X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=sql.lisp;h=27f6c4d3926eb1af43e6c380ef84419bb04b34b0;hp=94a7243e9da75dbbeeb019516f1405b4f1008de9;hb=HEAD;hpb=77d1409857f947a3fd9e8a07d19ff937952a25b5

diff --git a/sql.lisp b/sql.lisp
index 94a7243..97874c7 100644
--- a/sql.lisp
+++ b/sql.lisp
@@ -2,63 +2,88 @@
 ;;;; *************************************************************************
 ;;;; 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"
@@ -70,20 +95,20 @@
 (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)
@@ -94,87 +119,13 @@
 (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)))