From bfdd5c9d3d66970759fcdbee5a51da2ca93ddf06 Mon Sep 17 00:00:00 2001
From: "Kevin M. Rosenberg" <kevin@rosenberg.net>
Date: Wed, 9 Oct 2002 23:04:48 +0000
Subject: [PATCH] r2960: *** empty log message ***

---
 classes.lisp         | 92 +++++++++++++++++++++++++-------------------
 composite.lisp       | 27 ++++++++++---
 data-structures.lisp | 19 ++++++++-
 package.lisp         | 45 ++++++++++++++++++++--
 parse-2002.lisp      | 25 +++++++++---
 parse-common.lisp    | 24 +++++++++---
 parse-macros.lisp    | 24 +++++++++---
 sql-classes.lisp     | 64 +++++++++---------------------
 sql.lisp             | 23 ++++++++---
 umlisp.asd           | 19 ++++++++-
 utils.lisp           | 26 +++++++++----
 11 files changed, 262 insertions(+), 126 deletions(-)

diff --git a/classes.lisp b/classes.lisp
index b64c40f..9bbd171 100644
--- a/classes.lisp
+++ b/classes.lisp
@@ -1,14 +1,28 @@
-;;; $Id: classes.lisp,v 1.2 2002/10/09 02:23:22 kevin Exp $
-;;;
-;;; UMLS object defintions and printing routines
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          classes.lisp
+;;;; Purpose:       Class defintions for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: classes.lisp,v 1.3 2002/10/09 23:03:41 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)))
+(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
 
 (defclass umlsclass ()
   ()
-  (:metaclass kmrcl::ml-class)
-  (:documentation "Parent class of all UMLS objects"))
+  (:metaclass kmrcl:ml-class)
+  (:documentation "Parent class of all UMLS objects. It is based on the KMRCL:ML-CLASS metaclass that provides object printing functions."))
 
 
 (defmethod print-object ((obj umlsclass) (s stream))
@@ -20,14 +34,12 @@
 	      (funcall (funcall (kmrcl::obj-data-value-func fmt) obj) obj))))))
 
 
-
-  
 (defclass urank (umlsclass)
   ((rank :type fixnum :initarg :rank :reader rank)
    (sab :type string :initarg :sab :reader sab)
    (tty :type string :initarg :tty :reader tty)
    (supres :type string :initarg :supres :reader supres))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :rank nil :sab nil :tty nil :supres nil)
   (:title "Rank")
   (:fields (rank :fixnum) (sab :string) (tty :string) (supres :string)))
@@ -35,7 +47,7 @@
 (defclass udef (umlsclass)
   ((def :type string :initarg :def :reader def)
    (sab :type string :initarg :sab :reader sab))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :def nil :sab nil)
   (:title "Definition")
   (:ref-fields (sab find-bsab-sab))
@@ -46,7 +58,7 @@
    (code :type string :initarg :code :reader code)
    (atn :type string :initarg :atn :reader atn)
    (atv :type string :initarg :atv :reader atv))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :sab nil :code nil :atn nil :atv nil)
   (:title "Simple Attribute")
   (:ref-fields (sab find-bsab-sab))
@@ -57,7 +69,7 @@
    (code :type string :initarg :code :reader code)
    (tty :type string :initarg :tty :reader tty)
    (srl :type fixnum :initarg :srl :reader srl))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :sab nil :code nil :tty nil :srl nil)
   (:title "Source")
   (:ref-fields (sab find-bsab-sab) (tty find-btty-tty))
@@ -74,7 +86,7 @@
    (hcd :type string :initarg :hcd :reader hcd)
    (rela :type string :initarg :rela :reader rela)
    (xc :type string  :initarg :xc :reader xc))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :sab nil :code nil :rnk nil :cxn nil :cxl nil :cxs nil
 		     :cui2 nil :hcd nil :rela nil :xc nil)
   (:title "Context")
@@ -95,7 +107,7 @@
    (s#sat :reader s#sat)
    (s#so :reader s#so)
    (s#cxt :reader s#cxt))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs 
    :sui nil :cui nil :lui nil :cuisui nil :str nil :lrl nil :stt nil)
   (:title "String")
@@ -110,7 +122,7 @@
    (sui :type fixnum :initarg :sui :reader sui)
    (sna :type string :initarg :sna :reader sna)
    (soui :type string :initarg :soui :reader soui))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :isn nil :fr nil :un nil :sui nil :sna nil :soui nil)
   (:title "Locator")
   (:fields (isn :string) (fr :fixnum) (un :string) (sna :string)
@@ -124,7 +136,7 @@
    (lrl :type fixnum :initarg :lrl :reader lrl)
    (s#str :reader s#str)
    (s#sat :reader s#sat))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :lui nil :cui nil :lat nil :ts nil :lrl nil)
   (:title "Term")
   (:subobjects-lists (s#sat usat) (s#str ustr))
@@ -134,7 +146,7 @@
 (defclass usty (umlsclass)
   ((tui :type fixnum :initarg :tui :reader tui)
    (sty :type string :initarg :sty :reader sty))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :tui nil :sty nil)
   (:title "Semantic Type")
   (:ref-fields (tui find-ucon-tui (("subobjects" "no"))))
@@ -149,7 +161,7 @@
    (sab :type string :initarg :sab :reader sab)
    (sl :type string  :initarg :sl :reader sl)
    (mg :type string  :initarg :mg :reader mg))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs 
    :rel nil :cui1 nil :cui2 nil :pfstr2 nil :rela nil :sab nil :sl nil :mg nil)
   (:title "Relationship")
@@ -165,7 +177,7 @@
    (cot :type string :initarg :cot :reader cot)
    (cof :type fixnum :initarg :cof :reader cof)
    (coa :type string :initarg :coa :reader coa))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs 
    :cui1 nil :cui2 nil :pfstr2 nil :soc nil :cot nil :cof nil :coa nil)
   (:title "Co-occuring Concept")
@@ -178,7 +190,7 @@
   ((sab :type string :initarg :sab :reader sab)
    (rel :type string :initarg :rel :reader rel)
    (atx :type string :initarg :atx :reader atx))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :sab nil :rel nil :atx nil)
   (:title "Associated Expression")
   (:fields (sab :string) (rel :string) (atx :cdata)))
@@ -195,7 +207,7 @@
    (s#sat :reader s#sat)
    (s#atx :reader s#atx)
    (s#sty :reader s#sty))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :cui nil :pfstr nil :lrl nil)
   (:title "Concept")
   (:subobjects-lists 
@@ -209,7 +221,7 @@
    (cui :type fixnum :initform nil :initarg :cui :reader cui)
    (lui :type fixnum :initform nil :initarg :lui :reader lui)
    (sui :type fixnum :initform nil :initarg :sui :reader sui))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :wd nil :cui nil :lui nil :sui nil)
   (:title "XW Index")
   (:fields (wd :string) (cui :string fmt-cui) (lui :string fmt-lui) 
@@ -219,7 +231,7 @@
   ((lat :type string :initarg :lat :reader lat)
    (nwd :type string :initarg :nwd :reader nwd)
   (cuilist :type list :initarg :cuilist :reader uxnw-cuilist))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :lat nil :nwd nil :cuilist nil)
   (:title "XNW Index")
   (:fields (lat :string) (nwd :string) (cuilist :string)))
@@ -228,7 +240,7 @@
   ((lat :type string :initarg :lat :reader lat)
    (nstr :type string :initarg :nstr :reader nstr)
    (cuilist :type list :initarg :cuilist :reader cuilist))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :lat nil :nstr nil :cuilist nil)
   (:title "XNS Index")
   (:fields (lat :string) (nstr :string) (cuilist :string)))
@@ -249,7 +261,7 @@
    (s#spl :reader s#spl)
    (s#trm :reader s#trm)
    (s#typ :reader s#typ))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :wrd nil)
   (:title "Lexical Term")
   (:subobjects-lists 
@@ -265,7 +277,7 @@
    (abr :type string :initarg :abr :reader abr)
    (eui2 :type integer :initarg :eui2 :reader eui2)
    (bas2 :type string :initarg :bas2 :reader bas2))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :abr nil :eui2 nil :bas2 nil)
   (:title "Abbreviations and Acronyms")
   (:fields (eui :string fmt-eui) (bas :string) (abr :string) 
@@ -278,7 +290,7 @@
    (agr :type string :initarg :agr :reader agr)
    (cit :type string :initarg :cit :reader cit)
    (bas :type string :initarg :bas :reader bas))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :str nil :sca nil :agr nil :cit nil :bas nil)
   (:title "Agreement and Inflection")
   (:fields (eui :string fmt-eui) (str :string) (sca :string) (agr :string)
@@ -289,7 +301,7 @@
    (bas :type string :initarg :bas :reader bas)
    (sca :type string :initarg :sca :reader sca)
    (com :type string :initarg :com :reader com))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :sca nil :com nil)
   (:title "Complementation")
   (:fields (eui :string fmt-eui) (bas :string) (sca :string) (com :string)))
@@ -300,7 +312,7 @@
    (sca :type string :initarg :sca :reader sca)
    (psnmod :type string :initarg :psnmod :reader psnmod)
    (fea :type string :initarg :fea :reader fea))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :sca nil :psnmod nil :fea nil)
   (:title "Modifiers")
   (:fields (eui :string fmt-eui) (bas :string) (sca :string) (psnmod :string) 
@@ -313,7 +325,7 @@
    (eui2 :type integer :initarg :eui2 :reader eui2)
    (bas2 :type string :initarg :bas2 :reader bas2)
    (sca2 :type string :initarg :sca2 :reader sca2))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :sca nil :eui2 nil :bas2 nil :sca2 nil)
   (:title "Nominalizations")
   (:fields (eui :string fmt-eui) (bas :string) (sca :string) 
@@ -328,7 +340,7 @@
    (pos :type string :initarg :pos :reader pos)
    (qnt :type string :initarg :qnt :reader qnt)
    (fea :type string :initarg :fea :reader fea))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :num nil :gnd nil :cas nil
 		     :pos nil :qnt nil :fea nil)
   (:title "Pronouns")
@@ -341,7 +353,7 @@
    (str :type string :initarg :str :reader str)
    (sca :type string :initarg :sca :reader sca)
    (fea :type string :initarg :fea :reader fea))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :str nil :sca nil :fea nil)
   (:title "Properties")
   (:fields (eui :string fmt-eui) (bas :string) (str :string) (sca :string) 
@@ -352,7 +364,7 @@
   ((eui :type integer :initarg :eui :reader eui)
    (spv :type string :initarg :spv :reader spv)
    (bas :type string :initarg :bas :reader bas))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :spv nil :bas nil)
   (:title "Spelling Variants")
   (:fields (eui :string fmt-eui) (spv :string) (bas :string)))
@@ -363,7 +375,7 @@
   ((eui :type integer :initarg :eui :reader eui)
    (bas :type string :initarg :bas :reader bas)
    (gen :type string :initarg :gen :reader gen))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :gen nil)
   (:title "Trade Marks")
   (:fields (eui :string fmt-eui) (bas :string) (gen :string)))
@@ -373,7 +385,7 @@
    (bas :type string :initarg :bas :reader bas)
    (sca :type string :initarg :sca :reader sca)
    (typ :type string :initarg :typ :reader typ))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :eui nil :bas nil :sca nil :typ nil)
   (:title "Inflection Type")
   (:fields (eui :string fmt-eui) (bas :string) (sca :string) (typ :string)))
@@ -381,7 +393,7 @@
 (defclass lwd (umlsclass)
   ((wrd :type string :initarg :wrd :reader wrd)
    (euilist :type list :initarg :euilist :reader euilist))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :wrd nil :euilist nil)
   (:title "Lexical Word Index")
   (:fields (wrd :string) (euilist :string)))
@@ -399,7 +411,7 @@
    (rh :type string :initarg :rh :reader rh)
    (abr :type string :initarg :abr :reader abr)
    (rin :type string :initarg :rin :reader rin))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs 
    :rt nil :ui nil :styrl nil :stnrtn nil :def nil :ex nil :un nil :rh nil 
    :abr nil :rin nil)
@@ -414,7 +426,7 @@
    (rl :type string :initarg :rl :reader rl)
    (styrl2 :type string :initarg :styrl2 :reader styrl2)
    (ls :type string :initarg :ls :reader ls))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :styrl nil :rl nil :styrl2 nil :ls nil)
   (:title "Structure of the Network")
   (:fields (styrl :string) (rl :string) (styrl2 :string) (ls :string)))
@@ -423,7 +435,7 @@
   ((ui :type integer :initarg :ui :reader ui)
    (ui2 :type integer :initarg :ui2 :reader ui2)
    (ui3 :type integer :initarg :ui3 :reader ui3))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :ui nil :ui2 nil :ui3 nil)
   (:title "Fully Inherited Set of Releatons (TUI's)")
   (:fields (ui :string fmt-tui) (ui2 :string fmt-tui) (ui3 :string fmt-tui)))
@@ -432,7 +444,7 @@
   ((sty :type string :initarg :ui :reader sty)
    (rl :type string :initarg :ui2 :reader rl)
    (sty2 :type string :initarg :ui3 :reader sty2))
-  (:metaclass kmrcl::ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :sty nil :rl nil :sty2 nil)
   (:title "Fully Inherited Set of Releatons (strings)")
   (:fields (sty :string) (rl :string) (sty2 :string)))
diff --git a/composite.lisp b/composite.lisp
index 611dfd1..f363287 100644
--- a/composite.lisp
+++ b/composite.lisp
@@ -1,6 +1,23 @@
-;;;; $Id: composite.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:          composite.lisp
+;;;; Purpose:       Composite Classes for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: composite.lisp,v 1.3 2002/10/09 23:03:41 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)))
 
 
 ;;; Semantic type constants
@@ -51,7 +68,7 @@
 (defclass ucon_freq (umlsclass)
   ((ucon :type ucon :initarg :ucon :reader ucon)
    (freq :type fixnum :initarg :freq :accessor freq))
-  (:metaclass ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :cui nil :pfstr nil :freq nil)
   (:title "Concept and Count")
   (:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
@@ -67,7 +84,7 @@
 (defclass ustr_freq (umlsclass)
   ((ustr :type ustr :initarg :ustr :reader ustr)
    (freq :type fixnum :initarg :freq :accessor freq))
-  (:metaclass ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :cui nil :pfstr nil :freq nil)
   (:title "String and Count")
   (:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
@@ -89,7 +106,7 @@
 (defclass usty_freq (umlsclass)
   ((usty :type usty :initarg :usty :reader usty)
    (freq :type fixnum :initarg :freq :accessor freq))
-  (:metaclass ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :usty nil :freq nil)
   (:title "Semantic Type and Count")
   (:ref-fields (tui find-ucon-tui "subobjects=no"))
@@ -105,7 +122,7 @@
 (defclass usrl_freq (umlsclass)
   ((usrl :type usrl :initarg :usrl :reader usrl)
    (freq :type fixnum :initarg :freq :accessor freq))
-  (:metaclass ml-class)
+  (:metaclass kmrcl:ml-class)
   (:default-initargs :usrl nil :freq nil)
   (:title "Source and Count")
   (:ref-fields (sab find-ustr-sab))
diff --git a/data-structures.lisp b/data-structures.lisp
index a52c97d..15684eb 100644
--- a/data-structures.lisp
+++ b/data-structures.lisp
@@ -1,6 +1,23 @@
-;;;; $Id: data-structures.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:          data-structures.lisp
+;;;; Purpose:       Basic data objects for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: data-structures.lisp,v 1.3 2002/10/09 23:03:41 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)))
 
 
 ;;; Paths for files
diff --git a/package.lisp b/package.lisp
index 9cc3644..7dfc910 100644
--- a/package.lisp
+++ b/package.lisp
@@ -1,15 +1,54 @@
-;;;; $Id: package.lisp,v 1.3 2002/10/09 02:23:22 kevin Exp $
-;;;; 
-;;;; Package definition for UMLisp
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: cl-user -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          package.lisp
+;;;; Purpose:       Package definition for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: package.lisp,v 1.4 2002/10/09 23:03:41 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 :cl-user)
 
 (defpackage umlisp
   (:nicknames :u)
   (:export 
+   
+   ;; From classes.lisp
+   #:umlsclass
    #:ucon
    #:uterm
    #:ustr
+   #:sty
+   #:tui
+   
+   ;; From sql.lisp
+   #:umls-sql-user!
+   #:umls-sql-passwd!
+   #:with-sql-connection
+   #:mutex-sql-execute
+   #:mutex-sql-query
+   #:sql-query
+   #:sql-execute
+   
+   ;; From utils.lisp
+   #:fmt-cui
+   #:fmt-lui
+   #:fmt-sui
+   #:fmt-tui
+   
+   #:*current-srl*
+   
+   ;; From sql-classes.lisp
+   
    #:find-udef-cui
    #:find-usty-cui
    #:find-usty-word
diff --git a/parse-2002.lisp b/parse-2002.lisp
index 6f593eb..07f9b9c 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 1.3 2002/10/09 23:03:41 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)
diff --git a/parse-common.lisp b/parse-common.lisp
index 9610539..4c13a52 100644
--- a/parse-common.lisp
+++ b/parse-common.lisp
@@ -1,11 +1,23 @@
-;;; 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-common.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          parse-common.lisp
+;;;; Purpose:       Common, stable parsing routines for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: parse-common.lisp,v 1.2 2002/10/09 23:03:41 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)))
 
 (defun umls-pathname (filename &optional (extension ""))
 "Return pathname for a umls filename"
diff --git a/parse-macros.lisp b/parse-macros.lisp
index f3a8408..edccfe8 100644
--- a/parse-macros.lisp
+++ b/parse-macros.lisp
@@ -1,11 +1,23 @@
-;;; 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 $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          parse-macros.lisp
+;;;; Purpose:       Macros for UMLS file parsing
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: parse-macros.lisp,v 1.2 2002/10/09 23:03:41 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)))
 
 
 (defmacro with-umls-file ((line filename) &body body)
diff --git a/sql-classes.lisp b/sql-classes.lisp
index 920ee8d..5aae593 100644
--- a/sql-classes.lisp
+++ b/sql-classes.lisp
@@ -1,8 +1,24 @@
-;;; $Id: sql-classes.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:          sql-classes.lisp
+;;;; Purpose:       Routines for reading UMLS objects from SQL database
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: sql-classes.lisp,v 1.3 2002/10/09 23:03:41 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)))
 
-(declaim (optimize (speed 3) (safety 1)))
 
 (defvar *current-srl* nil)
 (defun current-srl ()
@@ -638,19 +654,6 @@
       (setq ucons (append ucons (find-ucon-word word :srl srl))))
     (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
 
-(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))))
-    (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui))))
-
 (defun find-ustr-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))
@@ -658,35 +661,6 @@
     (dolist (word words)
       (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
     (sort-score-ustr-str str (delete-duplicates ustrs :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))))
-    (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)))
 	
 (defun sort-score-ucon-str (str ucons)
   "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
diff --git a/sql.lisp b/sql.lisp
index 7e5ce88..e7ee3a4 100644
--- a/sql.lisp
+++ b/sql.lisp
@@ -1,11 +1,24 @@
-;;;;  -*- Mode: LISP; Syntax: Common-Lisp; Base: 10; Pkg: umlisp -*-
-;; SQL/UMLS database Layer over database backend
-;; Copyright (c) 2001 Kevin M. Rosenberg, M.D.
-;; $Id: sql.lisp,v 1.2 2002/10/08 22:13:41 kevin Exp $
+;;;; -*- 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 1.3 2002/10/09 23:03:41 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)))
 
-(declaim (optimize (speed 1) (safety 3)))
 
 (defvar *umls-sql-dsn* "KUMLS2002AC")
 (defun umls-sql-dsn ()
diff --git a/umlisp.asd b/umlisp.asd
index 2cd4756..da7a752 100644
--- a/umlisp.asd
+++ b/umlisp.asd
@@ -1,5 +1,20 @@
-;;;;  -*- Mode: LISP; Syntax: ANSI-Common-Lisp; Base: 10 -*-
-;;;; $Id: umlisp.asd,v 1.3 2002/10/09 00:34:47 kevin Exp $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          umlisp.asd
+;;;; Purpose:       ASDF system definition file for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: umlisp.asd,v 1.4 2002/10/09 23:03:41 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 :asdf)
 
diff --git a/utils.lisp b/utils.lisp
index 9bc35b8..c25cf1d 100644
--- a/utils.lisp
+++ b/utils.lisp
@@ -1,9 +1,24 @@
-;;;; $Id: utils.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name:          utils.lisp
+;;;; Purpose:       Low-level utility functions for UMLisp
+;;;; Programmer:    Kevin M. Rosenberg
+;;;; Date Started:  Apr 2000
+;;;;
+;;;; $Id: utils.lisp,v 1.2 2002/10/09 23:03:41 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 (inline xml-cdata make-cuisui make-cuilui parse-ui parse-cui))
-(declaim (optimize (speed 3) (safety 1)))
+(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
+(declaim (inline make-cuisui make-cuilui parse-ui parse-cui))
 
 (defmacro def-metaclass-reader (field)
   "Create function for reading slot of metaclass"
@@ -63,9 +78,6 @@
 	  (parse-integer eui)))
     eui))
     
-(defun xml-cdata (str)
-  (concatenate 'string "<![CDATA[" str "]]>"))
-
 (defconstant +cuisui-scale+ 10000000)
 
 (defun make-cuisui (cui sui)
-- 
2.34.1