;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: sql.lisp
-;;;; Purpose: Low-level SQL routines data for UMLisp
-;;;; Programmer: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
-;;;;
-;;;; $Id: sql.lisp,v 1.4 2002/10/16 15:22:28 kevin Exp $
+;;;; Name: sql.lisp
+;;;; Purpose: Low-level SQL routines data for UMLisp
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2012 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)))
-
-
-(defvar *umls-sql-dsn* "KUMLS2002AC")
-(defun umls-sql-dsn ()
- *umls-sql-dsn*)
-(defun umls-sql-dsn! (dbname)
- (sql-disconnect-pooled)
- (setq *umls-sql-dsn* dbname))
-
-(defvar *umls-sql-user* "secret")
+(in-package #:umlisp)
+
+(defparameter +umls-sql-map+
+ '((:2004aa . "KUMLS2004AA")
+ (:2006ac . "KUMLS2006AC")
+ (:2006ad . "MTS2006AD")
+ (:2009ab . "MTS2009AB")
+ (:2010aa . "MTS2010AA")
+ (:2012ab_all . "MTS2012AB_ALL")
+ (:2020ab_all . "MTS2020AB_ALL")))
+(defvar +default-umls-db+ "MTS2020AB_ALL")
+
+(defun lookup-db-name (db)
+ (cdr (assoc (ensure-keyword db) +umls-sql-map+)))
+
+(defvar *umls-sql-db* +default-umls-db+)
+(defun umls-sql-db ()
+ *umls-sql-db*)
+
+(defun set-umls-sql-db (db)
+ (etypecase db
+ (string
+ (setq *umls-sql-db* db))
+ (keyword
+ (setq *umls-sql-db* (lookup-db-name db)))))
+
+(defvar *umls-sql-user* "mts")
(defun umls-sql-user ()
*umls-sql-user*)
-(defun umls-sql-user! (u)
+(defun set-umls-sql-user (u)
(sql-disconnect-pooled)
(setq *umls-sql-user* u))
-(defvar *umls-sql-passwd* "secret")
+(defvar *umls-sql-passwd* "_mts")
(defun umls-sql-passwd ()
*umls-sql-passwd*)
-(defun umls-sql-passwd! (p)
+(defun set-umls-sql-passwd (p)
(sql-disconnect-pooled)
(setq *umls-sql-passwd* p))
-(defvar *umls-sql-host* "localhost")
+(defvar *umls-sql-host* "mysql.med-info.com")
(defun umls-sql-host ()
*umls-sql-host*)
-(defun umls-sql-host! (h)
+(defun set-umls-sql-host (h)
(sql-disconnect-pooled)
(setq *umls-sql-host* h))
(defvar *umls-sql-type* :mysql)
(defun umls-sql-type ()
*umls-sql-type*)
-(defun umls-sql-type! (h)
+(defun set-umls-sql-type (h)
(sql-disconnect-pooled)
(setq *umls-sql-type* h))
+(defun umls-connection-spec ()
+ (if (eql *umls-sql-type* :mysql)
+ (list *umls-sql-host* *umls-sql-db*
+ *umls-sql-user* *umls-sql-passwd*
+ nil '((:local-infile . 1))
+ )
+ (list *umls-sql-host* *umls-sql-db*
+ *umls-sql-user* *umls-sql-passwd*)))
+
(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))
+ (let ((db (clsql:connect (umls-connection-spec)
+ :database-type *umls-sql-type*
+ :encoding :utf-8
+ :pool t)))
+ db))
(defun sql-disconnect (conn)
"Disconnect from UMLS database, but put connection back into pool"
(defmacro with-sql-connection ((conn) &body body)
`(let ((,conn (sql-connect)))
(unwind-protect
- (progn ,@body)
+ (progn ,@body)
(when ,conn (clsql:disconnect :database ,conn)))))
+(defun sql-query (cmd conn &key (result-types :auto))
+ (clsql:query cmd :database conn :result-types result-types :field-names nil))
+
+(defun sql-execute (cmd conn)
+ (clsql:execute-command cmd :database conn))
+
(defun sql (stmt conn)
(if (string-equal "SELECT" (subseq stmt 0 6))
(sql-query stmt conn)
(sql-execute stmt conn)))
-(defun sql-query (cmd conn &key (types :auto))
- (clsql:query cmd :database conn :types types))
-
-(defun sql-execute (cmd conn)
- (clsql:execute-command cmd :database conn))
-
(defun umls-sql (stmt)
(check-type stmt string)
(with-sql-connection (conn)
(defmacro with-mutex-sql ((conn) &body body)
`(let ((,conn (sql-connect)))
(unwind-protect
- (progn ,@body)
+ (progn ,@body)
(when ,conn (sql-disconnect ,conn)))))
(defun mutex-sql-execute (cmd)
(with-mutex-sql (conn)
(sql-execute cmd conn)))
-(defun mutex-sql-query (cmd &key (types :auto))
+(defun mutex-sql-query (cmd &key (result-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)))
+ (sql-query cmd conn :result-types result-types)))
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