;;;;
;;;; Name: sql.lisp
;;;; Purpose: Low-level SQL routines data for UMLisp
-;;;; Programmer: Kevin M. Rosenberg
+;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: sql.lisp,v 1.4 2002/10/16 15:22:28 kevin Exp $
+;;;; $Id: sql.lisp,v 1.12 2003/06/10 22:30:16 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2003 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)))
+(in-package #:umlisp)
-
-(defvar *umls-sql-dsn* "KUMLS2002AC")
-(defun umls-sql-dsn ()
- *umls-sql-dsn*)
-(defun umls-sql-dsn! (dbname)
+(defvar *umls-sql-db* "KUMLS2003AA")
+(defun umls-sql-db ()
+ *umls-sql-db*)
+(defun umls-sql-db! (dbname)
(sql-disconnect-pooled)
- (setq *umls-sql-dsn* dbname))
+ (setq *umls-sql-db* dbname))
(defvar *umls-sql-user* "secret")
(defun umls-sql-user ()
(defun sql-connect ()
"Connect to UMLS database, automatically used pooled connections"
- (clsql:connect `(,(umls-sql-host) ,(umls-sql-dsn) ,(umls-sql-user) ,(umls-sql-passwd))
- :database-type *umls-sql-type* :pool t))
+ (clsql:connect
+ `(,(umls-sql-host) ,(umls-sql-db) ,(umls-sql-user) ,(umls-sql-passwd))
+ :database-type *umls-sql-type* :pool t))
(defun sql-disconnect (conn)
"Disconnect from UMLS database, but put connection back into pool"
(defun mutex-sql-query (cmd &key (types :auto))
(with-mutex-sql (conn)
(sql-query cmd conn :types types)))
-
-
-
-(defun make-usrl ()
- (with-sql-connection (conn)
- (sql-execute "drop table if exists USRL" conn)
- (sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
- (dolist (tuple (mutex-sql-query "select distinct SAB,SRL from MRSO order by SAB asc"))
- (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
- (car tuple) (ensure-integer (cadr tuple)))
- conn)))
- (find-usrl-all))
-
-(defun find-usrl-all ()
- (let ((usrls '())
- (tuples (mutex-sql-query "select SAB,SRL from USRL order by SAB desc")))
- (dolist (tuple tuples)
- (push (make-instance 'usrl :sab (nth 0 tuple)
- :srl (ensure-integer (nth 1 tuple))) usrls))
- usrls))
-
-;; already reversed by sql
-
-(defun find-usrl_freq-all ()
- (let ((freqs '()))
- (dolist (usrl (find-usrl-all))
- (let ((freq (ensure-integer
- (caar (mutex-sql-query
- (format nil "select count(*) from MRSO where SAB='~a'"
- (sab usrl)))))))
- (push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
- (sort freqs #'> :key #'usrl_freq-freq)))
-
-
-(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))))
- (umlisp::sort-score-ucon-str str (delete-duplicates ucons :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))))
- (umlisp::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)))