-;;; UMLS-Parse General
-;;; General purpose Lisp Routines for parsing UMLS files
-;;; and inserting into SQL databases
-;;;
-;;; Copyright (c) 2001 Kevin M. Rosenberg, M.D.
-;;; $Id: parse-macros.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
-
-(in-package :umlisp)
-
-
-(defmacro with-umls-file ((line filename) &body body)
-"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym)))
- `(with-open-file
- (,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-umls-line ,ustream) (read-umls-line ,ustream)))
- ((eq ,line 'eof) t)
- ,@body))))
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: parse-macros.lisp
+;;;; Purpose: Macros for UMLS file parsing
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
+;;;;
+;;;; $Id$
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2006 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.
+;;;; *************************************************************************
-(defmacro with-buffered-umls-file ((line filename) &body body)
-"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym))
- (buffer (gensym)))
- `(let ((,buffer (make-fields-buffer)))
- (with-open-file
- (,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-buffered-fields ,buffer ,ustream) (read-buffered-fields ,buffer ,ustream)))
- ((eq ,line 'eof) t)
- ,@body)))))
+(in-package #:umlisp)
+
+(defun read-umls-line (strm &optional (eof 'eof))
+ "Read a line from a UMLS stream, split into fields"
+ (let ((line (read-line strm nil eof)))
+ (if (eq line eof)
+ eof
+ (delimited-string-to-list line #\| t))))
-(defmacro with-buffered2-umls-file ((line filename) &body body)
-"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym))
- (buffer (gensym)))
- `(let ((,buffer (make-fields-buffer2)))
- (with-open-file
- (,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-buffered-fields2 ,buffer ,ustream) (read-buffered-fields2 ,buffer ,ustream)))
- ((eq ,line 'eof) t)
+(defun source-files (path)
+ (if (probe-file path)
+ (list path)
+ (sort
+ (directory (make-pathname :defaults path
+ :type :wild
+ :name (concatenate 'string (pathname-name path)
+ (aif (pathname-type path)
+ (concatenate 'string "." it)
+ ""))))
+ #'(lambda (a b)
+ (string-lessp (pathname-type a) (pathname-type b))))))
+
+(defmacro with-buffered-reading-umls-file ((line path) &body body)
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ (let ((ustream (gensym "STRM-"))
+ (buffer (gensym "BUF-"))
+ (eof (gensym "EOF-"))
+ (files (gensym "FILES-")))
+ `(let ((,eof (gensym "EOFSYM-"))
+ (,buffer (make-fields-buffer))
+ (,files (source-files ,path)))
+ (with-open-file (,ustream (first ,files) :direction :input
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (do ((,line (read-buffered-fields ,buffer ,ustream #\| ,eof)
+ (read-buffered-fields ,buffer ,ustream #\| ,eof)))
+ ((eq ,line ,eof) t)
+ (setq ,line (coerce ,line 'list))
+ (print ,line)
,@body)))))
+(defmacro with-reading-umls-file ((line path) &body body)
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ (let ((ustream (gensym "STRM-"))
+ (eof (gensym "EOF-"))
+ (files (gensym "FILES-")))
+ `(let ((,eof (gensym "EOFSYM-"))
+ (,files (source-files ,path)))
+ (unless ,files
+ (error "Can't find files for ~A~%" (namestring ,path)))
+ (with-open-file (,ustream (first ,files) :direction :input
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (do ((,line (read-umls-line ,ustream ,eof)
+ (read-umls-line ,ustream ,eof)))
+ ((eq ,line ,eof) t)
+ ,@body)))))
+
+(defmacro with-umls-ufile ((line ufile) &body body)
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ `(with-reading-umls-file (,line (ufile-pathname ,ufile))
+ ,@body))
+
+(defmacro with-umls-file ((line ufile) &body body)
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ `(with-reading-umls-file (,line (umls-pathname ,ufile))
+ ,@body))
+
+(defmacro with-buffered-umls-file ((line filename) &body body)
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ (let ((ustream (gensym "STRM-"))
+ (buffer (gensym "BUF-"))
+ (eof (gensym "EOF-")))
+ `(let ((,buffer (make-fields-buffer))
+ (,eof (gensym "EOFSYM-")))
+ (with-open-file
+ (,ustream (umls-pathname ,filename) :direction :input)
+ (do ((,line (read-buffered-fields ,buffer ,ustream #\| ,eof)
+ (read-buffered-fields ,buffer ,ustream #\| ,eof)))
+ ((eq ,line ,eof) t)
+ ,@body)))))
+
+