1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
6 ;;;; Purpose: Create SQL database for UMLisp
7 ;;;; Programmer: Kevin M. Rosenberg
8 ;;;; Date Started: Apr 2000
10 ;;;; $Id: sql-create.lisp,v 1.5 2003/05/04 08:52:13 kevin Exp $
12 ;;;; This file, part of UMLisp, is
13 ;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
15 ;;;; UMLisp users are granted the rights to distribute and use this software
16 ;;;; as governed by the terms of the GNU General Public License.
17 ;;;; *************************************************************************
20 (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
23 (defun create-table-cmd-old (file)
24 "Return sql command to create a table"
27 (let ((sqltype (umls-col-sqltype c)))
28 (concatenate 'string (umls-col-col c)
30 (if (or (string-equal sqltype "VARCHAR")
31 (string-equal sqltype "CHAR"))
32 (format nil "~a (~a)" sqltype (umls-col-max c))
35 (format nil "CREATE TABLE ~a (~a)" (umls-file-table file)
36 (string-trim-last-character
37 (mapcar-append-string col-func (umls-cols-for-umls-file file))))))
40 (defun create-table-cmd (file)
41 "Return sql command to create a table"
44 (let ((sqltype (umls-col-sqltype c)))
48 (if (or (string-equal sqltype "VARCHAR")
49 (string-equal sqltype "CHAR"))
50 (format nil "~a (~a)" sqltype (umls-col-max c))
52 (format nil "CREATE TABLE ~a (~{~a~^,~})" (umls-file-table file)
53 (mapcar col-func (umls-cols-for-umls-file file))))))
55 (defun create-custom-table-cmd (tablename sql-cmd)
56 "Return SQL command to create a custom table"
57 (format nil "CREATE TABLE ~a AS ~a;" tablename sql-cmd))
59 (defun insert-values-cmd-old (file values)
60 "Return sql insert command for a row of values"
65 (umls-col-quotechar col)
66 (if (null (umls-col-parsefunc col))
68 (format nil "~A" (funcall (umls-col-parsefunc col) value)))
69 (umls-col-quotechar col)
72 nil "INSERT INTO ~a (~a) VALUES (~a)"
73 (umls-file-table file)
74 (string-trim-last-character
75 (mapcar-append-string (lambda (c) (concatenate 'string c ","))
76 (umls-file-fields file)))
77 (string-trim-last-character
79 (mapcar2-append-string insert-func
80 (remove-custom-cols (umls-file-colstructs file))
82 (custom-col-values (custom-colstructs-for-file file) values "," t)))
85 (defun insert-col-value (col value)
86 (if (null (umls-col-parsefunc col))
88 (format nil "~A" (funcall (umls-col-parsefunc col) value))))
90 (defun insert-values-cmd (file values)
91 "Return sql insert command for a row of values"
94 (let ((q (umls-col-quotechar col)))
95 (concatenate 'string q (insert-col-value col value) q)))))
97 nil "INSERT INTO ~a (~{~a~^,~}) VALUES (~{~a~^,~})"
98 (umls-file-table file)
99 (umls-file-fields file)
101 (mapcar insert-func (remove-custom-cols (umls-file-colstructs file)) values)
102 (custom-col-values (custom-colstructs-for-file file) values t)))))
104 (defun custom-col-values-old (colstructs values delim doquote)
105 "Returns a string of column values for SQL inserts for custom columns"
107 (dolist (col colstructs)
108 (let* ((func (umls-col-custom-value-func col))
109 (custom-value (funcall func values)))
110 (string-append result
111 (if doquote (umls-col-quotechar col))
112 (escape-backslashes custom-value)
113 (if doquote (umls-col-quotechar col))
117 (defun col-value (col doquote values)
118 (let ((custom-value (funcall (umls-col-custom-value-func col) values)))
120 (let ((q (umls-col-quotechar col)))
121 (concatenate 'string q (escape-backslashes custom-value) q))
122 (escape-backslashes custom-value))))
124 (defun custom-col-values (colstructs values doquote)
125 "Returns a list of string column values for SQL inserts for custom columns"
126 (loop for col in colstructs collect (col-value col doquote values)))
129 (defun remove-custom-cols (cols)
130 "Remove custom cols from a list col umls-cols"
131 (remove-if #'umls-col-custom-value-func cols))
133 (defun find-custom-cols-for-filename (filename)
134 (remove-if-not (lambda (x) (string-equal filename (car x))) +custom-cols+))
136 (defun find-custom-col (filename col)
137 (find-if (lambda (x) (and (string-equal filename (car x))
138 (string-equal col (cadr x)))) +custom-cols+))
141 (defun custom-colnames-for-filename (filename)
142 (mapcar #'cadr (find-custom-cols-for-filename filename)))
144 (defun custom-colstructs-for-file (file)
145 (remove-if-not #'umls-col-custom-value-func (umls-file-colstructs file)))
147 (defun noneng-lang-index-files ()
148 (remove-if-not (lambda (f) (and (> (length (umls-file-fil f)) 4)
149 (string-equal (umls-file-fil f) "MRXW." :end1 5)
150 (not (string-equal (umls-file-fil f) "MRXW.ENG"))
151 (not (string-equal (umls-file-fil f) "MRXW.NONENG"))))
154 ;;; SQL Command Functions
156 (defun create-index-cmd (colname tablename length)
157 "Return sql create index command"
158 (format nil "CREATE INDEX ~a ON ~a (~a ~a)"
159 (concatenate 'string tablename "_" colname "_X") tablename colname
160 (if (integerp length)
161 (format nil "(~d)" length)
164 (defun create-all-tables-cmdfile ()
165 "Return sql commands to create all tables. Not need for automated SQL import"
166 (mapcar (lambda (f) (format nil "~a~%~%" (create-table-cmd f))) *umls-files*))
169 ;; SQL Execution functions
171 (defun sql-drop-tables (conn)
172 "SQL Databases: drop all tables"
176 (sql-execute (format nil "DROP TABLE ~a" (umls-file-table file)) conn)))
179 (defun sql-create-tables (conn)
180 "SQL Databases: create all tables"
181 (mapcar (lambda (file) (sql-execute (create-table-cmd file) conn)) *umls-files*))
183 (defun sql-create-custom-tables (conn)
184 "SQL Databases: create all custom tables"
186 (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn))
189 (defun sql-insert-values (conn file)
190 "SQL Databases: inserts all values for a file"
191 (with-umls-file (line (umls-file-fil file))
192 (sql-execute (insert-values-cmd file line) conn)))
194 (defun sql-insert-all-values (conn)
195 "SQL Databases: inserts all values for all files"
196 (mapcar (lambda (file) (sql-insert-values conn file)) *umls-files*))
198 (defun sql-create-indexes (conn &optional (indexes +index-cols+))
199 "SQL Databases: create all indexes"
202 (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn))
205 (defun make-usrl (conn)
206 (sql-execute "drop table if exists USRL" conn)
207 (sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
208 (dolist (tuple (mutex-sql-query "select distinct SAB,SRL from MRSO order by SAB asc"))
209 (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
210 (car tuple) (ensure-integer (cadr tuple)))
213 (defun sql-create-special-tables (conn)
216 (defun create-umls-db-by-insert ()
217 "SQL Databases: initializes entire database via SQL insert commands"
220 (with-sql-connection (conn)
221 (sql-drop-tables conn)
222 (sql-create-tables conn)
223 (sql-insert-all-values conn)
224 (sql-create-indexes conn)
225 (sql-create-custom-tables conn)
226 (sql-create-indexes conn +custom-index-cols+)
227 (sql-create-special-tables conn)))
229 (defun create-umls-db (&optional (extension ".trans")
230 (copy-cmd #'mysql-copy-cmd))
231 "SQL Databases: initializes entire database via SQL copy commands.
232 This is much faster that using create-umls-db-insert."
235 (translate-all-files extension)
236 (with-sql-connection (conn)
237 (sql-drop-tables conn)
238 (sql-create-tables conn)
240 #'(lambda (file) (sql-execute (funcall copy-cmd file extension) conn))
242 (sql-create-indexes conn)
243 (sql-create-custom-tables conn)
244 (sql-create-indexes conn +custom-index-cols+)
245 (sql-create-special-tables conn)))
247 (defun translate-all-files (&optional (extension ".trans"))
248 "Copy translated files and return postgresql copy commands to import"
249 (make-noneng-index-file extension)
250 (mapcar (lambda (f) (translate-file f extension)) *umls-files*))
252 (defun translate-file (file extension)
253 "Translate a umls file into a format suitable for sql copy cmd"
254 (let ((path (umls-pathname (umls-file-fil file) extension)))
255 (if (probe-file path)
257 (format t "File ~A already exists: skipping~%" path)
259 (with-open-file (ostream path :direction :output)
260 (with-umls-file (line (umls-file-fil file))
261 (princ (umls-translate file line) ostream)
262 (princ #\newline ostream))
265 (defun make-noneng-index-file (extension)
266 "Make non-english index file"
267 (let* ((outfile (find-umls-file "MRXW.NONENG"))
268 (path (umls-pathname (umls-file-fil outfile) extension)))
270 (if (probe-file path)
272 (format t "File ~A already exists: skipping~%" path)
275 (with-open-file (ostream path :direction :output)
276 (dolist (inputfile (noneng-lang-index-files))
277 (with-umls-file (line (umls-file-fil inputfile))
278 (princ (umls-translate outfile line) ostream) ;; use outfile for custom cols
279 (princ #\newline ostream))))
282 (defun pg-copy-cmd (file extension)
283 "Return postgresql copy statement for a file"
284 (format nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
285 (umls-file-table file) (umls-pathname (umls-file-fil file) extension)))
287 (defun mysql-copy-cmd (file extension)
288 "Return mysql copy statement for a file"
289 (format nil "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
290 (umls-pathname (umls-file-fil file) extension) (umls-file-table file)))
292 (defun umls-translate-old (file line)
293 "Translate a single line for sql output"
294 (string-trim-last-character
296 (mapcar2-append-string
300 (if (eq (umls-col-datatype col) 'sql-u)
301 (format nil "~d" (parse-ui value ""))
302 (escape-backslashes value))
304 (remove-custom-cols (umls-file-colstructs file))
306 (custom-col-values (custom-colstructs-for-file file) line "|" nil))))
308 (defun umls-translate (file line)
309 "Translate a single line for sql output"
310 (format nil "~{~A~^|~}"
316 (if (eq (umls-col-datatype col) 'sql-u)
317 (format nil "~d" (parse-ui value ""))
318 (escape-backslashes value))))
319 (remove-custom-cols (umls-file-colstructs file))
321 (custom-col-values (custom-colstructs-for-file file) line nil))))
324 ;;; Routines for analyzing cost of fixed size storage
327 (defun umls-fixed-size-waste ()
328 "Display storage waste if using all fixed size storage"
334 (dolist (file *umls-files*)
335 (dolist (col (umls-file-colstructs file))
336 (let* ((avwaste (- (umls-col-max col) (umls-col-av col)))
337 (cwaste (* avwaste (umls-file-rws file))))
338 (unless (zerop cwaste)
341 (incf totalunavoidable cwaste)
342 (setq unavoidable (append unavoidable (list (list (umls-file-fil file) (umls-col-col col) avwaste cwaste)))))
344 (incf totalavoidable cwaste)
345 (setq avoidable (append avoidable (list (list (umls-file-fil file) (umls-col-col col) avwaste cwaste))))))
346 (incf totalwaste cwaste)))))
347 (values totalwaste totalavoidable totalunavoidable avoidable unavoidable)))
349 (defun display-waste ()
352 (multiple-value-bind (tw ta tu al ul) (umls-fixed-size-waste)
353 (format t "Total waste: ~d~%" tw)
354 (format t "Total avoidable: ~d~%" ta)
355 (format t "Total unavoidable: ~d~%" tu)
356 (format t "Avoidable:~%")
358 (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
359 (format t "Unavoidable:~%")
361 (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
364 (defun max-umls-field ()
365 "Return length of longest field"
369 (declare (fixnum max))
370 (dolist (col *umls-cols*)
371 (when (> (umls-col-max col) max)
372 (setq max (umls-col-max col))))
375 (defun max-umls-row ()
376 "Return length of longest row"
378 6000 ;;; hack to use on systems without MRCOLS/MRFILES -- ok for UMLS2001
382 (let ((rowsizes '()))
383 (dolist (file *umls-files*)
385 (fields (umls-file-colstructs file)))
386 (dolist (field fields)
387 (incf row (1+ (umls-col-max field))))
388 (push row rowsizes)))
389 (car (sort rowsizes #'>))))))