1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
5 ;;;; Name: parse-rrf.lisp
6 ;;;; Purpose: Parsing and SQL insertion routines for UMLisp which may
7 ;;;; change from year to year
8 ;;;; Author: Kevin M. Rosenberg
11 ;;;; This file, part of UMLisp, is
12 ;;;; Copyright (c) 2000-2010 by Kevin M. Rosenberg, M.D.
14 ;;;; UMLisp users are granted the rights to distribute and use this software
15 ;;;; as governed by the terms of the GNU General Public License.
16 ;;;; *************************************************************************
20 ;;; Pre-read data for custom fields into hash tables
21 (defvar *preparse-hash-init?* nil)
23 (eval-when (:compile-toplevel :load-toplevel :execute)
25 (declaim (inline srl-to-srlus))
26 (defun srl-to-srlus (srl)
27 "Convert the standard SRL category to one oriented for use in the ~
28 United States. Specifically, SRL 4 in the USA has license restrictions ~
29 between SRL 1 and 2 when used in the United States. As of 2009AA, the
30 SNOMED SRL changed from 4 to 9. So we create a new scale ~
31 (SRLUS) where SRL to SRLUS mapping is: ~
32 (0->0, 1->1, 4->2, 9->2, 2->3, 3->4)."
33 (declare (type (integer 0 100) srl))
42 (defvar *vff-position-hash* (make-hash-table :size 100 :test 'eq))
44 (defmacro vff (filename fieldname record)
45 (let ((pos (gensym "POS-"))
46 (found (gensym "FOUND-"))
47 (key (kmrcl:ensure-keyword (concatenate 'string filename "^" fieldname))))
48 `(locally (declare (optimize (speed 3) (safety 0)))
49 (multiple-value-bind (,pos ,found) (gethash ,key *vff-position-hash*)
50 (declare (ignore ,found))
52 (locally (declare (type (integer 0 100000) ,pos))
54 (let ((,pos (position-field-file ,filename ,fieldname)))
56 (error "Did not find fieldname ~A in filename ~A." ,fieldname ,filename))
57 (locally (declare (type (integer 0 100000) ,pos))
58 (setf (gethash ,key *vff-position-hash*) ,pos)
59 (nth ,pos ,record))))))))
61 (let ((pfstr-hash nil) ;; Preferred concept strings by CUI
62 (cui-lrl-hash nil) ;; LRL by CUI
63 (lui-lrl-hash nil) ;; LRL by LUI
64 (sui-lrl-hash nil) ;; LRL by SUI
65 (cuisui-lrl-hash nil) ;; LRL by CUISUI
66 (cui-lrlus-hash nil) ;; LRLUS by CUI
67 (lui-lrlus-hash nil) ;; LRLUS by LUI
68 (sui-lrlus-hash nil) ;; LRLUS by SUI
69 (cuisui-lrlus-hash nil) ;; LRL by CUISUI
72 (sab-srlus-hash nil)) ;; SRL by SAB
74 (defun clear-preparse-hash-tables ()
76 (clrhash cui-lrl-hash)
77 (clrhash lui-lrl-hash)
78 (clrhash sui-lrl-hash)
79 (clrhash cuisui-lrl-hash)
80 (clrhash cui-lrlus-hash)
81 (clrhash lui-lrlus-hash)
82 (clrhash sui-lrlus-hash)
83 (clrhash cuisui-lrlus-hash)
84 (clrhash sab-srl-hash)
85 (clrhash sab-srlus-hash))
87 (defun make-preparse-hash-table ()
89 (clear-preparse-hash-tables)
91 pfstr-hash (make-hash-table :size 1500000)
92 cui-lrl-hash (make-hash-table :size 1500000)
93 lui-lrl-hash (make-hash-table :size 5000000)
94 sui-lrl-hash (make-hash-table :size 6000000)
95 cuisui-lrl-hash (make-hash-table :size 6000000)
96 cui-lrlus-hash (make-hash-table :size 1500000)
97 lui-lrlus-hash (make-hash-table :size 5000000)
98 sui-lrlus-hash (make-hash-table :size 6000000)
99 cuisui-lrlus-hash (make-hash-table :size 6000000)
100 sab-srl-hash (make-hash-table :size 200 :test 'equal)
101 sab-srlus-hash (make-hash-table :size 200 :test 'equal))))
103 (defun ensure-preparse (&optional (force-read nil))
104 (when (and *preparse-hash-init?* (not force-read))
105 (return-from ensure-preparse 'already-done))
106 (make-preparse-hash-table)
108 (declare (fixnum counter)
110 (with-umls-file (line "MRCONSO.RRF")
111 (let* ((cui (parse-ui (vff "MRCONSO.RRF" "CUI" line)))
112 (lui (parse-ui (vff "MRCONSO.RRF" "LUI" line)))
113 (sui (parse-ui (vff "MRCONSO.RRF" "SUI" line)))
114 (sab (vff "MRCONSO.RRF" "SAB" line))
115 (srl (parse-integer (vff "MRCONSO.RRF" "SRL" line)))
116 (srlus (srl-to-srlus srl))
117 (cuisui (make-cuisui cui sui)))
119 (when (= 0 (mod (incf counter) 100000)) (sb-ext:gc :full t))
121 ;; pfstr deprecated by KPFENG field in MRCONSO
123 (unless (gethash cui pfstr-hash) ;; if haven't stored pfstr for cui
124 (when (and (string-equal (vff "MRCONSO.RRF" "LAT" line) "ENG")
125 (string-equal (vff "MRCONSO.RRF" "TS" line) "P")
126 (string-equal (vff "MRCONSO.RRF" "STT" line) "PF"))
127 (setf (gethash cui pfstr-hash) (vff "MRCONSO.RRF" "STR" line))))
128 (set-lrl-hash cui srl cui-lrl-hash)
129 (set-lrl-hash lui srl lui-lrl-hash)
130 (set-lrl-hash sui srl sui-lrl-hash)
131 (set-lrl-hash cuisui srl cuisui-lrl-hash)
132 (set-lrl-hash cui srlus cui-lrlus-hash)
133 (set-lrl-hash lui srlus lui-lrlus-hash)
134 (set-lrl-hash sui srlus sui-lrlus-hash)
135 (set-lrl-hash cuisui srlus cuisui-lrlus-hash)
136 (multiple-value-bind (val found) (gethash sab sab-srl-hash)
137 (declare (ignore val))
139 (setf (gethash sab sab-srl-hash) srl)))
140 (multiple-value-bind (val found) (gethash sab sab-srlus-hash)
141 (declare (ignore val))
143 (setf (gethash sab sab-srlus-hash) srlus))))))
144 (setq *preparse-hash-init?* t)
147 #+nil (defun pfstr-hash (cui) (gethash cui pfstr-hash))
148 (defun cui-lrl (cui) (gethash cui cui-lrl-hash))
149 (defun lui-lrl (lui) (gethash lui lui-lrl-hash))
150 (defun sui-lrl (sui) (gethash sui sui-lrl-hash))
151 (defun cuisui-lrl (cuisui) (gethash cuisui cuisui-lrl-hash))
152 (defun cui-lrlus (cui) (gethash cui cui-lrlus-hash))
153 (defun lui-lrlus (lui) (gethash lui lui-lrlus-hash))
154 (defun sui-lrlus (sui) (gethash sui sui-lrlus-hash))
155 (defun cuisui-lrlus (cuisui) (gethash cuisui cuisui-lrlus-hash))
156 (defun sab-srl (sab) (aif (gethash sab sab-srl-hash) it 0))
157 (defun sab-srlus (sab) (aif (gethash sab sab-srlus-hash) it 0))
162 (defun set-lrl-hash (key srl hash)
163 "Set the least restrictive level in hash table"
164 (declare (fixnum srl))
165 (multiple-value-bind (hash-lrl found) (gethash key hash)
166 (declare (type (or null fixnum) hash-lrl)
168 (if (or (not found) (< srl hash-lrl))
169 (setf (gethash key hash) srl))))
171 ;; UMLS file and column structures
172 ;;; SQL datatypes symbols
173 ;;; sql-u - Unique identifier
174 ;;; sql-t - Tiny integer (8-bit)
175 ;;; sql-s - Small integer (16-bit)
176 ;;; sql-i - Integer (32-bit)
177 ;;; sql-l - Big integer (64-bit)
178 ;;; sql-f - Floating point
179 ;;; sql-c - Character data
181 (defparameter +col-datatypes+
182 '(("AV" sql-f) ("BTS" sql-i) ("CLS" sql-i) ("COF" sql-i) ("CUI1" sql-u)
183 ("AUI" sql-u) ("AUI1" sql-u) ("AUI2" sql-u) ("PCUI" sql-u)
184 ("PLUI" sql-u) ("PAUI" sql-u) ("RUI" sql-u)
185 ("CUI2" sql-u) ("CUI" sql-u) ("CXN" sql-s) ("FR" sql-i)
186 ("LUI" sql-u) ("MAX" sql-s) ("MIN" sql-s) ("RANK" sql-s) ("REF" sql-c)
188 ("RNK" sql-s) ("RWS" sql-i) ("SRL" sql-t) ("SUI" sql-u) ("TUI" sql-u)
191 ("KCUISUI" sql-l) ("KCUILUI" sql-l)
192 ("KSRL" sql-t) ("KSRLUS" sql-t) ("LRL" sql-t) ("LRLUS" sql-t)
193 ("KCUILRL" sql-t) ("KLUILRL" sql-t) ("KSUILRL" sql-t) ("KLRL" sql-t)
194 ("KCUILRLUS" sql-t) ("KLUILRLUS" sql-t) ("KSUILRLUS" sql-t) ("KLRLUS" sql-t)
196 ("EUI" sql-u) ("EUI2" sql-u)
197 ;;; Semantic net columns
198 ("UI" sql-u) ("UI2" sql-u) ("UI3" sql-u)
199 ;; New fields for 2002AD
200 ("RCUI" sql-u) ("VCUI" sql-u) ("CFR" sql-i) ("TFR" sql-i)
201 ;; New fields for 2004AA
204 "SQL data types for each non-string column")
206 (defparameter +custom-tables+
209 '(("KCON" "SELECT CUI,STR FROM MRCONSO WHERE STT='PF' AND TS='P' AND ISPREF='Y' AND LAT='ENG'"))
210 "Custom tables to create")
212 (defparameter +custom-cols+
213 '(#+nil ("MRCONSO.RRF" "KPFSTR" "TEXT"
214 (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)
215 (lambda (x) (pfstr-hash (parse-ui (vff "MRCONSO.RRF" "CUI" x)))))
216 ;; Set to 1 if term is prefered term for english
217 ("MRCONSO.RRF" "KPFENG" "TINYINT" 0
218 (lambda (x) (if (and (string-equal (vff "MRCONSO.RRF" "LAT" x) "ENG")
219 (string-equal (vff "MRCONSO.RRF" "TS" x) "P")
220 (string-equal (vff "MRCONSO.RRF" "STT" x) "PF"))
223 ("MRCONSO.RRF" "KCUISUI" "BIGINT" 0
224 (lambda (x) (write-to-string (make-cuisui (parse-ui (vff "MRCONSO.RRF" "CUI" x))
225 (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
226 ("MRCONSO.RRF" "KCUILUI" "BIGINT" 0
227 (lambda (x) (write-to-string (make-cuilui (parse-ui (vff "MRCONSO.RRF" "CUI" x))
228 (parse-ui (vff "MRCONSO.RRF" "LUI" x))))))
229 ("MRCONSO.RRF" "KCUILRL" "TINYINT" 0
230 (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRCONSO.RRF" "CUI" x))))))
231 ("MRCONSO.RRF" "KCUILRLUS" "TINYINT" 0
232 (lambda (x) (write-to-string (cui-lrlus (parse-ui (vff "MRCONSO.RRF" "CUI" x))))))
233 ("MRCONSO.RRF" "KLUILRL" "TINYINT" 0
234 (lambda (x) (write-to-string (lui-lrl (parse-ui (vff "MRCONSO.RRF" "LUI" x))))))
235 ("MRCONSO.RRF" "KLUILRLUS" "TINYINT" 0
236 (lambda (x) (write-to-string (lui-lrlus (parse-ui (vff "MRCONSO.RRF" "LUI" x))))))
237 ("MRCONSO.RRF" "KSUILRL" "TINYINT" 0
238 (lambda (x) (write-to-string (sui-lrl (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
239 ("MRCONSO.RRF" "KSUILRLUS" "TINYINT" 0
240 (lambda (x) (write-to-string (sui-lrlus (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
241 ("MRCONSO.RRF" "KSRLUS" "TINYINT" 0
242 (lambda (x) (write-to-string (srl-to-srlus (parse-integer (vff "MRCONSO.RRF" "SRL" x))))))
243 ("MRSAB.RRF" "KSRLUS" "TINYINT" 0
244 (lambda (x) (write-to-string (srl-to-srlus (parse-integer (vff "MRSAB.RRF" "SRL" x))))))
245 ("MRSTY.RRF" "KLRL" "TINYINT" 0
246 (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
247 ("MRSTY.RRF" "KLRLUS" "TINYINT" 0
248 (lambda (x) (write-to-string (cui-lrlus (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
249 #+mrcoc ("MRCOC.RRF" "KLRL" "TINYINT" 0
250 (lambda (x) (write-to-string
251 (max (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
252 (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
253 #+mrcoc ("MRCOC.RRF" "KLRLUS" "TINYINT" 0
254 (lambda (x) (write-to-string
255 (max (cui-lrlus (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
256 (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
257 ("MRSAT.RRF" "KSRL" "TINYINT" 0
258 (lambda (x) (write-to-string (sab-srl (vff "MRSAT.RRF" "SAB" x)))))
259 ("MRSAT.RRF" "KSRLUS" "TINYINT" 0
260 (lambda (x) (write-to-string (sab-srlus (vff "MRSAT.RRF" "SAB" x)))))
261 ("MRREL.RRF" "KSRL" "TINYINT" 0
262 (lambda (x) (write-to-string (sab-srl (vff "MRREL.RRF" "SAB" x)))))
263 ("MRREL.RRF" "KSRLUS" "TINYINT" 0
264 (lambda (x) (write-to-string (sab-srlus (vff "MRREL.RRF" "SAB" x)))))
265 ("MRRANK.RRF" "KSRL" "TINYINT" 0
266 (lambda (x) (write-to-string (sab-srl (vff "MRRANK.RRF" "SAB" x)))))
267 ("MRRANK.RRF" "KSRLUS" "TINYINT" 0
268 (lambda (x) (write-to-string (sab-srlus (vff "MRRANK.RRF" "SAB" x)))))
269 ("MRHIER.RRF" "KSRL" "TINYINT" 0
270 (lambda (x) (write-to-string (sab-srl (vff "MRHIER.RRF" "SAB" x)))))
271 ("MRHIER.RRF" "KSRLUS" "TINYINT" 0
272 (lambda (x) (write-to-string (sab-srlus (vff "MRHIER.RRF" "SAB" x)))))
273 ("MRMAP.RRF" "KSRL" "TINYINT" 0
274 (lambda (x) (write-to-string (sab-srl (vff "MRMAP.RRF" "MAPSETSAB" x)))))
275 ("MRMAP.RRF" "KSRLUS" "TINYINT" 0
276 (lambda (x) (write-to-string (sab-srlus (vff "MRMAP.RRF" "MAPSETSAB" x)))))
277 ("MRSMAP.RRF" "KSRL" "TINYINT" 0
278 (lambda (x) (write-to-string (sab-srl (vff "MRSMAP.RRF" "MAPSETSAB" x)))))
279 ("MRSMAP.RRF" "KSRLUS" "TINYINT" 0
280 (lambda (x) (write-to-string (sab-srlus (vff "MRSMAP.RRF" "MAPSETSAB" x)))))
281 ("MRDEF.RRF" "KSRL" "TINYINT" 0
282 (lambda (x) (write-to-string (sab-srl (vff "MRDEF.RRF" "SAB" x)))))
283 ("MRDEF.RRF" "KSRLUS" "TINYINT" 0
284 (lambda (x) (write-to-string (sab-srlus (vff "MRDEF.RRF" "SAB" x)))))
285 ("MRXW_ENG.RRF" "KLRL" "TINYINT" 0
286 (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
287 (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
288 (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))
289 ("MRXW_ENG.RRF" "KLRLUS" "TINYINT" 0
290 (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
291 (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
292 (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))
293 ("MRXW_NONENG.RRF" "KLRL" "TINYINT" 0
294 (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
295 (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
296 (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))
297 ("MRXW_NONENG.RRF" "KLRLUS" "TINYINT" 0
298 (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
299 (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
300 (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))
301 ("MRXNW_ENG.RRF" "KLRL" "TINYINT" 0
302 (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
303 (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
304 (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))
305 ("MRXNW_ENG.RRF" "KLRLUS" "TINYINT" 0
306 (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
307 (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
308 (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))
309 ("MRXNS_ENG.RRF" "KLRL" "TINYINT" 0
310 (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
311 (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
312 (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))
313 ("MRXNS_ENG.RRF" "KLRLUS" "TINYINT" 0
314 (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
315 (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
316 (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))
318 #+nil ("MRREL.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRREL.RRF" "CUI2" x)))))
319 #+mrcoc ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRCOC.RRF" "CUI2" x)))))
321 ("MRSAT.RRF" "KCUILUI" "BIGINT" 0
322 (lambda (x) (write-to-string (make-cuilui
323 (parse-ui (vff "MRSAT.RRF" "CUI" x))
324 (parse-ui (vff "MRSAT.RRF" "LUI" x))))))
325 ("MRSAT.RRF" "KCUISUI" "BIGINT" 0
326 (lambda (x) (write-to-string (make-cuisui
327 (parse-ui (vff "MRSAT.RRF" "CUI" x))
328 (parse-ui (vff "MRSAT.RRF" "SUI" x))))))
329 ("MRXW_ENG.RRF" "KCUISUI" "BIGINT" 0
330 (lambda (x) (write-to-string (make-cuisui
331 (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
332 (parse-ui (vff "MRXW_ENG.RRF" "SUI" x))))))
333 ("MRXNW_ENG.RRF" "KCUISUI" "BIGINT" 0
334 (lambda (x) (write-to-string (make-cuisui
335 (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
336 (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x))))))
337 ("MRXNS_ENG.RRF" "KCUISUI" "BIGINT" 0
338 (lambda (x) (write-to-string (make-cuisui
339 (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
340 (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x))))))
341 ("MRXW_NONENG.RRF" "LAT" "VARCHAR" 3 (lambda (x) (vff "MRXW_NONENG.RRF" "LAT" x)))
342 ("MRXW_NONENG.RRF" "WD" "VARCHAR" 200 (lambda (x) (vff "MRXW_NONENG.RRF" "WD" x)))
343 ("MRXW_NONENG.RRF" "CUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x)))))
344 ("MRXW_NONENG.RRF" "LUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (vff "MRXW_NONENG.RRF" "LUI" x)))))
345 ("MRXW_NONENG.RRF" "SUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))
346 ("MRXW_NONENG.RRF" "KCUISUI" "BIGINT" 0
347 (lambda (x) (write-to-string (make-cuisui
348 (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
349 (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))
350 "Custom columns to create.(filename, col, sqltype, value-func).")
352 (defparameter +index-cols+
353 '( #+mrcoc ("CUI1" "MRCOC") #+mrcoc ("KLRL" "MRCOC") #+mrcoc ("KLRLUS" "MRCOC")
354 ("CUI" "MRCONSO") ("LUI" "MRCONSO")
355 ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
356 ("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
359 ("CUI1" "MRREL") ("CUI2" "MRREL") ("SAB" "MRREL")
360 ("RUI" "MRREL") ("AUI1" "MRREL") ("AUI2" "MRREL")
361 ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
362 ("METAUI" "MRSAT") ("ATN" "MRSAT")
363 ("CUI" "MRSTY") ("TUI" "MRSTY") ("CUI" "MRXNS_ENG")
364 ("AUI" "MRHIER") ("CUI" "MRHIER") ("CXN" "MRHIER") ("RELA" "MRHIER")
365 ("PAUI" "MRHIER") ("SAB" "MRHIER")
366 ("NSTR" "MRXNS_ENG" 255)
367 ("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
368 ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO")
369 ("KCUILRL" "MRCONSO") ("KLUILRL" "MRCONSO") ("KSUILRL" "MRCONSO")
370 ("KCUILRLUS" "MRCONSO") ("KLUILRLUS" "MRCONSO") ("KSUILRLUS" "MRCONSO")
371 ("KCUISUI" "MRSAT") ("KCUILUI" "MRSAT")
372 ("KCUISUI" "MRXW_ENG") ("KCUISUI" "MRXNW_ENG")
373 ("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
374 ("KSRL" "MRDEF") ("KSRL" "MRRANK")("KSRL" "MRREL") ("KSRL" "MRSAT")
375 ("KSRLUS" "MRDEF") ("KSRLUS" "MRRANK")("KSRLUS" "MRREL") ("KSRLUS" "MRSAT")
376 ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
377 ("KLRLUS" "MRSTY") ("KLRLUS" "MRXW_ENG") ("KLRLUS" "MRXNW_ENG")
378 ("KLRL" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
379 ("KLRLUS" "MRXNS_ENG") ("KLRLUS" "MRXW_NONENG")
381 ("EUI" "LRABR") ("EUI2" "LRABR") ("EUI" "LRAGR") ("EUI" "LRCMP") ("EUI" "LRMOD")
382 ("EUI" "LRNOM") ("EUI2" "LRNOM") ("EUI" "LRPRN") ("EUI" "LRPRP") ("EUI" "LRSPL")
383 ("EUI" "LRTRM") ("EUI" "LRTYP") ("EUI" "LRWD") ("WRD" "LRWD")
385 ;; Semantic NET indices
386 ("UI" "SRSTRE1") ("UI2" "SRSTRE1") ("UI3" "SRSTRE1")
387 ("STY_RL" "SRDEF") ("RT" "SRDEF") ("STY_RL" "SRSTR") ("STY_RL2" "SRSTR")
390 ("SRL" "MRSAB") ("KSRLUS" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
391 ("VCUI" "MRSAB") ("LAT" "MRSAB") ("MAPSETCUI" "MRMAP") ("MAPSETCUI" "MRSMAP"))
392 "Columns in files to index")
395 (defparameter +custom-index-cols+
398 '(("CUI" "KCON") ("LRL" "KCON"))
399 "Indexes to custom tables")
401 ;; File & Column functions
404 (add-ucols (gen-ucols-meta))
405 (add-ucols (gen-ucols-generic "LRFLD"))
406 (add-ucols (gen-ucols-generic "SRFLD"))
407 (add-ucols (gen-ucols-custom)))
409 (defun gen-ucols-meta ()
410 "Initialize all umls columns"
412 (with-umls-file (line "MRCOLS.RRF")
413 (destructuring-bind (col des ref min av max fil dty) line
414 (push (make-ucol col des ref (parse-integer min) (read-from-string av)
415 (parse-integer max) fil dty)
419 (defun gen-ucols-custom ()
420 "Initialize umls columns for custom columns"
421 (loop for customcol in +custom-cols+
423 (make-ucol (nth 1 customcol) "" 0 0 0 (eval (nth 3 customcol))
424 (nth 0 customcol) nil :sqltype (canonicalize-column-type (nth 2 customcol))
425 :custom-value-fun (compile nil (nth 4 customcol)))))
427 (defun gen-ucols-generic (col-filename)
428 "Initialize for generic (LEX/NET) columns"
430 (with-umls-file (line col-filename)
431 (destructuring-bind (nam des ref fil) line
432 (setq nam (escape-column-name nam))
433 (dolist (file (delimited-string-to-list fil #\,))
435 (make-ucol nam des ref nil nil nil file nil)
441 (add-ufiles (gen-ufiles-generic "MRFILES.RRF" "META"))
442 (add-ufiles (gen-ufiles-generic "LRFIL" "LEX"))
443 (add-ufiles (gen-ufiles-generic "SRFIL" "NET"))
444 ;; needs to come last
445 (add-ufiles (gen-ufiles-custom)))
448 (defun gen-ufiles-generic (files-filename dir)
449 "Initialize generic UMLS file structures"
451 (with-umls-file (line files-filename)
452 (destructuring-bind (fil des fmt cls rws bts) line
456 (parse-integer rws) (parse-integer bts)
457 (concatenate 'list (umls-field-string-to-list fmt)
458 (custom-colnames-for-filename fil)))
462 (defun gen-ufiles-custom ()
463 (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"
464 5 0 0 (fields (find-ufile "MRXW_ENG.RRF"))))