-;;; $Id: sql-classes.lisp,v 1.2 2002/10/09 00:34:47 kevin Exp $
-
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: sql-classes.lisp
+;;;; Purpose: Routines for reading UMLS objects from SQL database
+;;;; Programmer: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
+;;;;
+;;;; $Id: sql-classes.lisp,v 1.5 2002/10/14 15:25:11 kevin Exp $
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;;
+;;;; UMLisp users are granted the rights to distribute and use this software
+;;;; as governed by the terms of the GNU General Public License.
+;;;; *************************************************************************
+
(in-package :umlisp)
+(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
-(declaim (optimize (speed 3) (safety 1)))
(defvar *current-srl* nil)
(defun current-srl ()
;;; Lookup functions for uterms,ustr in ucons
(defun find-uterm-in-ucon (ucon lui)
- (find lui (s#term ucon) :key #'uterm-lui :test 'equal))
+ (find lui (s#term ucon) :key #'lui :test 'equal))
(defun find-ustr-in-uterm (uterm sui)
- (find sui (s#str uterm) :key #'ustr-sui :test 'equal))
+ (find sui (s#str uterm) :key #'sui :test 'equal))
(defun find-ustr-in-ucon (ucon sui)
(let ((found-ustr nil))
(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
(mapcar
- #'(lambda (cui) (find-ucon-cui cui :key srl))
+ #'(lambda (cui) (find-ucon-cui cui :srl srl))
(remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))))
(defun find-ucoc-cui (cui &key (srl *current-srl*))
(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
"List of ucon with co-occurance cui2"
(mapcar
- #'(lambda (cui) (find-ucon-cui cui :key srl))
+ #'(lambda (cui) (find-ucon-cui cui :srl srl))
(remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
(defun find-ulo-cui (cui &key (srl *current-srl*))
ulos))
(nreverse ulos)))
+(defgeneric suistr (lo))
(defmethod suistr ((lo ulo))
"Return the string for a ulo object"
(find-string-sui (sui lo)))
(push (find-usty-tui (nth 0 tuple)) ustys))
(nreverse ustys)))
-(defun find-usty_freq-all ()
- (let ((usty_freqs '()))
- (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
- (let* ((tui (car tuple))
- (freq (ensure-integer
- (caar (mutex-sql-query
- (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
- (push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
- (sort usty_freqs #'> :key #'usty_freq-freq)))
-
-
-
(defun find-cui-max ()
(let ((cui (caar (mutex-sql-query "select max(CUI) from MRCON"))))
(setq ucons (append ucons (find-ucon-word word :srl srl))))
(sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
-(defun find-ucon-normalized-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 '())
- (nwords '()))
- (dolist (word words)
- (let ((nws (lvg:process-terms word)))
- (dolist (nword nws)
- (push nword nwords))))
- (dolist (word nwords)
- (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))
(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-ustr-normalized-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 '())
- (nwords '()))
- (dolist (word words)
- (let ((nws (lvg:process-terms word)))
- (dolist (nword nws)
- (push nword nwords))))
- (dolist (word nwords)
- (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
- (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'ustr-cui))))
-
-(defun a (str)
- (find-normalized-matches-for-str str #'find-ustr-normalized-word #'ustr-sui))
-
-(defun find-normalized-matches-for-str (str lookup-func key-func)
- "Return list of objects that normalize match for words in string,
-eliminate duplicates."
- (let ((objs '())
- (nwords '()))
- (dolist (word (delimited-string-to-list str #\space))
- (dolist (nword (lvg:process-terms word))
- (unless (member nword nwords :test #'string-equal)
- (push nword nwords))))
- (dolist (nw nwords)
- (setq objs (append objs (funcall lookup-func nw))))
- (delete-duplicates objs :key key-func :test #'eql)))
(defun sort-score-ucon-str (str ucons)
"Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"