--- /dev/null
+.PHONY: all clean test test-acl test-sbcl
+
+test-file:=`pwd`/run-tests.lisp
+all:
+
+clean:
+ @find . -type f -name "*.fasl*" -or -name "*.ufsl" -or -name "*.x86f" \
+ -or -name "*.fas" -or -name "*.pfsl" -or -name "*.dfsl" \
+ -or -name "*~" -or -name ".#*" -or -name "#*#" | xargs rm -f
+
+test: test-alisp
+
+test-alisp:
+ alisp8 -q -L $(test-file)
+
+test-mlisp:
+ mlisp -q -L $(test-file)
+
+test-sbcl:
+ sbcl --noinform --disable-debugger --userinit $(test-file)
+
+test-cmucl:
+ lisp -init $(test-file)
+
+test-lw:
+ lw-console -init $(test-file)
+
+test-scl:
+ scl -init $(test-file)
+
+test-clisp:
+ clisp -norc -q -i $(test-file)
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: classes-support.lisp
-;;;; Purpose: Class defintions for UMLisp
-;;;; Programmer: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
+;;;; Name: classes-support.lisp
+;;;; Purpose: Support for UMLisp classes
+;;;; Author: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: class-support.lisp,v 1.3 2003/05/06 02:15:41 kevin Exp $
+;;;; $Id: class-support.lisp,v 1.4 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: sql-create
+;;;; Purpose: Create SQL database for UMLisp
+;;;; Author: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
+;;;;
+;;;; $Id: create-sql.lisp,v 1.1 2003/05/07 21:57:06 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)
+
+(eval-when (:compile-toplevel)
+ (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
+
+(defun create-table-cmd (file)
+ "Return sql command to create a table"
+ (let ((col-func
+ (lambda (c)
+ (let ((sqltype (sqltype c)))
+ (concatenate 'string
+ (col c)
+ " "
+ (if (or (string-equal sqltype "VARCHAR")
+ (string-equal sqltype "CHAR"))
+ (format nil "~a (~a)" sqltype (cmax c))
+ sqltype))))))
+ (format nil "CREATE TABLE ~a (~{~a~^,~})" (table file)
+ (mapcar col-func (ucols file)))))
+
+(defun create-custom-table-cmd (tablename sql-cmd)
+ "Return SQL command to create a custom table"
+ (format nil "CREATE TABLE ~a AS ~a;" tablename sql-cmd))
+
+(defun insert-col-value (col value)
+ (if (null (parse-fun col))
+ value
+ (format nil "~A" (funcall (parse-fun col) value))))
+
+(defun insert-values-cmd (file values)
+ "Return sql insert command for a row of values"
+ (let ((insert-func
+ (lambda (col value)
+ (let ((q (quotechar col)))
+ (concatenate 'string q (insert-col-value col value) q)))))
+ (format
+ nil "INSERT INTO ~a (~{~a~^,~}) VALUES (~A)"
+ (table file)
+ (fields file)
+ (concat-separated-strings
+ ","
+ (mapcar insert-func (remove-custom-cols (ucols file)) values)
+ (custom-col-values (custom-ucols-for-file file) values t)))))
+
+
+(defun custom-col-value (col values doquote)
+ (let ((custom-value (funcall (custom-value-fun col) values)))
+ (if custom-value
+ (if doquote
+ (let ((q (quotechar col)))
+ (concatenate 'string q (escape-backslashes custom-value) q))
+ (escape-backslashes custom-value))
+ "")))
+
+(defun custom-col-values (ucols values doquote)
+ "Returns a list of string column values for SQL inserts for custom columns"
+ (loop for col in ucols collect (custom-col-value col values doquote)))
+
+(defun remove-custom-cols (cols)
+ "Remove custom cols from a list col umls-cols"
+ (remove-if #'custom-value-fun cols))
+
+(defun find-custom-cols-for-filename (filename)
+ (remove-if-not (lambda (x) (string-equal filename (car x))) +custom-cols+))
+
+(defun find-custom-col (filename col)
+ (find-if (lambda (x) (and (string-equal filename (car x))
+ (string-equal col (cadr x)))) +custom-cols+))
+
+(defun custom-colnames-for-filename (filename)
+ (mapcar #'cadr (find-custom-cols-for-filename filename)))
+
+(defun custom-ucols-for-file (file)
+ (remove-if-not #'custom-value-fun (ucols file)))
+
+(defun noneng-lang-index-files ()
+ (remove-if-not
+ (lambda (f) (and (> (length (fil f)) 4)
+ (string-equal (fil f) "MRXW." :end1 5)
+ (not (string-equal (fil f) "MRXW.ENG"))
+ (not (string-equal (fil f) "MRXW.NONENG"))))
+ *umls-files*))
+
+;;; SQL Command Functions
+
+(defun create-index-cmd (colname tablename length)
+ "Return sql create index command"
+ (format nil "CREATE INDEX ~a ON ~a (~a ~a)"
+ (concatenate 'string tablename "_" colname "_X")
+ tablename colname
+ (if (integerp length) (format nil "(~d)" length) "")))
+
+(defun create-all-tables-cmdfile ()
+ "Return sql commands to create all tables. Not need for automated SQL import"
+ (mapcar (lambda (f) (format nil "~a~%~%" (create-table-cmd f))) *umls-files*))
+
+;; SQL Execution functions
+
+(defun sql-drop-tables (conn)
+ "SQL Databases: drop all tables"
+ (dolist (file *umls-files*)
+ (ignore-errors
+ (sql-execute (format nil "DROP TABLE ~a" (table file)) conn))))
+
+(defun sql-create-tables (conn)
+ "SQL Databases: create all tables"
+ (dolist (file *umls-files*)
+ (sql-execute (create-table-cmd file) conn)))
+
+(defun sql-create-custom-tables (conn)
+ "SQL Databases: create all custom tables"
+ (dolist (ct +custom-tables+)
+ (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn)))
+
+(defun sql-insert-values (conn file)
+ "SQL Databases: inserts all values for a file"
+ (with-umls-file (line (fil file))
+ (sql-execute (insert-values-cmd file line) conn)))
+
+(defun sql-insert-all-values (conn)
+ "SQL Databases: inserts all values for all files"
+ (dolist (file *umls-files*)
+ (sql-insert-values conn file)))
+
+(defun sql-create-indexes (conn &optional (indexes +index-cols+))
+ "SQL Databases: create all indexes"
+ (dolist (idx indexes)
+ (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
+
+(defun make-usrl (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)))
+
+(defun sql-create-special-tables (conn)
+ (make-usrl conn))
+
+(defun create-umls-db-by-insert ()
+ "SQL Databases: initializes entire database via SQL insert commands"
+ (ensure-init-umls)
+ (init-hash-table)
+ (with-sql-connection (conn)
+ (sql-drop-tables conn)
+ (sql-create-tables conn)
+ (sql-insert-all-values conn)
+ (sql-create-indexes conn)
+ (sql-create-custom-tables conn)
+ (sql-create-indexes conn +custom-index-cols+)
+ (sql-create-special-tables conn)))
+
+(defun create-umls-db (&optional (extension ".trans")
+ (copy-cmd #'mysql-copy-cmd))
+ "SQL Databases: initializes entire database via SQL copy commands.
+This is much faster that using create-umls-db-insert."
+ (ensure-init-umls)
+ (init-hash-table)
+ (translate-all-files extension)
+ (with-sql-connection (conn)
+ (sql-drop-tables conn)
+ (sql-create-tables conn)
+ (dolist (file *umls-files*)
+ (sql-execute (funcall copy-cmd file extension) conn))
+ (sql-create-indexes conn)
+ (sql-create-custom-tables conn)
+ (sql-create-indexes conn +custom-index-cols+)
+ (sql-create-special-tables conn)))
+
+(defun translate-all-files (&optional (extension ".trans"))
+ "Copy translated files and return postgresql copy commands to import"
+ (make-noneng-index-file extension)
+ (dolist (f *umls-files*) (translate-umls-file f extension)))
+
+(defun translate-umls-file (file extension)
+ "Translate a umls file into a format suitable for sql copy cmd"
+ (translate-files file extension (list file)))
+
+(defun make-noneng-index-file (extension)
+ "Make non-english index file"
+ (translate-files (find-ufile "MRXW.NONENG")
+ extension (noneng-lang-index-files)))
+
+(defun translate-files (out-ufile extension input-ufiles)
+ "Translate a umls file into a format suitable for sql copy cmd"
+ (let ((output-path (umls-pathname (fil out-ufile) extension)))
+ (if (probe-file output-path)
+ (format t "File ~A already exists: skipping~%" output-path)
+ (with-open-file (ostream output-path :direction :output)
+ (dolist (input-ufile input-ufiles)
+ (with-umls-file (line (fil input-ufile))
+ (translate-line out-ufile line ostream)
+ (princ #\newline ostream)))))))
+
+(defun translate-line (file line strm)
+ "Translate a single line for sql output"
+ (flet ((col-value (col value)
+ (if (eq (datatype col) 'sql-u)
+ (let ((ui (parse-ui value "")))
+ (if (stringp ui)
+ ui
+ (write-to-string ui)))
+ (escape-backslashes value))))
+ (print-separated-strings
+ strm "|"
+ (mapcar #'col-value (remove-custom-cols (ucols file)) line)
+ (custom-col-values (custom-ucols-for-file file) line nil))))
+
+(defun pg-copy-cmd (file extension)
+ "Return postgresql copy statement for a file"
+ (format
+ nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
+ (table file) (umls-pathname (fil file) extension)))
+
+(defun mysql-copy-cmd (file extension)
+ "Return mysql copy statement for a file"
+ (format
+ nil
+ "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
+ (umls-pathname (fil file) extension) (table file)))
+
+
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+;;;
+;;; Routines for analyzing cost of fixed size storage
+;;;
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+
+(defun umls-fixed-size-waste ()
+ "Display storage waste if using all fixed size storage"
+ (let ((totalwaste 0)
+ (totalunavoidable 0)
+ (totalavoidable 0)
+ (unavoidable '())
+ (avoidable '()))
+ (dolist (file *umls-files*)
+ (dolist (col (ucols file))
+ (let* ((avwaste (- (cmax col) (av col)))
+ (cwaste (* avwaste (rws file))))
+ (when (plusp cwaste)
+ (if (<= avwaste 6)
+ (progn
+ (incf totalunavoidable cwaste)
+ (push (list (fil file) (col col)
+ avwaste cwaste)
+ unavoidable))
+ (progn
+ (incf totalavoidable cwaste)
+ (push (list (fil file) (col col)
+ avwaste cwaste)
+ avoidable)))
+ (incf totalwaste cwaste)))))
+ (values totalwaste totalavoidable totalunavoidable
+ (nreverse avoidable) (nreverse unavoidable))))
+
+(defun display-waste ()
+ (ensure-init-umls)
+ (multiple-value-bind (tw ta tu al ul) (umls-fixed-size-waste)
+ (format t "Total waste: ~d~%" tw)
+ (format t "Total avoidable: ~d~%" ta)
+ (format t "Total unavoidable: ~d~%" tu)
+ (format t "Avoidable:~%")
+ (dolist (w al)
+ (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
+ (format t "Unavoidable:~%")
+ (dolist (w ul)
+ (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
+ ))
+
+(defun max-umls-field ()
+ "Return length of longest field"
+ (declare (optimize (speed 3) (space 0)))
+ (ensure-init-umls)
+ (let ((max 0))
+ (declare (fixnum max))
+ (dolist (ucol *umls-cols*)
+ (when (> (cmax ucol) max)
+ (setq max (cmax ucol))))
+ max))
+
+(defun max-umls-row ()
+ "Return length of longest row"
+ (declare (optimize (speed 3) (space 0)))
+ (ensure-init-umls)
+ (let ((rowsizes '()))
+ (dolist (file *umls-files*)
+ (let ((row 0))
+ (dolist (ucol (ucols file))
+ (incf row (1+ (cmax ucol))))
+ (push row rowsizes)))
+ (car (sort rowsizes #'>))))
;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: data-structures.lisp,v 1.9 2003/05/06 07:20:31 kevin Exp $
+;;;; $Id: data-structures.lisp,v 1.10 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
(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)
- (quotechar :initarg :quotechar :accessor quotechar)
+ (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
;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-2002.lisp,v 1.9 2003/05/06 07:55:15 kevin Exp $
+;;;; $Id: parse-2002.lisp,v 1.10 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
;; File & Column functions
-(defun init-umls (&optional (alwaysclear nil))
-"Initialize all UMLS file and column structures if not already initialized"
- (when (or alwaysclear (null *umls-files*))
- (init-umls-cols)
- (init-umls-files)
- (init-field-lengths)))
+(defun gen-ucols ()
+ (add-ucols (gen-ucols-meta))
+ (add-ucols (gen-ucols-custom))
+ (add-ucols (gen-ucols-generic "LRFLD"))
+ (add-ucols (gen-ucols-generic "SRFLD")))
-(defun init-umls-cols ()
- (setq *umls-cols* (append
- (init-meta-cols)
- (init-custom-cols)
- (init-generic-cols "LRFLD")
- (init-generic-cols "SRFLD"))))
-
-(defun init-meta-cols ()
+(defun gen-ucols-meta ()
"Initialize all umls columns"
(let ((cols '()))
(with-umls-file (line "MRCOLS")
(destructuring-bind (col des ref min av max fil dty) line
- (let ((c (make-instance 'ucol
- :col col
- :des des
- :ref ref
- :min (parse-integer min)
- :av (read-from-string av)
- :max (parse-integer max)
- :fil fil
- :dty dty ;; new in 2002 UMLS
- :sqltype "VARCHAR" ; default data type
- :parse-fun #'add-sql-quotes
- :custom-value-fun nil
- :quotechar "'")))
- (add-datatype-to-col c (datatype-for-col col))
- (push c cols))))
+ (push (make-ucol col des ref (parse-integer min) (read-from-string av)
+ (parse-integer max) fil dty)
+ cols)))
(nreverse cols)))
-(defun init-custom-cols ()
+(defun gen-ucols-custom ()
"Initialize umls columns for custom columns"
- (let ((cols '()))
- (dolist (customcol +custom-cols+)
- (let ((c (make-instance 'ucol
- :col (nth 1 customcol) :des "" :ref 0 :min 0 :max (nth 3 customcol)
- :av 0 :dty nil :fil (nth 0 customcol) :sqltype (nth 2 customcol)
- :parse-fun #'add-sql-quotes :custom-value-fun (nth 4 customcol)
- :quotechar "'")))
- (add-datatype-to-col c (datatype-for-col (nth 1 customcol)))
- (push c cols)))
- (nreverse cols)))
-
-(defun escape-column-name (name)
- (substitute #\_ #\/ name))
+ (loop for customcol in +custom-cols+
+ collect
+ (make-ucol (nth 1 customcol) "" 0 0 0 (nth 3 customcol)
+ (nth 0 customcol) nil :sqltype (nth 2 customcol))))
-(defun init-generic-cols (col-filename)
+(defun gen-ucols-generic (col-filename)
"Initialize for generic (LEX/NET) columns"
(let ((cols '()))
(with-umls-file (line col-filename)
(destructuring-bind (nam des ref fil) line
(setq nam (escape-column-name nam))
(dolist (file (delimited-string-to-list fil #\,))
- (let ((c (make-instance 'ucol
- :col nam
- :des des
- :ref ref
- :min nil
- :av nil
- :max nil
- :fil file
- :dty nil
- :sqltype "VARCHAR" ; default data type
- :parse-fun #'add-sql-quotes
- :custom-value-fun nil
- :quotechar "'")))
- (add-datatype-to-col c (datatype-for-col nam))
- (push c cols)))))
+ (push
+ (make-ucol nam des ref nil nil nil file nil)
+ cols))))
(nreverse cols)))
-(defun init-umls-files ()
- (setq *umls-files* (append
- (init-generic-files "MRFILES")
- (init-generic-files "LRFIL")
- (init-generic-files "SRFIL")))
- ;; need to separate this since init-custom-files depends on *umls-files*
- (setq *umls-files* (append *umls-files* (init-custom-files))))
+(defun gen-ufiles ()
+ (add-ufiles (gen-ufiles-generic "MRFILES"))
+ (add-ufiles (gen-ufiles-generic "LRFIL"))
+ (add-ufiles (gen-ufiles-generic "SRFIL"))
+ ;; needs to come last
+ (add-ufiles (gen-ufiles-custom)))
-(defun umls-field-string-to-list (fmt)
- "Converts a comma delimited list of fields into a list of field names. Will
-append a unique number (starting at 2) onto a column name that is repeated in the list"
- (let ((field-list (delimited-string-to-list (escape-column-name fmt) #\,))
- (col-count (make-hash-table :test 'equal)))
- (dotimes (i (length field-list))
- (declare (fixnum i))
- (let ((col (nth i field-list)))
- (multiple-value-bind (key found) (gethash col col-count)
- (if found
- (let ((next-id (1+ key)))
- (setf (nth i field-list) (concatenate 'string col (write-to-string next-id)))
- (setf (gethash col col-count) next-id))
- (setf (gethash col col-count) 1)))))
- field-list))
-
-(defun init-generic-files (files-filename)
+
+(defun gen-ufiles-generic (files-filename)
"Initialize all LEX file structures"
(let ((files '()))
- (with-umls-file (line files-filename)
- (destructuring-bind (fil des fmt cls rws bts) line
- (let ((f (make-instance 'ufile
- :fil fil
- :table (substitute #\_ #\. fil)
- :des des
- :fmt (escape-column-name fmt)
- :cls (parse-integer cls)
- :rws (parse-integer rws)
- :bts (parse-integer bts)
- :fields (concatenate 'list
- (umls-field-string-to-list fmt)
- (custom-colnames-for-filename fil)))))
- (setf (ucols f) (ucols-for-ufile f))
- (push f files))))
- (nreverse files)))
-
-(defun init-custom-files ()
- (let ((ffile (make-instance 'ufile
- :fil "MRXW.NONENG" :des "Custom NonEnglish Index" :table "MRXW_NONENG"
- :cls 5 :rws 0 :bts 0 :fields (fields (find-ufile "MRXW.ENG")))))
- (setf (ucols ffile)
- (ucols-for-ufile ffile))
- (list ffile)))
-
-(defun datatype-for-col (colname)
-"Return datatype for column name"
- (car (cdr (find colname +col-datatypes+ :key #'car :test #'string-equal))))
+ (with-umls-file (line files-filename)
+ (destructuring-bind (fil des fmt cls rws bts) line
+ (push (make-ufile
+ fil des (substitute #\_ #\. fil) (parse-integer cls)
+ (parse-integer rws) (parse-integer bts)
+ (concatenate 'list (umls-field-string-to-list fmt)
+ (custom-colnames-for-filename fil)))
+ files)))
+ (nreverse files)))
-(defun add-datatype-to-col (col datatype)
-"Add data type information to column"
- (setf (datatype col) datatype)
- (case datatype
- (sql-u (setf (sqltype col) "INTEGER"
- (parse-fun col) #'parse-ui
- (quotechar col) ""))
- (sql-s (setf (sqltype col) "SMALLINT"
- (parse-fun col) #'parse-integer
- (quotechar col) ""))
- (sql-l (setf (sqltype col) "BIGINT"
- (parse-fun col) #'parse-integer
- (quotechar col) ""))
- (sql-i (setf (sqltype col) "INTEGER"
- (parse-fun col) #'parse-integer
- (quotechar col) ""))
- (sql-f (setf (sqltype col) "NUMERIC"
- (parse-fun col) #'read-from-string
- (quotechar col) ""))
- (t ; Default column type, optimized text storage
- (setf (parse-fun col) #'add-sql-quotes
- (quotechar col) "'")
- (when (and (cmax col) (av col))
- (if (> (cmax col) 255)
- (setf (sqltype col) "TEXT")
- (if (< (- (cmax col) (av col)) 4)
- (setf (sqltype col) "CHAR") ; if average bytes wasted < 4
- (setf (sqltype col) "VARCHAR")))))))
+(defun gen-ufiles-custom ()
+ (make-ufile "MRXW.NONENG" "Custom NonEnglish Index" "MRXW_NONENG"
+ 5 0 0 (fields (find-ufile "MRXW.ENG"))))
;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-common.lisp,v 1.8 2003/05/06 07:44:07 kevin Exp $
+;;;; $Id: parse-common.lisp,v 1.9 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
(eval-when (:compile-toplevel)
(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
+(defun ensure-init-umls (&optional (alwaysclear nil))
+"Initialize all UMLS file and column structures if not already initialized"
+ (when (or alwaysclear (null *umls-files*))
+ (gen-ucols)
+ (gen-ufiles)
+ (ensure-field-lengths)))
+
+(defun add-ucols (ucols)
+ "Adds a ucol or list of ucols to *umls-cols*. Returns input value."
+ (setq *umls-cols* (append (mklist ucols) *umls-cols*))
+ ucols)
+
+(defun add-ufiles (ufiles)
+ "Adds a ufile or list of ufiles to *umls-filess*. Returns input value."
+ (setq *umls-files* (append (mklist ufiles) *umls-files*))
+ ufiles)
+
(defun umls-pathname (filename &optional (extension ""))
-"Return pathname for a umls filename"
+"Return pathname for a umls filename with an optional extension"
(etypecase filename
(string
(merge-pathnames
;;; Find field lengths for LEX and NET files
-(defun file-field-lengths (files)
- (let ((lengths '()))
- (dolist (file files)
- (setq file (fil file))
- (let (max-field count-field num-fields (count-lines 0))
- (with-umls-file (fields file)
- (unless num-fields
- (setq num-fields (length fields))
- (setq max-field (make-array num-fields :element-type 'fixnum
- :initial-element 0))
- (setq count-field (make-array num-fields :element-type 'number
- :initial-element 0)))
- (dotimes (i (length fields))
- (declare (fixnum i))
- (let ((len (length (nth i fields))))
- (incf (aref count-field i) len)
- (when (> len (aref max-field i))
- (setf (aref max-field i) len))))
- (incf count-lines))
- (dotimes (i num-fields)
- (setf (aref count-field i) (float (/ (aref count-field i) count-lines))))
- (push (list file max-field count-field) lengths)))
- (nreverse lengths)))
-
-(defun init-field-lengths ()
+(defun ensure-field-lengths ()
"Initial colstruct field lengths for files that don't have a measurement.
Currently, these are the LEX and NET files."
- (let ((measure-files '()))
- (dolist (file *umls-files*)
- (let ((filename (fil file)))
- (unless (or (char= #\M (char filename 0))
- (char= #\m (char filename 0)))
- (push file measure-files))))
- (let ((length-lists (file-field-lengths measure-files)))
- (dolist (length-list length-lists)
- (let* ((filename (car length-list))
- (max-field (cadr length-list))
- (av-field (caddr length-list))
- (file (find-ufile filename)))
- (when file
- (if (/= (length max-field) (length (fields file)))
- (format t "Warning: Number of file fields ~A doesn't match length of fields in file structure ~S"
- max-field file)
- (dotimes (i (max (length max-field) (length (fields file))))
- (declare (fixnum i))
- (let* ((field (nth i (fields file)))
- (col (find-ucol field filename)))
- (if col
- (progn
- (setf (cmax col) (aref max-field i))
- (setf (av col) (aref av-field i))
- (add-datatype-to-col col (datatype-for-col (col col))))
- (error "can't find column ~A" field)))))))))))
+ (dolist (length-list (ufiles-field-lengths (ufiles-to-measure)))
+ (destructuring-bind (filename fields-max fields-av) length-list
+ (let ((file (find-ufile filename)))
+ (unless file
+ (error "Can't find ~A filename in ufiles"))
+ (unless (= (length fields-max) (length (fields file)))
+ (error
+ "Number of file fields ~A not equal to field count in ufile ~S"
+ fields-max file))
+ (dotimes (i (length (fields file)))
+ (declare (fixnum i))
+ (let* ((field (nth i (fields file)))
+ (col (find-ucol field filename)))
+ (unless col
+ (error "can't find column ~A" field))
+ (setf (cmax col) (aref fields-max i))
+ (setf (av col) (aref fields-av i))
+ (ensure-ucol-datatype col (datatype-for-colname (col col)))))))))
-
+(defun ufiles-to-measure ()
+ "Returns a list of ufiles to measure"
+ (loop for ufile in *umls-files*
+ unless (or (char= #\M (char (fil ufile) 0))
+ (char= #\m (char (fil ufile) 0)))
+ collect ufile))
+
+
+(defun ufiles-field-lengths (ufiles)
+ "Returns a list of lists of containing (FILE MAX AV)"
+ (loop for ufile in ufiles collect (file-field-lengths (fil ufile))))
+
+(defun file-field-lengths (filename)
+ "Returns a list of FILENAME MAX AV"
+ (let (fields-max fields-av num-fields (count-lines 0))
+ (with-umls-file (line filename)
+ (unless num-fields
+ (setq num-fields (length line))
+ (setq fields-max (make-array num-fields :element-type 'fixnum
+ :initial-element 0))
+ (setq fields-av (make-array num-fields :element-type 'number
+ :initial-element 0)))
+ (dotimes (i num-fields)
+ (declare (fixnum i))
+ (let ((len (length (nth i line))))
+ (incf (aref fields-av i) len)
+ (when (> len (aref fields-max i))
+ (setf (aref fields-max i) len))))
+ (incf count-lines))
+ (dotimes (i num-fields)
+ (setf (aref fields-av i) (float (/ (aref fields-av i) count-lines))))
+ (list filename fields-max fields-av)))
;;; UMLS column/file functions
-(defun find-col-in-columns (colname filename cols)
+(defun find-ucol-of-colname (colname filename ucols)
"Returns list of umls-col structure for a column name and a filename"
- (dolist (col cols)
- (when (and (string-equal filename (fil col))
- (string-equal colname (col col)))
- (return-from find-col-in-columns col)))
- nil)
-
-(defun find-or-make-col-in-columns (colname filename cols)
- (let ((col (find-col-in-columns colname filename cols)))
- (if col
- col
- ;; try to find column name without a terminal digit
- (let* ((last-char (char colname (1- (length colname))))
- (digit (- (char-code last-char) (char-code #\0))))
- (if (and (>= digit 0) (<= digit 9))
- (let ((base-colname (subseq colname 0 (1- (length colname)))))
- (setq col (find-col-in-columns base-colname filename cols))
- (if col
- (let ((new-col (make-instance 'ucol
- :col (copy-seq colname)
- :des (copy-seq (des col))
- :ref (copy-seq (ref col))
- :min (cmin col)
- :max (cmax col)
- :fil (copy-seq (fil col))
- :sqltype (copy-seq (sqltype col))
- :dty (copy-seq (dty col))
- :parse-fun (parse-fun col)
- :quotechar (copy-seq (quotechar col))
- :datatype (datatype col)
- :custom-value-fun (custom-value-fun col))))
- (push new-col *umls-cols*)
- new-col)
- (error "Couldn't find a base column for col ~A in file ~A"
- colname filename)))
- (let ((new-col (make-instance 'ucol
- :col (copy-seq colname)
- :des "Unknown"
- :ref ""
- :min nil
- :max nil
- :fil filename
- :sqltype "VARCHAR"
- :dty nil
- :parse-fun #'add-sql-quotes
- :quotechar "'"
- :datatype nil
- :custom-value-fun nil)))
- (push new-col *umls-cols*)
- new-col))))))
+ (dolist (ucol ucols nil)
+ (when (and (string-equal filename (fil ucol))
+ (string-equal colname (col ucol)))
+ (return-from find-ucol-of-colname ucol))))
+
+(defun ensure-col-in-columns (colname filename ucols)
+ (aif (find-ucol-of-colname colname filename ucols)
+ it
+ (add-ucols (make-ucol-for-column colname filename ucols))))
+
+(defun make-ucol-for-column (colname filename ucols)
+ ;; try to find column name without a terminal digit
+ (let* ((len (length colname))
+ (last-digit? (digit-char-p (char colname (1- len))))
+ (base-colname (if last-digit?
+ (subseq colname 0 (1- len))
+ colname))
+ (ucol (when last-digit?
+ (find-ucol-of-colname base-colname filename ucols))))
+ (when (and last-digit? (null ucol))
+ (error "Couldn't find a base column for col ~A in file ~A"
+ colname filename))
+ (copy-or-new-ucol colname filename ucol)))
+
+(defun copy-or-new-ucol (colname filename ucol)
+ (if ucol
+ (make-instance
+ 'ucol
+ :col (copy-seq colname) :des (copy-seq (des ucol)) :ref (copy-seq (ref ucol))
+ :min (cmin ucol) :max (cmax ucol) :fil (copy-seq (fil ucol))
+ :sqltype (copy-seq (sqltype ucol)) :dty (copy-seq (dty ucol))
+ :parse-fun (parse-fun ucol) :quote-str (copy-seq (quote-str ucol))
+ :datatype (datatype ucol) :custom-value-fun (custom-value-fun ucol))
+ (make-empty-ucol colname filename)))
+
+(defun make-ucol (col des ref min av max fil dty
+ &key (sqltype "VARCHAR") (parse-fun #'add-sql-quotes)
+ (quote-str "'") (custom-value-fun))
+ (let ((ucol (make-instance
+ 'ucol
+ :col col :des des :ref ref :min min :av av :max max :fil fil
+ :dty dty :sqltype sqltype :parse-fun parse-fun
+ :quote-str quote-str :custom-value-fun custom-value-fun)))
+ (ensure-ucol-datatype ucol (datatype-for-colname col))
+ ucol))
+
+(defun make-empty-ucol (colname filename)
+ (make-ucol (copy-seq colname) "Unknown" "" nil nil nil filename nil))
(defun find-ucol (colname filename)
"Returns list of umls-col structure for a column name and a filename"
- (find-or-make-col-in-columns colname filename *umls-cols*))
+ (ensure-col-in-columns colname filename *umls-cols*))
(defun find-ufile (filename)
"Returns umls-file structure for a filename"
- (find-if (lambda (f) (string-equal filename (fil f))) *umls-files*))
-
-(defun ucols-for-ufile (file)
- "Returns list of umls-cols for a file structure"
- (let ((filename (fil file)))
- (mapcar (lambda (col) (find-ucol col filename))
- (fields file))))
-
-
+ (find-if #'(lambda (f) (string-equal filename (fil f))) *umls-files*))
+
+(defun find-ucols-for-filename (filename)
+ "Returns list of umls-cols for a file structure"
+ (loop for colname in (fields (find-ufile filename))
+ collect (find-ucol colname filename)))
+
+(defun umls-field-string-to-list (fmt)
+ "Converts a comma delimited list of fields into a list of field names. Will
+append a unique number (starting at 2) onto a column name that is repeated in the list"
+ (let ((col-counts (make-hash-table :test 'equal)))
+ (loop for colname in (delimited-string-to-list (escape-column-name fmt) #\,)
+ collect
+ (multiple-value-bind (value found) (gethash col col-counts)
+ (cond
+ (found
+ (incf (gethash col col-counts))
+ (concatenate 'string colname (write-to-string (1+ value))))
+ (t
+ (setf (gethash col col-counts) 1)
+ colname))))))
+
+(defun make-ufile (fil des table cls rws bts fields)
+ (let ((ufile
+ (make-instance
+ 'ufile :fil fil :des des :table table :cls cls :rws rws :bts bts
+ :fields fields)))
+ (setf (ucols ufile) (find-ucols-for-filename fil))
+ ufile))
+
+(defun datatype-for-colname (colname)
+"Return datatype for column name"
+ (second (find colname +col-datatypes+ :key #'car :test #'string-equal)))
+
+(defun ensure-ucol-datatype (col datatype)
+"Add data type information to column"
+ (setf (datatype col) datatype)
+ (case datatype
+ (sql-u (setf (sqltype col) "INTEGER"
+ (parse-fun col) #'parse-ui
+ (quote-str col) ""))
+ (sql-s (setf (sqltype col) "SMALLINT"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-l (setf (sqltype col) "BIGINT"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-i (setf (sqltype col) "INTEGER"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-f (setf (sqltype col) "NUMERIC"
+ (parse-fun col) #'read-from-string
+ (quote-str col) ""))
+ (t ; Default column type, optimized text storage
+ (setf (parse-fun col) #'add-sql-quotes
+ (quote-str col) "'")
+ (when (and (cmax col) (av col))
+ (if (> (cmax col) 255)
+ (setf (sqltype col) "TEXT")
+ (if (< (- (cmax col) (av col)) 4)
+ (setf (sqltype col) "CHAR") ; if average bytes wasted < 4
+ (setf (sqltype col) "VARCHAR")))))))
+
+(defun escape-column-name (name)
+ (substitute #\_ #\/ name))
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: parse-macros.lisp
-;;;; Purpose: Macros for UMLS file parsing
-;;;; Programmer: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
+;;;; Name: parse-macros.lisp
+;;;; Purpose: Macros for UMLS file parsing
+;;;; Author: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-macros.lisp,v 1.6 2003/05/06 06:09:29 kevin Exp $
+;;;; $Id: parse-macros.lisp,v 1.7 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
--- /dev/null
+(defpackage #:run-tests (:use #:cl))
+(in-package #:run-tests)
+
+(require 'rt)
+(require 'kmrcl)
+(require 'clsql-mysql)
+(require 'clsql)
+(require 'hyperobject)
+(load "umlisp.asd")
+(asdf:oos 'asdf:test-op 'umlisp)
+
+(defun quit (&optional (code 0))
+ "Function to exit the Lisp implementation. Copied from CLOCC's QUIT function."
+ #+allegro (excl:exit code)
+ #+clisp (#+lisp=cl ext:quit #-lisp=cl lisp:quit code)
+ #+(or cmu scl) (ext:quit code)
+ #+cormanlisp (win32:exitprocess code)
+ #+gcl (lisp:bye code)
+ #+lispworks (lw:quit :status code)
+ #+lucid (lcl:quit code)
+ #+sbcl (sb-ext:quit :unix-status (typecase code (number code) (null 0) (t 1)))
+ #+mcl (ccl:quit code)
+ #-(or allegro clisp cmu scl cormanlisp gcl lispworks lucid sbcl mcl)
+ (error 'not-implemented :proc (list 'quit code)))
+
+(quit)
+
+++ /dev/null
-;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
-;;;; *************************************************************************
-;;;; FILE IDENTIFICATION
-;;;;
-;;;; Name: sql-create
-;;;; Purpose: Create SQL database for UMLisp
-;;;; Author: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
-;;;;
-;;;; $Id: sql-create.lisp,v 1.21 2003/05/06 08:15:47 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)
-
-(eval-when (:compile-toplevel)
- (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
-
-(defun create-table-cmd (file)
- "Return sql command to create a table"
- (let ((col-func
- (lambda (c)
- (let ((sqltype (sqltype c)))
- (concatenate 'string
- (col c)
- " "
- (if (or (string-equal sqltype "VARCHAR")
- (string-equal sqltype "CHAR"))
- (format nil "~a (~a)" sqltype (cmax c))
- sqltype))))))
- (format nil "CREATE TABLE ~a (~{~a~^,~})" (table file)
- (mapcar col-func (ucols-for-ufile file)))))
-
-(defun create-custom-table-cmd (tablename sql-cmd)
- "Return SQL command to create a custom table"
- (format nil "CREATE TABLE ~a AS ~a;" tablename sql-cmd))
-
-(defun insert-col-value (col value)
- (if (null (parse-fun col))
- value
- (format nil "~A" (funcall (parse-fun col) value))))
-
-(defun insert-values-cmd (file values)
- "Return sql insert command for a row of values"
- (let ((insert-func
- (lambda (col value)
- (let ((q (quotechar col)))
- (concatenate 'string q (insert-col-value col value) q)))))
- (format
- nil "INSERT INTO ~a (~{~a~^,~}) VALUES (~A)"
- (table file)
- (fields file)
- (concat-separated-strings
- ","
- (mapcar insert-func (remove-custom-cols (ucols file)) values)
- (custom-col-values (custom-ucols-for-file file) values t)))))
-
-
-(defun custom-col-value (col values doquote)
- (let ((custom-value (funcall (custom-value-fun col) values)))
- (if custom-value
- (if doquote
- (let ((q (quotechar col)))
- (concatenate 'string q (escape-backslashes custom-value) q))
- (escape-backslashes custom-value))
- "")))
-
-(defun custom-col-values (ucols values doquote)
- "Returns a list of string column values for SQL inserts for custom columns"
- (loop for col in ucols collect (custom-col-value col values doquote)))
-
-(defun remove-custom-cols (cols)
- "Remove custom cols from a list col umls-cols"
- (remove-if #'custom-value-fun cols))
-
-(defun find-custom-cols-for-filename (filename)
- (remove-if-not (lambda (x) (string-equal filename (car x))) +custom-cols+))
-
-(defun find-custom-col (filename col)
- (find-if (lambda (x) (and (string-equal filename (car x))
- (string-equal col (cadr x)))) +custom-cols+))
-
-(defun custom-colnames-for-filename (filename)
- (mapcar #'cadr (find-custom-cols-for-filename filename)))
-
-(defun custom-ucols-for-file (file)
- (remove-if-not #'custom-value-fun (ucols file)))
-
-(defun noneng-lang-index-files ()
- (remove-if-not
- (lambda (f) (and (> (length (fil f)) 4)
- (string-equal (fil f) "MRXW." :end1 5)
- (not (string-equal (fil f) "MRXW.ENG"))
- (not (string-equal (fil f) "MRXW.NONENG"))))
- *umls-files*))
-
-;;; SQL Command Functions
-
-(defun create-index-cmd (colname tablename length)
- "Return sql create index command"
- (format nil "CREATE INDEX ~a ON ~a (~a ~a)"
- (concatenate 'string tablename "_" colname "_X")
- tablename colname
- (if (integerp length) (format nil "(~d)" length) "")))
-
-(defun create-all-tables-cmdfile ()
- "Return sql commands to create all tables. Not need for automated SQL import"
- (mapcar (lambda (f) (format nil "~a~%~%" (create-table-cmd f))) *umls-files*))
-
-;; SQL Execution functions
-
-(defun sql-drop-tables (conn)
- "SQL Databases: drop all tables"
- (dolist (file *umls-files*)
- (ignore-errors
- (sql-execute (format nil "DROP TABLE ~a" (table file)) conn))))
-
-(defun sql-create-tables (conn)
- "SQL Databases: create all tables"
- (dolist (file *umls-files*)
- (sql-execute (create-table-cmd file) conn)))
-
-(defun sql-create-custom-tables (conn)
- "SQL Databases: create all custom tables"
- (dolist (ct +custom-tables+)
- (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn)))
-
-(defun sql-insert-values (conn file)
- "SQL Databases: inserts all values for a file"
- (with-umls-file (line (fil file))
- (sql-execute (insert-values-cmd file line) conn)))
-
-(defun sql-insert-all-values (conn)
- "SQL Databases: inserts all values for all files"
- (dolist (file *umls-files*)
- (sql-insert-values conn file)))
-
-(defun sql-create-indexes (conn &optional (indexes +index-cols+))
- "SQL Databases: create all indexes"
- (dolist (idx indexes)
- (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
-
-(defun make-usrl (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)))
-
-(defun sql-create-special-tables (conn)
- (make-usrl conn))
-
-(defun create-umls-db-by-insert ()
- "SQL Databases: initializes entire database via SQL insert commands"
- (init-umls)
- (init-hash-table)
- (with-sql-connection (conn)
- (sql-drop-tables conn)
- (sql-create-tables conn)
- (sql-insert-all-values conn)
- (sql-create-indexes conn)
- (sql-create-custom-tables conn)
- (sql-create-indexes conn +custom-index-cols+)
- (sql-create-special-tables conn)))
-
-(defun create-umls-db (&optional (extension ".trans")
- (copy-cmd #'mysql-copy-cmd))
- "SQL Databases: initializes entire database via SQL copy commands.
-This is much faster that using create-umls-db-insert."
- (init-umls)
- (init-hash-table)
- (translate-all-files extension)
- (with-sql-connection (conn)
- (sql-drop-tables conn)
- (sql-create-tables conn)
- (map 'nil
- #'(lambda (file) (sql-execute (funcall copy-cmd file extension) conn))
- *umls-files*)
- (sql-create-indexes conn)
- (sql-create-custom-tables conn)
- (sql-create-indexes conn +custom-index-cols+)
- (sql-create-special-tables conn)))
-
-(defun translate-all-files (&optional (extension ".trans"))
- "Copy translated files and return postgresql copy commands to import"
- (make-noneng-index-file extension)
- (dolist (f *umls-files*) (translate-umls-file f extension)))
-
-(defun translate-umls-file (file extension)
- "Translate a umls file into a format suitable for sql copy cmd"
- (translate-files file extension (list file)))
-
-(defun make-noneng-index-file (extension)
- "Make non-english index file"
- (translate-files (find-ufile "MRXW.NONENG")
- extension (noneng-lang-index-files)))
-
-(defun translate-files (out-ufile extension input-ufiles)
- "Translate a umls file into a format suitable for sql copy cmd"
- (let ((output-path (umls-pathname (fil out-ufile) extension)))
- (if (probe-file output-path)
- (format t "File ~A already exists: skipping~%" output-path)
- (with-open-file (ostream output-path :direction :output)
- (dolist (input-ufile input-ufiles)
- (with-umls-file (line (fil input-ufile))
- (translate-line out-ufile line ostream)
- (princ #\newline ostream)))))))
-
-(defun pg-copy-cmd (file extension)
- "Return postgresql copy statement for a file"
- (format
- nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
- (table file) (umls-pathname (fil file) extension)))
-
-(defun mysql-copy-cmd (file extension)
- "Return mysql copy statement for a file"
- (format
- nil
- "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
- (umls-pathname (fil file) extension) (table file)))
-
-(defun col-value (col value)
- (if (eq (datatype col) 'sql-u)
- (let ((ui (parse-ui value "")))
- (if (stringp ui)
- ui
- (write-to-string ui)))
- (escape-backslashes value)))
-
-(defun translate-line (file line strm)
- "Translate a single line for sql output"
- (print-separated-strings
- strm "|"
- (mapcar #'col-value (remove-custom-cols (ucols file)) line)
- (custom-col-values (custom-ucols-for-file file) line nil)))
-
-
-;;; Routines for analyzing cost of fixed size storage
-
-
-(defun umls-fixed-size-waste ()
- "Display storage waste if using all fixed size storage"
- (let ((totalwaste 0)
- (totalunavoidable 0)
- (totalavoidable 0)
- (unavoidable '())
- (avoidable '()))
- (dolist (file *umls-files*)
- (dolist (col (ucols file))
- (let* ((avwaste (- (cmax col) (av col)))
- (cwaste (* avwaste (rws file))))
- (when (plusp cwaste)
- (if (<= avwaste 6)
- (progn
- (incf totalunavoidable cwaste)
- (push (list (fil file) (col col)
- avwaste cwaste)
- unavoidable))
- (progn
- (incf totalavoidable cwaste)
- (push (list (fil file) (col col)
- avwaste cwaste)
- avoidable)))
- (incf totalwaste cwaste)))))
- (values totalwaste totalavoidable totalunavoidable
- (nreverse avoidable) (nreverse unavoidable))))
-
-(defun display-waste ()
- (unless *umls-files*
- (init-umls))
- (multiple-value-bind (tw ta tu al ul) (umls-fixed-size-waste)
- (format t "Total waste: ~d~%" tw)
- (format t "Total avoidable: ~d~%" ta)
- (format t "Total unavoidable: ~d~%" tu)
- (format t "Avoidable:~%")
- (dolist (w al)
- (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
- (format t "Unavoidable:~%")
- (dolist (w ul)
- (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
- ))
-
-(defun max-umls-field ()
- "Return length of longest field"
- (unless *umls-files*
- (init-umls))
- (let ((max 0))
- (declare (fixnum max))
- (dolist (col *umls-cols*)
- (when (> (cmax col) max)
- (setq max (cmax col))))
- max))
-
-(defun max-umls-row ()
- "Return length of longest row"
- (unless *umls-files*
- (init-umls))
- (let ((rowsizes '()))
- (dolist (file *umls-files*)
- (let ((row 0)
- (fields (ucols file)))
- (dolist (field fields)
- (incf row (1+ (cmax field))))
- (push row rowsizes)))
- (car (sort rowsizes #'>))))
;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: umlisp.asd,v 1.16 2003/05/03 17:10:08 kevin Exp $
+;;;; $Id: umlisp.asd,v 1.17 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
(:file "parse-macros" :depends-on ("sql"))
(:file "parse-2002" :depends-on ("parse-macros"))
(:file "parse-common" :depends-on ("parse-2002"))
- (:file "sql-create" :depends-on ("parse-common"))
+ (:file "create-sql" :depends-on ("parse-common"))
(:file "classes" :depends-on ("utils"))
(:file "class-support" :depends-on ("classes"))
(:file "sql-classes" :depends-on ("class-support" "sql"))
projects / umlisp.git / commitdiff