon-lui (lui &key (srl *current-srl*))
"Find list of ucon for lui"
(ensure-lui-integer lui)
- (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui lui
+ (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui
:distinct t)
(make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(defun find-ucon-sui (sui &key (srl *current-srl*))
"Find list of ucon for sui"
(ensure-sui-integer sui)
- (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl sui sui :distinct t)
+ (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t)
(make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(ensure-cui-integer cui)
(ensure-sui-integer sui)
(when (and cui sui)
- (collect-umlisp-query (mrcon (kpfstr kcuilrl) srl kcuisui
+ (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl kcuisui
(make-cuisui cui sui))
(make-instance 'ucon :cui cui
:pfstr kpfstr
(defun find-ucon-str (str &key (srl *current-srl*))
"Find ucon that are exact match for str"
- (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl str str :distinct t)
+ (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t)
(make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(with-sql-connection (db)
(clsql:map-query
'list
- #'(lambda (cui pfstr cuilrl)
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer cuilrl)))
- (query-string mrcon (cui kpfstr kcuilrl) srl nil nil
+ #'(lambda (tuple)
+ (destructuring-bind (cui pfstr cuilrl) tuple
+ (make-instance 'ucon :cui (ensure-integer cui)
+ :pfstr pfstr
+ :lrl (ensure-integer cuilrl))))
+ (query-string mrconso (cui kpfstr kcuilrl) srl nil nil
:order (cui asc) :distinct t)
:database db)))
(defun find-ucon-all2 (&key (srl *current-srl*))
"Return list of all ucon's"
- (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
:distinct t)
(make-instance 'ucon :cui (ensure-integer cui)
:pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
+(defun find-cui-ucon-all (&key (srl *current-srl*))
+ "Return list of CUIs for all ucons"
+ (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
+ :distinct t)
+ cui))
+
(defun map-ucon-all (fn &key (srl *current-srl*))
"Map a function over all ucon's"
(with-sql-connection (db)
(clsql:map-query
nil
- #'(lambda (cui pfstr cuilrl)
- (funcall fn
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer cuilrl))))
- (query-string mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ #'(lambda (tuple)
+ (destructuring-bind (cui pfstr cuilrl) tuple
+ (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
+ :pfstr pfstr
+ :lrl (ensure-integer cuilrl)))))
+ (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
:distinct t)
:database db)))
:cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl
:mg mg :pfstr2 kpfstr2)))
+(defun find-cui2-urel-cui (cui &key (srl *current-srl*))
+ "Return a list of urel for cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrrel (cui2) srl cui1
+ cui :lrl "KSRL")
+ cui2))
+
(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
"Return a list of urel for cui2"
(ensure-cui-integer cui2)
(collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1
cui :lrl klrl :order (cof asc))
(setq cui2 (ensure-integer cui2))
- (when (zerop cui2) (setq cui2 nil))
+ (when (eql 0 cui2) (setq cui2 nil))
(make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2)
:soc soc :cot cot :cof (ensure-integer cof) :coa coa
:pfstr2 kpfstr2)))
(make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un
:sui (ensure-integer sui) :sna sna :soui soui)))
-(defun find-uatx-cui (cui &key (srl *current-srl*))
- "Return a list of uatx for cui"
- (ensure-cui-integer cui)
- (collect-umlisp-query (mratx (sab rel atx) srl cui cui :lrl ksrl)
- (make-instance 'uatx :sab sab :rel rel :atx atx)))
-
(defun find-uterm-cui (cui &key (srl *current-srl*))
"Return a list of uterm for cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrcon (lui lat ts kluilrl) srl cui cui
+ (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
:lrl kluilrl :distinct t)
(make-instance 'uterm :lui (ensure-integer lui) :cui cui
:lat lat :ts ts :lrl (ensure-integer kluilrl))))
(defun find-uterm-lui (lui &key (srl *current-srl*))
"Return a list of uterm for lui"
(ensure-lui-integer lui)
- (collect-umlisp-query (mrcon (cui lat ts kluilrl) srl lui lui
+ (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
:lrl kluilrl :distinct t)
(make-instance 'uterm :cui (ensure-integer cui) :lui lui
:lat lat :ts ts :lrl (ensure-integer kluilrl))))
"Return single uterm for cui/lui"
(ensure-cui-integer cui)
(ensure-lui-integer lui)
- (collect-umlisp-query (mrcon (lat ts kluilrl) srl kcuilui
+ (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
(make-cuilui cui lui)
:lrl kluilrl :single t)
(make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
"Return a list of ustr for cui/lui"
(ensure-cui-integer cui)
(ensure-lui-integer lui)
- (collect-umlisp-query (mrcon (sui stt str lrl) srl kcuilui
- (make-cuilui cui lui) :lrl lrl)
- (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
+ (collect-umlisp-query (mrconso (sui stt str ksuilrl) srl kcuilui
+ (make-cuilui cui lui) :lrl ksuilrl)
+ (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
:cuisui (make-cuisui cui sui) :stt stt :str str
- :lrl (ensure-integer lrl))))
+ :lrl (ensure-integer ksuilrl))))
(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
"Return the single ustr for cuisui"
(ensure-cui-integer cui)
(ensure-sui-integer sui)
- (collect-umlisp-query (mrcon (lui stt str lrl) srl kcuisui
- (make-cuisui cui sui) :lrl lrl :single t)
+ (collect-umlisp-query (mrconso (lui stt str ksuilrl) srl kcuisui
+ (make-cuisui cui sui) :lrl lsuilrl :single t)
(make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
:lui (ensure-integer lui) :stt stt :str str
- :lrl (ensure-integer lrl))))
+ :lrl (ensure-integer ksuilrl))))
(defun find-ustr-sui (sui &key (srl *current-srl*))
"Return the list of ustr for sui"
(ensure-sui-integer sui)
- (collect-umlisp-query (mrcon (cui lui stt str lrl) srl sui sui
- :lrl lrl)
+ (collect-umlisp-query (mrconso (cui lui stt str ksuilrl) srl sui sui
+ :lrl ksuilrl)
(make-instance 'ustr :sui sui :cui cui :stt stt :str str
:cuisui (make-cuisui (ensure-integer cui) sui)
- :lui (ensure-integer lui) :lrl (ensure-integer lrl))))
+ :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
(defun find-ustr-sab (sab &key (srl *current-srl*))
"Return the list of ustr for sab"
- (collect-umlisp-query (mrso (kcuisui) srl sab sab :lrl srl)
+ (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
(let ((cuisui (ensure-integer kcuisui)))
(apply #'find-ustr-cuisui
(append
(with-sql-connection (db)
(clsql:map-query
'list
- #'(lambda (cui lui sui stt lrl pfstr)
- (make-instance 'ustr :cui (ensure-integer cui)
- :lui (ensure-integer lui) :sui (ensure-integer sui)
- :stt stt :str pfstr
- :cuisui (make-cuisui (ensure-integer cui)
- (ensure-integer sui))
- :lrl (ensure-integer lrl)))
- (query-string mrcon (cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl
+ #'(lambda (tuple)
+ (destructuring-bind (cui lui sui stt ksuilrl pfstr) tuple
+ (make-instance 'ustr :cui (ensure-integer cui)
+ :lui (ensure-integer lui) :sui (ensure-integer sui)
+ :stt stt :str pfstr
+ :cuisui (make-cuisui (ensure-integer cui)
+ (ensure-integer sui))
+ :lrl (ensure-integer ksuilrl))))
+ (query-string mrconso (cui lui sui stt ksuilrl kpfstr) srl nil nil :lrl ksuilrl
:distinct t
:order (sui asc))
:database db)))
(defun find-string-sui (sui &key (srl *current-srl*))
"Return the string associated with sui"
(ensure-sui-integer sui)
- (collect-umlisp-query (mrcon (str) srl sui sui :lrl lrl :single t)
+ (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
str))
(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
(ensure-sui-integer sui)
(ensure-cui-integer cui)
- (collect-umlisp-query (mrso (sab code srl tty) srl kcuisui
+ (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui
(make-cuisui cui sui) :lrl srl)
- (make-instance 'uso :sab sab :code code :srl srl :tty tty)))
+ (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
+ :cui cui :sui sui :saui saui :sdui sdui :scui scui)))
+
+(defun find-uso-aui (aui &key (srl *current-srl*))
+ (ensure-sui-integer aui)
+ (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui) srl aui
+ aui :lrl srl :single t)
+ (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
+ :sui sui :saui saui :sdui sdui :scui scui)))
(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
(ensure-cui-integer cui)
(ensure-sui-integer sui)
(let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
(cond
- (sui (string-append ls "KCUISUI="
- (integer-string (make-cuisui cui sui) 14)))
- (lui (string-append ls "KCUILUI="
+ (sui (string-append ls "KCUISUI='"
+ (integer-string (make-cuisui cui sui) 14)
+ "'"))
+ (lui (string-append ls "KCUILUI='"
(integer-string (make-cuilui cui lui) 14)
- " and sui=0"))
- (t (string-append ls "cui=" (prefixed-fixnum-string cui nil 7)
- " and lui=0 and sui=0")))
+ "' and sui='0'"))
+ (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
+ "' and lui='0' and sui='0'")))
(when srl
(string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
(loop for tuple in (mutex-sql-query ls) collect
(defun find-usab-all ()
"Find usab for a key"
- (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta
+ (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
rmeta slc scc srl tfr cfr cxty ttyl atnl lat
cenc curver sabin) nil nil nil)
(make-instance 'usab :vcui (ensure-integer vcui)
:rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
- :sf sf :sver sver :mstart mstart :mend mend :imeta imeta
+ :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
:rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
:tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
:cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
(defun find-usab-by-key (key-name key)
"Find usab for a key"
- (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver mstart
- mend imeta rmeta slc scc srl tfr cfr cxty
+ (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
+ vend imeta rmeta slc scc srl tfr cfr cxty
ttyl atnl lat cenc curver sabin)
nil key-name key :single t)
(make-instance 'usab :vcui (ensure-integer vcui)
:rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
- :sf sf :sver sver :mstart mstart :mend mend :imeta imeta
+ :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
:rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
:tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
:cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
:lrl 'klrl :order '(cui asc))
(find-ucon-cui cui :srl srl)))
+(defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
+ "Return list of cui that match word, optionally use SQL's LIKE syntax"
+ (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
+ :lrl 'klrl :order '(cui asc))
+ cui))
+
+(defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
+ "Return list of cui that match word, optionally use SQL's LIKE syntax"
+ (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
+ :lrl 'klrl :order '(cui asc))
+ lui))
+
+(defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
+ "Return list of cui that match word, optionally use SQL's LIKE syntax"
+ (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
+ :lrl 'klrl :order '(cui asc))
+ sui))
+
(defun find-ustr-word (word &key (srl *current-srl*))
"Return list of ustrs that match word"
(collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
(defun find-uterm-word (word &key (srl *current-srl*))
"Return list of uterms that match word"
- (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
- :order (cui asc sui asc))
- (find-uterm-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
+ (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
+ :order (cui asc lui asc))
+ (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
(defun find-uterm-normalized-word (word &key (srl *current-srl*))
"Return list of uterms that match word"
- (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl
- :order (cui asc sui asc))
- (find-uterm-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
+ (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
+ :order (cui asc lui asc))
+ (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
(defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
"Return list of ucons that match non-english word"
;;; Multiword lookup and score functions
-(defun find-ucon-multiword (str &key (srl *current-srl*))
- "Return sorted list of ucon's that match a multiword string"
- (let* ((words (delimited-string-to-list str #\space))
- (ucons '()))
- (dolist (word words)
- (setq ucons (append ucons (find-ucon-word word :srl srl))))
- (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
-
-(defun find-ustr-multiword (str &key (srl *current-srl*))
- "Return sorted list of ustr's that match a multiword string"
- (let* ((words (delimited-string-to-list str #\space))
- (ustrs '()))
- (dolist (word words)
- (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
- (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'cui))))
+(defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
+ only-exact-if-match)
+ (let ((uobjs '()))
+ (dolist (word (delimited-string-to-list str #\space))
+ (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl))))
+ (let ((sorted
+ (funcall sort-fun str
+ (delete-duplicates uobjs :test #'= :key key))))
+ (if (and (plusp (length sorted))
+ only-exact-if-match
+ (multiword-match str (pfstr (first sorted))))
+ (first sorted)
+ sorted))))
+
+(defun find-ucon-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
+ #'cui srl only-exact-if-match))
+
+(defun find-uterm-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
+ #'lui srl only-exact-if-match))
+
+(defun find-ustr-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
+ #'sui srl only-exact-if-match))
-(defun sort-score-ucon-str (str ucons)
+(defun sort-score-pfstr-str (str uobjs)
"Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
- (sort-score-umlsclass-str ucons str #'pfstr))
+ (sort-score-umlsclass-str uobjs str #'pfstr))
(defun sort-score-ustr-str (str ustrs)
"Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
scored))
(mapcar #'car (sort scored #'> :key #'cadr))))
-(defun score-multiword-match (s1 s2)
- "Score a match between two strings with s1 being reference string"
- (let* ((word-list-1 (delimited-string-to-list s1 #\space))
- (word-list-2 (delimited-string-to-list s2 #\space))
- (n1 (length word-list-1))
- (n2 (length word-list-2))
- (unmatched n1)
- (score 0)
- (nlong 0)
- (nshort 0)
- short-list long-list)
- (declare (fixnum n1 n2 nshort nlong score unmatched))
- (if (> n1 n2)
- (progn
- (setq nlong n1)
- (setq nshort n2)
- (setq long-list word-list-1)
- (setq short-list word-list-2))
- (progn
- (setq nlong n2)
- (setq nshort n1)
- (setq long-list word-list-2)
- (setq short-list word-list-1)))
- (decf score (- nlong nshort)) ;; reduce score for extra words
- (dotimes (iword nshort)
- (declare (fixnum iword))
- (kmrcl:aif (position (nth iword short-list) long-list :test #'string-equal)
- (progn
- (incf score (- 10 (abs (- kmrcl::it iword))))
- (decf unmatched))))
- (decf score (* 2 unmatched))
- score))
-
;;; LEX SQL functions
(make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
(defun find-lwd-wrd (wrd)
- (make-instance 'lwd :wrd
+ (make-instance 'lwd :wrd wrd
:euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
- (ensure-integer eui))))
+ (ensure-integer eui))))
;;; Semantic Network SQL access functions
(defun find-sstr-styrl (styrl)
(collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
(make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
+
+
+;;; **************************
+;;; Local Classes
+;;; **************************
+
+
+(defun make-ustats ()
+ (with-sql-connection (conn)
+ (ignore-errors (sql-execute "drop table USTATS" conn))
+ (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
+
+ (dotimes (srl 4)
+ (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
+ (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
+ (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
+ (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
+ (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
+ (insert-ustats-count conn "Context Count" "MRCXT" "*" "KSRL" srl)
+ (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
+ (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
+ #+ignore
+ (insert-ustats-count conn "Locator Count" "MRLO" "*" "KLRL" srl)
+ (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
+ (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
+ (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
+ (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
+ (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
+ (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
+ (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
+ (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
+ (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
+ (find-ustats-all))
+
+(defun insert-ustats-count (conn name table count-variable srl-control srl)
+ (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
+
+(defun find-count-table (conn table srl count-variable srl-control)
+ (cond
+ ((stringp srl-control)
+ (ensure-integer
+ (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
+ count-variable table srl-control srl)
+ conn))))
+ ((null srl-control)
+ (ensure-integer
+ (caar (sql-query (format nil "select count(~a) from ~a"
+ count-variable table )
+ conn))))
+ (t
+ (error "Unknown srl-control")
+ 0)))
+
+(defun insert-ustats (conn name count srl)
+ (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
+ name count (if srl srl 3))
+ conn))
+
+(defun find-ustats-all (&key (srl *current-srl*))
+ (if srl
+ (collect-umlisp-query (ustats (name count srl) nil srl srl
+ :order (name asc))
+ (make-instance 'ustats :name name
+ :hits (ensure-integer count)
+ :srl (ensure-integer srl)))
+ (collect-umlisp-query (ustats (name count srl) nil nil nil
+ :order (name asc))
+ (make-instance 'ustats :name name
+ :hits (ensure-integer count)
+ :srl (ensure-integer srl)))))
+
+(defun find-ustats-srl (srl)
+ (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
+ (make-instance 'ustats :name name :hits (ensure-integer count))))
+
+
+
+(defun find-bsab-sab (sab)
+ (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t)
+ (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
+
+(defun find-bsab-all ()
+ (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc))
+ (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
+
+(defun find-btty-tty (tty)
+ (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t)
+ (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
+
+(defun find-btty-all ()
+ (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc))
+ (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
+
+(defun find-brel-rel (rel)
+ (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel)
+ (make-instance 'brel :sab sab :sl sl :rel rel :rela rela
+ :hits (ensure-integer count))))