;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: data-structures.lisp
-;;;; Purpose: Basic data objects for UMLisp
-;;;; Author: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
-;;;;
-;;;; $Id: data-structures.lisp,v 1.7 2003/05/06 06:09:29 kevin Exp $
+;;;; Name: data-structures.lisp
+;;;; Purpose: Basic data objects 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) 2000-2011 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)
-(eval-when (:compile-toplevel)
- (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
-
;;; Paths for files
-(defvar *umls-path*
- (make-pathname :directory '(:absolute "data" "umls" "2003AA"))
+(defparameter *release* "2017AA")
+
+(defparameter *umls-path*
+ (make-pathname :directory (list :absolute "srv" "umls" *release* *release*))
"Path for base of UMLS data files")
-(defvar *meta-path*
- (merge-pathnames
- (make-pathname :directory '(:relative "META"))
- *umls-path*))
+(defparameter *meta-dir*
+ (make-pathname :directory '(:relative "META")))
+
+(defparameter *lex-dir*
+ (make-pathname :directory '(:relative "LEX")))
+
+(defparameter *net-dir*
+ (make-pathname :directory '(:relative "NET")))
+
+(defparameter *meta-path*
+ (merge-pathnames *meta-dir* *umls-path*))
-(defvar *lex-path*
- (merge-pathnames
- (make-pathname :directory '(:relative "LEX"))
- *umls-path*))
+(defparameter *lex-path*
+ (merge-pathnames *lex-dir* *umls-path*))
-(defvar *net-path*
- (merge-pathnames
- (make-pathname :directory '(:relative "NET"))
- *umls-path*))
+(defparameter *net-path*
+ (merge-pathnames *net-dir* *umls-path*))
-(defun umls-path! (p)
- (setq *umls-path* p))
+(defun set-umls-path (p)
+ (setq *umls-path* (etypecase p
+ (string (parse-namestring p))
+ (pathname p)))
+ (setq *meta-path* (merge-pathnames *meta-dir* *umls-path*))
+ (setq *lex-path* (merge-pathnames *lex-dir* *umls-path*))
+ (setq *net-path* (merge-pathnames *net-dir* *umls-path*)))
;;; Structures for parsing UMLS text files
-
-(defparameter *umls-files* nil
+
+(defparameter *umls-files* nil
"List of umls file structures. Used when parsing text files.")
-(defparameter *umls-cols* nil
+(defparameter *umls-cols* nil
"List of meta column structures. Used when parsing text files.")
+;; Special variables
+
+(defvar *has-fixnum-class* (when (ignore-errors (find-class 'fixnum)) t))
+
+(defvar *octet-sql-storage* t
+ "Used to deciding field lengths. Use nil if using UTF-8 database encoding. But, UTF-8 will cause MySQL to double the bytes used for fixed field sizes.")
+
;; Preliminary objects to replace structures
(defclass ufile ()
- ((fil :initarg :fil)
- (table :initarg :table)
- (des :initarg :des)
- (fmt :initarg :fmt)
- (cls :initarg :cls)
- (rws :initarg :rws)
- (bts :initarg :bts)
- (fields :initarg :fields)
- (ucols :initarg ucols))
- (:documentation "A UMLS File"))
+ ((subdir :initarg :subdir :accessor subdir)
+ (dir :initarg :dir :accessor dir)
+ (fil :initarg :fil :accessor fil)
+ (table :initarg :table :accessor table)
+ (des :initarg :des :accessor des)
+ (fmt :initarg :fmt :accessor fmt)
+ (cls :initarg :cls :accessor cls)
+ (rws :initarg :rws :accessor rws)
+ (bts :initarg :bts :accessor bts)
+ (fields :initarg :fields :accessor fields)
+ (ucols :initarg :ucols :accessor ucols))
+ (:default-initargs :fil nil :table nil :des nil :fmt nil :cls nil :rws nil :bts nil
+ :fields nil :ucols nil :subdir nil :dir nil)
+ (:documentation "UMLS File"))
(defclass ucol ()
- ((col :initarg :col)
- (des :initarg des)
- (ref :initarg ref)
- (min :initarg :min)
- (av :initarg :av)
- (max :initarg :max)
- (fil :initarg :fil)
- (sqltype :initarg :sqltype)
- (dty :initarg :dty :documentation "new in 2002: suggested SQL datatype")
- (parsefunc :initarg :parsefunc)
- (quotechar :initarg :quotechar)
- (datatype :initarg :datatype)
- (custom-value-func :initarg :custom-value-func))
- (:documentation "A UMLS column"))
-
-(defstruct (umls-file)
- "Record for each UMLS File"
- fil table des fmt cls rws bts fields colstructs)
-
-(defstruct (umls-col)
- "Record for each UMLS Column in each file"
- col des ref min av max fil sqltype
- dty ;; new in 2002 umls: suggested SQL datatype
- parsefunc quotechar datatype custom-value-func)
-
+ ((col :initarg :col :accessor col)
+ (des :initarg :des :accessor des)
+ (ref :initarg :ref :accessor ref)
+ (min :initarg :min :accessor cmin)
+ (av :initarg :av :accessor av)
+ (max :initarg :max :accessor cmax)
+ (fil :initarg :fil :accessor fil)
+ (sqltype :initarg :sqltype :accessor sqltype)
+ (dty :initarg :dty :accessor dty :documentation "new in 2002: suggested SQL datatype")
+ (parse-fun :initarg :parse-fun :accessor parse-fun)
+ (quote-str :initarg :quote-str :accessor quote-str)
+ (datatype :initarg :datatype :accessor datatype)
+ (custom-value-fun :initarg :custom-value-fun :accessor custom-value-fun))
+ (:default-initargs :col nil :des nil :ref nil :min nil :av nil :max nil :fil nil
+ :sqltype nil :dty nil :parse-fun nil :datatype nil
+ :custom-value-fun nil)
+ (:documentation "UMLS column"))
+
+
+(defmethod print-object ((obj ufile) s)
+ (print-unreadable-object (obj s :type t)
+ (format s "~A" (fil obj))))
+
+(defmethod print-object ((obj ucol) s)
+ (print-unreadable-object (obj s :type t)
+ (format s "~A" (col obj))))
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