;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
;;;; *************************************************************************
;;;; 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 $
;;;;
;;;; 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)))


(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")
(defun umls-sql-user ()
  *umls-sql-user*)
(defun umls-sql-user! (u)
  (sql-disconnect-pooled)
  (setq *umls-sql-user* u))

(defvar *umls-sql-passwd* "secret")
(defun umls-sql-passwd ()
  *umls-sql-passwd*)
(defun umls-sql-passwd! (p)
  (sql-disconnect-pooled)
  (setq *umls-sql-passwd* p))

(defvar *umls-sql-host* "localhost")
(defun umls-sql-host ()
  *umls-sql-host*)
(defun 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)
  (sql-disconnect-pooled)
  (setq *umls-sql-type* h))

(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))

(defun sql-disconnect (conn)
  "Disconnect from UMLS database, but put connection back into pool"
  (clsql:disconnect :database conn))

(defun sql-disconnect-pooled ()
  (clsql:disconnect-pooled))

(defmacro with-sql-connection ((conn) &body body)
  `(let ((,conn (sql-connect)))
     (unwind-protect
	 (progn ,@body)
       (when ,conn (clsql:disconnect :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)
    (sql stmt conn)))

;;; Pool of open connections

(defmacro with-mutex-sql ((conn) &body body)
  `(let ((,conn (sql-connect)))
     (unwind-protect
	 (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))
  (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)))