1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
6 ;;;; Purpose: Low-level SQL routines data for UMLisp
7 ;;;; Programmer: Kevin M. Rosenberg
8 ;;;; Date Started: Apr 2000
10 ;;;; $Id: sql.lisp,v 1.4 2002/10/16 15:22:28 kevin Exp $
12 ;;;; This file, part of UMLisp, is
13 ;;;; Copyright (c) 2000-2002 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 ;;;; *************************************************************************
20 (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
23 (defvar *umls-sql-dsn* "KUMLS2002AC")
24 (defun umls-sql-dsn ()
26 (defun umls-sql-dsn! (dbname)
27 (sql-disconnect-pooled)
28 (setq *umls-sql-dsn* dbname))
30 (defvar *umls-sql-user* "secret")
31 (defun umls-sql-user ()
33 (defun umls-sql-user! (u)
34 (sql-disconnect-pooled)
35 (setq *umls-sql-user* u))
37 (defvar *umls-sql-passwd* "secret")
38 (defun umls-sql-passwd ()
40 (defun umls-sql-passwd! (p)
41 (sql-disconnect-pooled)
42 (setq *umls-sql-passwd* p))
44 (defvar *umls-sql-host* "localhost")
45 (defun umls-sql-host ()
47 (defun umls-sql-host! (h)
48 (sql-disconnect-pooled)
49 (setq *umls-sql-host* h))
51 (defvar *umls-sql-type* :mysql)
52 (defun umls-sql-type ()
54 (defun umls-sql-type! (h)
55 (sql-disconnect-pooled)
56 (setq *umls-sql-type* h))
59 "Connect to UMLS database, automatically used pooled connections"
60 (clsql:connect `(,(umls-sql-host) ,(umls-sql-dsn) ,(umls-sql-user) ,(umls-sql-passwd))
61 :database-type *umls-sql-type* :pool t))
63 (defun sql-disconnect (conn)
64 "Disconnect from UMLS database, but put connection back into pool"
65 (clsql:disconnect :database conn))
67 (defun sql-disconnect-pooled ()
68 (clsql:disconnect-pooled))
70 (defmacro with-sql-connection ((conn) &body body)
71 `(let ((,conn (sql-connect)))
74 (when ,conn (clsql:disconnect :database ,conn)))))
76 (defun sql (stmt conn)
77 (if (string-equal "SELECT" (subseq stmt 0 6))
79 (sql-execute stmt conn)))
81 (defun sql-query (cmd conn &key (types :auto))
82 (clsql:query cmd :database conn :types types))
84 (defun sql-execute (cmd conn)
85 (clsql:execute-command cmd :database conn))
87 (defun umls-sql (stmt)
88 (check-type stmt string)
89 (with-sql-connection (conn)
92 ;;; Pool of open connections
94 (defmacro with-mutex-sql ((conn) &body body)
95 `(let ((,conn (sql-connect)))
98 (when ,conn (sql-disconnect ,conn)))))
100 (defun mutex-sql-execute (cmd)
101 (with-mutex-sql (conn)
102 (sql-execute cmd conn)))
104 (defun mutex-sql-query (cmd &key (types :auto))
105 (with-mutex-sql (conn)
106 (sql-query cmd conn :types types)))
111 (with-sql-connection (conn)
112 (sql-execute "drop table if exists USRL" conn)
113 (sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
114 (dolist (tuple (mutex-sql-query "select distinct SAB,SRL from MRSO order by SAB asc"))
115 (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
116 (car tuple) (ensure-integer (cadr tuple)))
120 (defun find-usrl-all ()
122 (tuples (mutex-sql-query "select SAB,SRL from USRL order by SAB desc")))
123 (dolist (tuple tuples)
124 (push (make-instance 'usrl :sab (nth 0 tuple)
125 :srl (ensure-integer (nth 1 tuple))) usrls))
128 ;; already reversed by sql
130 (defun find-usrl_freq-all ()
132 (dolist (usrl (find-usrl-all))
133 (let ((freq (ensure-integer
134 (caar (mutex-sql-query
135 (format nil "select count(*) from MRSO where SAB='~a'"
137 (push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
138 (sort freqs #'> :key #'usrl_freq-freq)))
141 (defun find-ucon-normalized-multiword (str &key (srl *current-srl*))
142 "Return sorted list of ucon's that match a multiword string"
143 (let* ((words (delimited-string-to-list str #\space))
147 (let ((nws (lvg:process-terms word)))
149 (push nword nwords))))
150 (dolist (word nwords)
151 (setq ucons (append ucons (find-ucon-word word :srl srl))))
152 (umlisp::sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
153 (defun find-ustr-normalized-multiword (str &key (srl *current-srl*))
154 "Return sorted list of ustr's that match a multiword string"
155 (let* ((words (delimited-string-to-list str #\space))
159 (let ((nws (lvg:process-terms word)))
161 (push nword nwords))))
162 (dolist (word nwords)
163 (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
164 (umlisp::sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'ustr-cui))))
167 (find-normalized-matches-for-str str #'find-ustr-normalized-word #'ustr-sui))
169 (defun find-normalized-matches-for-str (str lookup-func key-func)
170 "Return list of objects that normalize match for words in string,
171 eliminate duplicates."
174 (dolist (word (delimited-string-to-list str #\space))
175 (dolist (nword (lvg:process-terms word))
176 (unless (member nword nwords :test #'string-equal)
177 (push nword nwords))))
179 (setq objs (append objs (funcall lookup-func nw))))
180 (delete-duplicates objs :key key-func :test #'eql)))