(sui-lrl-hash nil) ;; LRL by SUI
(cuisui-lrl-hash nil) ;; LRL by CUISUI
(sab-srl-hash nil)) ;; SRL by SAB
-
+
(defun make-preparse-hash-table ()
(if sui-lrl-hash
(progn
sui-lrl-hash (make-hash-table :size 1500000)
cuisui-lrl-hash (make-hash-table :size 1800000)
sab-srl-hash (make-hash-table :size 100 :test 'equal))))
-
+
(defun ensure-preparse (&optional (force-read nil))
- (when (or force-read (not *preparse-hash-init?*))
- (make-preparse-hash-table))
+ (when (and *preparse-hash-init?* (not force-read))
+ (return-from ensure-preparse 'already-done))
+ (make-preparse-hash-table)
(with-umls-file (line "MRCONSO.RRF")
(let ((cui (parse-ui (nth 0 line)))
- (lui (parse-ui (nth 3 line)))
- (sui (parse-ui (nth 5 line)))
- (sab (nth 11 line))
- (srl (parse-integer (nth 15 line))))
- (unless (gethash cui pfstr-hash) ;; if haven't stored pfstr for cui
- (if (and (string-equal (nth 1 line) "ENG") ; LAT
- (string-equal (nth 2 line) "P") ; ts
- (string-equal (nth 4 line) "PF")) ; stt
+ (lui (parse-ui (nth 3 line)))
+ (sui (parse-ui (nth 5 line)))
+ (sab (nth 11 line))
+ (srl (parse-integer (nth 15 line))))
+ (unless (gethash cui pfstr-hash) ;; if haven't stored pfstr for cui
+ (if (and (string-equal (nth 1 line) "ENG") ; LAT
+ (string-equal (nth 2 line) "P") ; ts
+ (string-equal (nth 4 line) "PF")) ; stt
(setf (gethash cui pfstr-hash) (nth 14 line))))
- (set-lrl-hash cui srl cui-lrl-hash)
- (set-lrl-hash lui srl lui-lrl-hash)
- (set-lrl-hash sui srl sui-lrl-hash)
- (set-lrl-hash (make-cuisui cui sui) srl cuisui-lrl-hash)
+ (set-lrl-hash cui srl cui-lrl-hash)
+ (set-lrl-hash lui srl lui-lrl-hash)
+ (set-lrl-hash sui srl sui-lrl-hash)
+ (set-lrl-hash (make-cuisui cui sui) srl cuisui-lrl-hash)
(multiple-value-bind (val found) (gethash sab sab-srl-hash)
(declare (ignore val))
(unless found
(setf (gethash sab sab-srl-hash) srl)))))
- (setq *preparse-hash-init?* t))
-
+ (setq *preparse-hash-init?* t)
+ t)
+
(defun pfstr-hash (cui) (gethash cui pfstr-hash))
(defun cui-lrl (cui) (gethash cui cui-lrl-hash))
(defun lui-lrl (lui) (gethash lui lui-lrl-hash))
(defun sui-lrl (sui) (gethash sui sui-lrl-hash))
(defun sab-srl (sab) (aif (gethash sab sab-srl-hash) it 0))
(defun cuisui-lrl (cuisui) (gethash cuisui cuisui-lrl-hash))
-
+
)) ;; closure
(defun set-lrl-hash (key lrl hash)
("RCUI" sql-u) ("VCUI" sql-u) ("CFR" sql-i) ("TFR" sql-i)
;; New fields for 2004AA
("MAPSETCUI" sql-u)
- )
+ )
"SQL data types for each non-string column")
(defparameter +custom-tables+
;; Deprecated, last in 2004AA -- skip index
#+ignore
("MRLO.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string
+ (lambda (x) (write-to-string
(if (zerop (length (nth 4 x)))
(cui-lrl (parse-ui (nth 0 x)))
(cuisui-lrl (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 4 x))))))))
("MRSTY.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cui-lrl (parse-ui (nth 0 x))))))
("MRCOC.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string
+ (lambda (x) (write-to-string
(max (cui-lrl (parse-ui (nth 0 x)))
(kmrcl:aif (cui-lrl (parse-ui (nth 1 x))) kmrcl::it 0)))))
("MRSAT.RRF" "KSRL" "SMALLINT" 0
("MRCXT.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 2 x)))))
("MRXW_ENG.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
+ (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
("MRXW_NONENG.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
+ (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
("MRXNW_ENG.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
+ (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
("MRXNS_ENG.RRF" "KLRL" "SMALLINT" 0
- (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
+ (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
("MRREL.RRF" "KPFSTR2" "TEXT" 1024
(lambda (x) (pfstr-hash (parse-ui (nth 4 x)))))
("MRCOC.RRF" "KPFSTR2" "TEXT" 1024
(lambda (x) (pfstr-hash (parse-ui (nth 2 x)))))
- ("MRCXT.RRF" "KCUISUI" "BIGINT" 0
+ ("MRCXT.RRF" "KCUISUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 1 x))))))
("MRSAT.RRF" "KCUILUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuilui (parse-ui (nth 0 x)) (parse-ui (nth 1 x))))))
("MRXW_NONENG.RRF" "CUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (nth 2 x)))))
("MRXW_NONENG.RRF" "LUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (nth 3 x)))))
("MRXW_NONENG.RRF" "SUI" "INTEGER" 0 (lambda (x) (write-to-string (parse-ui (nth 4 x)))))
- ("MRXW_NONENG.RRF" "KCUISUI" "BIGINT" 0
+ ("MRXW_NONENG.RRF" "KCUISUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuisui (parse-ui (nth 2 x)) (parse-ui (nth 4 x)))))))
"Custom columns to create.(filename, col, sqltype, value-func).")
(defparameter +index-cols+
- '(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
+ '(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
("SRL" "MRCONSO") ("AUI" "MRCONSO")
("SUI" "MRCONSO") ("CUI" "MRCXT") ("CUI" "MRDEF") ("CUI" "MRLO")
("CUI1" "MRREL") ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
("CUI" "MRSTY")
- ("TUI" "MRSTY") ("CUI" "MRXNS_ENG")
+ ("TUI" "MRSTY") ("CUI" "MRXNS_ENG")
#+ignore ("NSTR" "MRXNS_ENG" 10)
("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO") ("KCUILRL" "MRCONSO")
- ("KLUILRL" "MRCONSO") ("KCUISUI" "MRCXT")
+ ("KLUILRL" "MRCONSO") ("KCUISUI" "MRCXT")
("KCUISUI" "MRSAT") ("KCUILUI" "MRSAT")
- ("KCUISUI" "MRXW_ENG") ("KCUISUI" "MRXNW_ENG")
+ ("KCUISUI" "MRXW_ENG") ("KCUISUI" "MRXNW_ENG")
("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
- ("KSRL" "MRCXT") ("KSRL" "MRDEF") ("KSRL" "MRRANK")
- ("KSRL" "MRREL") ("KSRL" "MRSAT") ("KLRL" "MRCOC")
+ ("KSRL" "MRCXT") ("KSRL" "MRDEF") ("KSRL" "MRRANK")
+ ("KSRL" "MRREL") ("KSRL" "MRSAT") ("KLRL" "MRCOC")
#+ignore ("KLRL" "MRLO") ;; deprecated
("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
("KLRL" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
("EUI" "LRABR") ("EUI2" "LRABR") ("EUI" "LRAGR") ("EUI" "LRCMP") ("EUI" "LRMOD")
("EUI" "LRNOM") ("EUI2" "LRNOM") ("EUI" "LRPRN") ("EUI" "LRPRP") ("EUI" "LRSPL")
("EUI" "LRTRM") ("EUI" "LRTYP") ("EUI" "LRWD") ("WRD" "LRWD")
- ("BAS" "LRABR")
+ ("BAS" "LRABR")
;; Semantic NET indices
- ("UI" "SRSTRE1") ("UI2" "SRSTRE1") ("UI3" "SRSTRE1")
+ ("UI" "SRSTRE1") ("UI2" "SRSTRE1") ("UI3" "SRSTRE1")
("STY_RL" "SRDEF") ("RT" "SRDEF") ("STY_RL" "SRSTR") ("STY_RL2" "SRSTR")
("RL" "SRSTR")
-
+
("SRL" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
("VCUI" "MRSAB") ("LAT" "MRSAB") ("MAPSETCUI" "MRMAP") ("MAPSETCUI" "MRSMAP")
("CUI" "MRHIER") ("AUI" "MRHIER") ("PAUI" "MRHIER"))
(add-ucols (gen-ucols-generic "SRFLD")))
(defun gen-ucols-meta ()
-"Initialize all umls columns"
+"Initialize all umls columns"
(let ((cols '()))
(with-umls-file (line "MRCOLS.RRF")
(destructuring-bind (col des ref min av max fil dty) line
(nreverse cols)))
(defun gen-ucols-custom ()
-"Initialize umls columns for custom columns"
+"Initialize umls columns for custom columns"
(loop for customcol in +custom-cols+
collect
(make-ucol (nth 1 customcol) "" 0 0 0 (eval (nth 3 customcol))
:custom-value-fun (nth 4 customcol))))
(defun gen-ucols-generic (col-filename)
-"Initialize for generic (LEX/NET) columns"
+"Initialize for generic (LEX/NET) columns"
(let ((cols '()))
(with-umls-file (line col-filename)
(destructuring-bind (nam des ref fil) line
;; needs to come last
(add-ufiles (gen-ufiles-custom)))
-
+
(defun gen-ufiles-generic (files-filename dir)
-"Initialize all LEX file structures"
+"Initialize all LEX file structures"
(let ((files '()))
(with-umls-file (line files-filename)
(destructuring-bind (fil des fmt cls rws bts) line
(push (make-ufile
- dir fil des
+ dir fil des
(parse-integer cls)
(parse-integer rws) (parse-integer bts)
(concatenate 'list (umls-field-string-to-list fmt)
(nreverse files)))
(defun gen-ufiles-custom ()
- (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"
+ (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"
5 0 0 (fields (find-ufile "MRXW_ENG.RRF"))))
projects / umlisp.git / commitdiff