X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=parse-2002.lisp;h=9d76d2e15382265c96ae4676b81186f1bb43a0ce;hb=baef3e3eba503d04fe6d19ac3087bf9d3dbc37b9;hp=6f593ebeedef63241b5621ccd5e77a907a631f9a;hpb=f513e7b50135115f3c56b840c2cb0d1c9c8ffa82;p=umlisp.git

diff --git a/parse-2002.lisp b/parse-2002.lisp
index 6f593eb..9d76d2e 100644
--- a/parse-2002.lisp
+++ b/parse-2002.lisp
@@ -1,11 +1,24 @@
- ;;; UMLS-Parse
-;;; Lisp Routines for parsing UMLS files
-;;;   and inserting into SQL databases
-;;;
-;;; Copyright (c) 2001 Kevin M. Rosenberg, M.D.
-;;; $Id: parse-2002.lisp,v 1.2 2002/10/09 00:34:47 kevin Exp $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          parse-2002.lisp
+;;;; Purpose:       Parsing and SQL insertion routines for UMLisp which may
+;;;;                change from year to year
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: parse-2002.lisp,v 1.5 2002/11/10 22:39:15 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)))
 
 ;;; Pre-read data for custom fields into hash tables
 (defvar *parse-hash-init?* nil)
@@ -38,9 +51,9 @@
       (setq *parse-hash-init?* t))
     (with-buffered-umls-file (line "MRCON")
       (let ((cui (parse-ui (aref line 0)))
-	    (lui (parse-ui (nth 3 line)))
-	    (sui (parse-ui (nth 5 line)))
-	    (lrl (parse-integer (nth 7 line))))
+	    (lui (parse-ui (aref line 3)))
+	    (sui (parse-ui (aref line 5)))
+	    (lrl (parse-integer (aref line 7))))
 	(unless (gethash cui pfstr-hash)  ;; if haven't stored pfstr for cui
 	  (if (and (string-equal (aref line 1) "ENG") ; LAT
 		   (string-equal (aref line 2) "P") ; ts
@@ -50,9 +63,9 @@
 	(set-lrl-hash lui lrl lui-lrl-hash)
 	(set-lrl-hash (make-cuisui cui sui) lrl cuisui-lrl-hash)))
     (with-buffered-umls-file (line "MRSO")
-      (let ((sab (aref 3 line)))
+      (let ((sab (aref line 3)))
 	(unless (gethash sab sab-srl-hash)  ;; if haven't stored
-	  (setf (gethash sab sab-srl-hash) (aref 6 line))))))
+	  (setf (gethash sab sab-srl-hash) (aref line 6))))))
   
   (defun init-hash-table (&optional (force-read nil))
     (when (or force-read (not *parse-hash-init?*))
@@ -119,7 +132,7 @@
 ;;; sql-l - Big integer (64-bit)
 ;;; sql-f - Floating point
 
-(defconstant +col-datatypes+
+(defparameter +col-datatypes+
     '(("AV" sql-f) ("BTS" sql-i) ("CLS" sql-i) ("COF" sql-i) ("CUI1" sql-u)
       ("CUI2" sql-u) ("CUI" sql-u) ("CXN" sql-s) ("FR" sql-i) ("LRL" sql-s)
       ("LUI" sql-u) ("MAX" sql-s) ("MIN" sql-s) ("RANK" sql-s) ("REF" sql-s)
@@ -130,17 +143,20 @@
       ;;; LEX columns
       ("EUI" sql-u) ("EUI2" sql-u)
       ;;; Semantic net columns
-      ("UI" sql-u) ("UI2" sql-u) ("UI3" sql-u)) 
+      ("UI" sql-u) ("UI2" sql-u) ("UI3" sql-u)
+      ;; New fields for 2002AD
+      ("RCUI" sql-u) ("VCUI" sql-u) ("CFR" sql-i) ("TFR" sql-i)
+      ) 
     "SQL data types for each non-string column")
 
-(defconstant +custom-tables+
+(defparameter +custom-tables+
     nil
   #+ignore
   '(("MRCONSO" "SELECT m.CUI, m.LAT, m.TS, m.LUI, m.STT, m.SUI, m.STR, m.LRL, s.SAB, s.TTY, s.SCD, s.SRL FROM MRCON m, MRSO s WHERE m.CUI=s.CUI AND m.LUI=s.LUI AND m.SUI=s.SUI")
     ("MRCONFULL" "SELECT m.CUI, m.LAT, m.TS, m.LUI, m.STT, m.SUI, m.STR, m.LRL, s.SAB, s.TTY, s.SCD, s.SRL, t.TUI FROM MRCON m, MRSO s, MRSTY t WHERE m.CUI=s.CUI AND m.LUI=s.LUI AND m.SUI=s.SUI AND m.CUI=t.CUI AND s.CUI=t.CUI"))
   "Custom tables to create")
 
-(defconstant +custom-cols+
+(defparameter +custom-cols+
     '(("MRCON" "KPFSTR" "TEXT" 1024
 	       (lambda (x) (pfstr-hash (parse-ui (nth 0 x)))))
       ("MRCON" "KCUISUI" "BIGINT" 0
@@ -217,7 +233,7 @@
        (lambda (x) (format nil "~d" (make-cuisui (parse-ui (nth 2 x)) (parse-ui (nth 4 x)))))))
   "Custom columns to create.(filename, col, sqltype, value-func).")
 
-(defconstant +index-cols+
+(defparameter +index-cols+
     '(("CUI" "MRATX") ("CUI1" "MRCOC") ("CUI" "MRCON") ("LUI" "MRCON") 
       ("LRL" "MRCON")
       ("SUI" "MRCON") ("CUI" "MRCXT") ("CUI" "MRDEF") ("CUI" "MRLO")
@@ -242,11 +258,12 @@
       ;; Semantic NET indices
       ("UI" "SRSTRE1") ("UI2" "SRSTRE1") ("UI3" "SRSTRE1") 
       ("STY_RL" "SRDEF") ("RT" "SRDEF") ("STY_RL" "SRSTR") ("STY_RL2" "SRSTR")
-      ("RL" "SRSTR"))
+      ("RL" "SRSTR")
+      ("SRL" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
+      ("VCUI" "MRSAB") ("LAT" "MRSAB"))
   "Columns in files to index")
 
-
-(defconstant +custom-index-cols+
+(defparameter +custom-index-cols+
   nil
   #+ignore
   '(("CUI" "MRCONFULL") ("SAB" "MRCONFULL") ("TUI" "MRCONFULL"))