;;;; Programmer: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: package.lisp,v 1.16 2003/05/02 05:37:16 kevin Exp $
+;;;; $Id: package.lisp,v 1.17 2003/05/06 01:34:57 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
;; From classes.lisp
#:umlsclass
- #:ucon #:uterm #:ustr #:usrl #:uso #:ucxt #:urank #:udef #:usat #:usab #:ulo #:urel
- #:ucoc #:usty #:uatx #:uxw #:uxnw #:uxns
- #:lexterm #:labr #:lagr #:lcmp #:lmod #:lnom #:lprn #:lprp #:lspl #:ltrm #:ltyp #:lwd
- #:sdef #:sstr #:sstre1 #:sstre2
- #:sty #:tui #:def #:sab #:srl #:tty #:rank #:supres #:atn #:atv #:vcui #:rcui #:vsab
+ #:ucon #:uterm #:ustr #:usrl #:uso #:ucxt #:urank #:udef #:usat #:usab #:ulo
+ #:urel #:ucoc #:usty #:uatx #:uxw #:uxnw #:uxns
+ #:lexterm #:labr #:lagr #:lcmp #:lmod #:lnom #:lprn #:lprp #:lspl #:ltrm
+ #:ltyp #:lwd #:sdef #:sstr #:sstre1 #:sstre2
+ #:sty #:tui #:def #:sab #:srl #:tty #:rank #:supres #:atn #:atv #:vcui
+ #:rcui #:vsab
#:rl #:sty2 #:ui #:ui2 #:ui3 #:eui #:bas #:eui2 #:bas2
#:cui #:lui #:sui #:wd #:lat #:nstr :cuilist
- #:rsab
- #:lat
- #:s#def #:s#sty #:s#term #:s#str #:s#atx #:s#lo #:s#sat #:s#rel #:s#coc #:s#so #:s#cxt
-
+ #:rsab #:lat
+ #:s#def #:s#sty #:s#term #:s#str #:s#atx #:s#lo #:s#sat #:s#rel #:s#coc
+ #:s#so #:s#cxt
+
;; From class-support.lisp
#:ucon-has-tui
#:english-term-p
#:ustr_freq
#:usty_freq
#:usrl_freq
-
- #:urank
- #:urel
- #:usat
- #:uso
- #:ucxt
- #:ustr
- #:ulo
- #:uterm
- #:usty
- #:urel
- #:ucoc
- #:uatx
- #:ucon
- #:uxw
- #:uxnw
- #:uxns
- #:lexterm
- #:labr
- #:lagr
- #:lcmp
- #:lmod
- #:lmod
- #:lprn
- #:prp
- #:lspl
- #:ltrm
- #:ltyp
- #:sdef
- #:sstr
- #:sstre1
- #:sstre2
-
- #:english-term-p
))
;;;; Programmer: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-common.lisp,v 1.5 2003/05/05 23:13:28 kevin Exp $
+;;;; $Id: parse-common.lisp,v 1.6 2003/05/06 01:34:57 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
;;;; 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)))
+(in-package #:umlisp)
+
+(eval-when (:compile-toplevel)
+ (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
(defun umls-pathname (filename &optional (extension ""))
"Return pathname for a umls filename"
(pathname
filename)))
-(defun read-umls-line-new (strm)
- "Read a line from a UMLS stream, split into fields"
- (let ((line (read-line strm nil 'eof)))
- (if (stringp line) ;; ensure not 'eof
- (delimited-string-to-list line #\| t)
- line)))
-
-(defun read-umls-line (strm)
+(defun read-umls-line (strm &optional (eof 'eof))
"Read a line from a UMLS stream, split into fields"
- (let ((line (read-line strm nil 'eof)))
- (if (stringp line) ;; ensure not 'eof
- (delimited-string-to-list line #\| t)
- line)))
+ (let ((line (read-line strm nil eof)))
+ (if (eq line eof)
+ eof
+ (delimited-string-to-list line #\| t))))
;;; Find field lengths for LEX and NET files
;;;; Programmer: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-macros.lisp,v 1.3 2003/05/05 23:13:28 kevin Exp $
+;;;; $Id: parse-macros.lisp,v 1.4 2003/05/06 01:34:57 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
;;;; 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)))
+(in-package #:umlisp)
(defmacro with-umls-file ((line filename) &body body)
"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym)))
+ (let ((ustream (gensym "STRM-"))
+ (eof (gensym "EOF-")))
`(with-open-file
- (,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-umls-line ,ustream) (read-umls-line ,ustream)))
- ((eq ,line 'eof) t)
- ,@body))))
+ (,ustream (umls-pathname ,filename) :direction :input)
+ (do ((,line (read-umls-line ,ustream ,eof)
+ (read-umls-line ,ustream ,eof)))
+ ((eq ,line 'eof) t)
+ ,@body))))
(defmacro with-buffered-umls-file ((line filename) &body body)
-"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym))
- (buffer (gensym)))
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ (let ((ustream (gensym "STRM-"))
+ (buffer (gensym "BUF-"))
+ (eof (gensym "EOF-")))
`(let ((,buffer (make-fields-buffer)))
(with-open-file
- (,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-buffered-fields ,buffer ,ustream) (read-buffered-fields ,buffer ,ustream)))
- ((eq ,line 'kl::eof) t)
+ (,ustream (umls-pathname ,filename) :direction :input)
+ (do ((,line (read-buffered-fields ,buffer ,ustream #\| ,eof)
+ (read-buffered-fields ,buffer ,ustream #\| ,eof)))
+ ((eq ,line ,eof) t)
,@body)))))
(defmacro with-buffered2-umls-file ((line filename) &body body)
-"Opens a UMLS and processes each parsed line with (body) argument"
- (let ((ustream (gensym))
- (buffer (gensym)))
+ "Opens a UMLS and processes each parsed line with (body) argument"
+ (let ((ustream (gensym "STRM-"))
+ (buffer (gensym "BUF-"))
+ (eof (gensym "EOF-")))
`(let ((,buffer (make-fields-buffer2)))
(with-open-file
(,ustream (umls-pathname ,filename)
- :direction :input :if-exists :overwrite)
- (do ((,line (read-buffered-fields2 ,buffer ,ustream) (read-buffered-fields2 ,buffer ,ustream)))
- ((eq ,line 'eof) t)
+ :direction :input :if-exists :overwrite)
+ (do ((,line (read-buffered-fields ,buffer ,ustream #\| ,eof)
+ (read-buffered-fields ,buffer ,ustream #\| ,eof)))
+ ((eq ,line ,eof) t)
,@body)))))
-
;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: sql-classes.lisp,v 1.70 2003/05/05 23:13:28 kevin Exp $
+;;;; $Id: sql-classes.lisp,v 1.71 2003/05/06 01:34:57 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
&key (lrl "KCUILRL") single distinct order like)
(let* ((%%fields (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
(if distinct "distinct " "") fields table))
- (%%order (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) ""))
+ (%%order (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}"
+ order)
+ ""))
(%%lrl (format nil " and ~:@(~A~)<=" lrl))
(%%where (when where-name
(format nil " where ~:@(~A~)~A" where-name
(defun find-ucon-lui (lui &key (srl *current-srl*))
"Find list of ucon for lui"
- (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui (parse-lui lui) :distinct t)
+ (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui (parse-lui lui)
+ :distinct t)
(make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(defun find-ucon-sui (sui &key (srl *current-srl*))
"Find list of ucon for sui"
- (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl sui (parse-sui sui) :distinct t)
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr kpfstr
+ (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl sui (parse-sui sui)
+ :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
(defun find-ucon-all2 (&key (srl *current-srl*))
"Return list of all ucon's"
- (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t)
+ (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ :distinct t)
(make-instance 'ucon :cui (ensure-integer cui)
:pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
(make-instance 'ucon :cui (ensure-integer cui)
:pfstr pfstr
:lrl (ensure-integer cuilrl))))
- (query-string mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t)
+ (query-string mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ :distinct t)
:database db)))
(defun find-usty-word (word &key (srl *current-srl*))
"Return a list of usty that match word"
- (with-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t :distinct t)
+ (with-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
+ :distinct t)
(make-instance 'usty :tui (ensure-integer tui) :sty sty)))
(defun find-urel-cui (cui &key (srl *current-srl*))
"Return a list of urel for cui"
- (with-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1 (parse-cui cui) :lrl "KSRL")
- (make-instance 'urel :cui1 (parse-cui cui) :rel rel :cui2 (ensure-integer cui2)
- :rela rela :sab sab :sl sl :mg mg :pfstr2 kpfstr2)))
+ (with-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1
+ (parse-cui cui) :lrl "KSRL")
+ (make-instance 'urel :cui1 (parse-cui cui) :rel rel
+ :cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl
+ :mg mg :pfstr2 kpfstr2)))
(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
"Return a list of urel for cui2"
- (with-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2 (parse-cui cui2) :lrl "KSRL")
- (make-instance 'urel :cui2 (parse-cui cui2) :rel rel :cui1 (ensure-integer cui1)
- :rela rela :sab sab :sl sl :mg mg :pfstr2 kpfstr2)))
+ (with-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2
+ (parse-cui cui2) :lrl "KSRL")
+ (make-instance 'urel :cui2 (parse-cui cui2) :rel rel
+ :cui1 (ensure-integer cui1) :rela rela :sab sab :sl sl
+ :mg mg :pfstr2 kpfstr2)))
(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
(mapcar
(defun find-ucoc-cui (cui &key (srl *current-srl*))
"Return a list of ucoc for cui"
- (with-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1 (parse-cui cui)
- :lrl "KSRL" :order (cof asc))
+ (with-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1
+ (parse-cui cui) :lrl "KSRL" :order (cof asc))
(setq cui2 (ensure-integer cui2))
(when (zerop cui2) (setq cui2 nil))
- (make-instance 'ucoc :cui1 (parse-cui cui) :cui2 (ensure-integer cui2) :soc soc
- :cot cot :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2)))
+ (make-instance 'ucoc :cui1 (parse-cui cui) :cui2 (ensure-integer cui2)
+ :soc soc :cot cot :cof (ensure-integer cof) :coa coa
+ :pfstr2 kpfstr2)))
(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
"Return a list of ucoc for cui2"
- (with-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2 (parse-cui cui2)
- :lrl "KSRL" :order (cof asc))
+ (with-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2
+ (parse-cui cui2) :lrl "KSRL" :order (cof asc))
(setq cui2 (ensure-integer cui2))
(when (zerop cui2) (setq cui2 nil))
- (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 (parse-cui cui2) :soc soc
- :cot cot :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2)))
+ (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 (parse-cui cui2)
+ :soc soc :cot cot :cof (ensure-integer cof) :coa coa
+ :pfstr2 kpfstr2)))
(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
"List of ucon with co-occurance cui2"
(defun find-ulo-cui (cui &key (srl *current-srl*))
"Return a list of ulo for cui"
- (with-umlisp-query (mrlo (isn fr un sui sna soui) srl cui (parse-cui cui) :lrl "KLRL")
- (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un :sui (ensure-integer sui)
- :sna sna :soui soui)))
+ (with-umlisp-query (mrlo (isn fr un sui sna soui) srl cui (parse-cui cui)
+ :lrl "KLRL")
+ (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un
+ :sui (ensure-integer sui) :sna sna :soui soui)))
(defgeneric suistr (lo))
(defmethod suistr ((lo ulo))
(defun find-uterm-cui (cui &key (srl *current-srl*))
"Return a list of uterm for cui"
- (with-umlisp-query (mrcon (lui lat ts kluilrl) srl cui (parse-cui cui) :lrl kluilrl
- :distinct t)
+ (with-umlisp-query (mrcon (lui lat ts kluilrl) srl cui (parse-cui cui)
+ :lrl kluilrl :distinct t)
(make-instance 'uterm :lui (ensure-integer lui) :cui (parse-cui cui)
:lat lat :ts ts :lrl (ensure-integer kluilrl))))
(defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
"Return a list of ustr for cui/lui"
- (with-umlisp-query (mrcon (sui stt str lrl) srl kcuilui (make-cuilui cui lui) :lrl lrl)
+ (with-umlisp-query (mrcon (sui stt str lrl) srl kcuilui
+ (make-cuilui cui lui) :lrl lrl)
(make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
:cuisui (make-cuisui cui sui) :stt stt :str str
:lrl (ensure-integer lrl))))
(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
"Return the single ustr for cuisui"
- (with-umlisp-query (mrcon (lui stt str lrl) srl kcuisui (make-cuisui cui sui) :lrl lrl :single t)
+ (with-umlisp-query (mrcon (lui stt str lrl) srl kcuisui
+ (make-cuisui cui sui) :lrl lrl :single t)
(make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
- :lui (ensure-integer lui) :stt stt :str str :lrl (ensure-integer lrl))))
+ :lui (ensure-integer lui) :stt stt :str str
+ :lrl (ensure-integer lrl))))
(defun find-ustr-sui (sui &key (srl *current-srl*))
"Return the list of ustr for sui"
- (with-umlisp-query (mrcon (cui lui stt str lrl) srl sui (parse-sui sui) :lrl lrl)
+ (with-umlisp-query (mrcon (cui lui stt str lrl) srl sui (parse-sui sui)
+ :lrl lrl)
(make-instance 'ustr :sui sui :cui cui :stt stt :str str
:cuisui (make-cuisui (ensure-integer cui) (parse-sui sui))
:lui (ensure-integer lui) :lrl (ensure-integer lrl))))
(let ((cuisui (ensure-integer kcuisui)))
(apply #'find-ustr-cuisui
(append
- (multiple-value-list (decompose-cuisui cuisui)) (list :srl srl))))))
+ (multiple-value-list (decompose-cuisui cuisui))
+ (list :srl srl))))))
(defun find-ustr-all (&key (srl *current-srl*))
"Return list of all ustr's"
(clsql:map-query
'list
#'(lambda (cui lui sui stt lrl pfstr)
- (make-instance 'ustr :cui (ensure-integer cui) :lui (ensure-integer lui)
- :sui (ensure-integer sui) :stt stt :str pfstr
- :cuisui (make-cuisui (ensure-integer cui) (ensure-integer sui))
+ (make-instance 'ustr :cui (ensure-integer cui)
+ :lui (ensure-integer lui) :sui (ensure-integer sui)
+ :stt stt :str pfstr
+ :cuisui (make-cuisui (ensure-integer cui)
+ (ensure-integer sui))
:lrl (ensure-integer lrl)))
- (query-string mrcon (cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl :distinct t
+ (query-string mrcon (cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl
+ :distinct t
:order (sui asc))
:database db)))
str))
(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
- (with-umlisp-query (mrso (sab code srl tty) srl kcuisui (make-cuisui cui sui) :lrl srl)
+ (with-umlisp-query (mrso (sab code srl tty) srl kcuisui
+ (make-cuisui cui sui) :lrl srl)
(make-instance 'uso :sab sab :code code :srl srl :tty tty)))
(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
- (with-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc) srl kcuisui
- (make-cuisui cui sui) :lrl ksrl)
+ (with-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc)
+ srl kcuisui (make-cuisui cui sui) :lrl ksrl)
(make-instance 'ucxt :sab sab :code code
- :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd :rela rela :xc xc
- :rnk (ensure-integer rnk) :cui2 (ensure-integer cui2))))
+ :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd
+ :rela rela :xc xc :rnk (ensure-integer rnk)
+ :cui2 (ensure-integer cui2))))
(defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
(let ((ls (format nil "select CODE,ATN,SAB,ATV from MRSAT where ")))
(cond
- (sui (string-append ls (format nil "KCUISUI=~d" (make-cuisui cui sui))))
- (lui (string-append ls (format nil "KCUILUI=~d and sui=0" (make-cuilui cui lui))))
- (t (string-append ls (format nil "cui=~d and lui=0 and sui=0" cui))))
+ (sui (string-append ls (format nil "KCUISUI=~D" (make-cuisui cui sui))))
+ (lui (string-append ls (format nil "KCUILUI=~D and sui=0"
+ (make-cuilui cui lui))))
+ (t (string-append ls (format nil "cui=~D and lui=0 and sui=0" cui))))
(when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (string-append ls (format nil " and KSRL <= ~D" srl)))
(loop for tuple in (mutex-sql-query ls) collect
(destructuring-bind (code atn sab atv) tuple
(make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
(defun find-usab-all ()
"Find usab for a key"
- (with-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc
- scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin)
- nil nil nil)
+ (with-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta
+ rmeta slc scc srl tfr cfr cxty ttyl atnl lat
+ cenc curver sabin) nil nil nil)
(make-instance 'usab :vcui (ensure-integer vcui)
- :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son :sf sf
- :sver sver :mstart mstart :mend mend :imeta imeta :rmeta rmeta
- :slc slc :scc scc :srl (ensure-integer srl) :tfr (ensure-integer tfr)
- :cfr (ensure-integer cfr) :cxty cxty :ttyl ttyl :atnl atnl :lat lat
- :cenc cenc :curver curver :sabin sabin)))
+ :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
+ :sf sf :sver sver :mstart mstart :mend mend :imeta imeta
+ :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
+ :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
+ :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
+ :curver curver :sabin sabin)))
(defun find-usab-by-key (key-name key)
"Find usab for a key"
- (with-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver mstart mend imeta
- rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc
- curver sabin) nil key-name key :single t)
+ (with-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver mstart
+ mend imeta rmeta slc scc srl tfr cfr cxty
+ ttyl atnl lat cenc curver sabin)
+ nil key-name key :single t)
(make-instance 'usab :vcui (ensure-integer vcui)
- :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son :sf sf
- :sver sver :mstart mstart :mend mend :imeta imeta :rmeta rmeta
- :slc slc :scc scc :srl (ensure-integer srl) :tfr (ensure-integer tfr)
- :cfr (ensure-integer cfr) :cxty cxty :ttyl ttyl :atnl atnl :lat lat
- :cenc cenc :curver curver :sabin sabin)))
+ :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
+ :sf sf :sver sver :mstart mstart :mend mend :imeta imeta
+ :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
+ :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
+ :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
+ :curver curver :sabin sabin)))
(defun find-usab-rsab (rsab)
"Find usab for rsab"
;;;; Programmer: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: sql-create.lisp,v 1.7 2003/05/05 23:13:28 kevin Exp $
+;;;; $Id: sql-create.lisp,v 1.8 2003/05/06 01:34:57 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
;;;; *************************************************************************
(in-package :umlisp)
-(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
-
-
-(defun create-table-cmd-old (file)
- "Return sql command to create a table"
- (let ((col-func
- (lambda (c)
- (let ((sqltype (umls-col-sqltype c)))
- (concatenate 'string (umls-col-col c)
- " "
- (if (or (string-equal sqltype "VARCHAR")
- (string-equal sqltype "CHAR"))
- (format nil "~a (~a)" sqltype (umls-col-max c))
- sqltype)
- ",")))))
- (format nil "CREATE TABLE ~a (~a)" (umls-file-table file)
- (string-trim-last-character
- (mapcar-append-string col-func (umls-cols-for-umls-file file))))))
+(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"
"Return SQL command to create a custom table"
(format nil "CREATE TABLE ~a AS ~a;" tablename sql-cmd))
-(defun insert-values-cmd-old (file values)
- "Return sql insert command for a row of values"
- (let ((insert-func
- (lambda (col value)
- (concatenate
- 'string
- (umls-col-quotechar col)
- (if (null (umls-col-parsefunc col))
- value
- (format nil "~A" (funcall (umls-col-parsefunc col) value)))
- (umls-col-quotechar col)
- ","))))
- (format
- nil "INSERT INTO ~a (~a) VALUES (~a)"
- (umls-file-table file)
- (string-trim-last-character
- (mapcar-append-string (lambda (c) (concatenate 'string c ","))
- (umls-file-fields file)))
- (string-trim-last-character
- (concatenate 'string
- (mapcar2-append-string insert-func
- (remove-custom-cols (umls-file-colstructs file))
- values)
- (custom-col-values-old (custom-colstructs-for-file file) values "," t)))
- )))
-
(defun insert-col-value (col value)
(if (null (umls-col-parsefunc col))
value
(mapcar insert-func (remove-custom-cols (umls-file-colstructs file)) values)
(custom-col-values (custom-colstructs-for-file file) values t)))))
-(defun custom-col-values-old (colstructs values delim doquote)
- "Returns a string of column values for SQL inserts for custom columns"
- (let ((result ""))
- (dolist (col colstructs)
- (let* ((func (umls-col-custom-value-func col))
- (custom-value (funcall func values)))
- (string-append result
- (if doquote (umls-col-quotechar col))
- (escape-backslashes custom-value)
- (if doquote (umls-col-quotechar col))
- delim)))
- result))
(defun custom-col-value (col doquote values)
(let ((custom-value (funcall (umls-col-custom-value-func col) values)))
(remove-if-not #'umls-col-custom-value-func (umls-file-colstructs file)))
(defun noneng-lang-index-files ()
- (remove-if-not (lambda (f) (and (> (length (umls-file-fil f)) 4)
- (string-equal (umls-file-fil f) "MRXW." :end1 5)
- (not (string-equal (umls-file-fil f) "MRXW.ENG"))
- (not (string-equal (umls-file-fil f) "MRXW.NONENG"))))
- *umls-files*))
+ (remove-if-not
+ (lambda (f) (and (> (length (umls-file-fil f)) 4)
+ (string-equal (umls-file-fil f) "MRXW." :end1 5)
+ (not (string-equal (umls-file-fil f) "MRXW.ENG"))
+ (not (string-equal (umls-file-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)
- "")))
+ (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"
- (mapcar
- (lambda (file)
- (ignore-errors
- (sql-execute (format nil "DROP TABLE ~a" (umls-file-table file)) conn)))
- *umls-files*))
+ (dolist (file *umls-files*)
+ (ignore-errors
+ (sql-execute (format nil "DROP TABLE ~a" (umls-file-table file)) conn))))
(defun sql-create-tables (conn)
"SQL Databases: create all tables"
- (mapcar (lambda (file) (sql-execute (create-table-cmd file) conn)) *umls-files*))
+ (dolist (file *umls-files*)
+ (sql-execute (create-table-cmd file) conn)))
(defun sql-create-custom-tables (conn)
"SQL Databases: create all custom tables"
- (mapcar (lambda (ct)
- (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn))
- +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"
(defun sql-insert-all-values (conn)
"SQL Databases: inserts all values for all files"
- (mapcar (lambda (file) (sql-insert-values conn file)) *umls-files*))
+ (dolist (file *umls-files*)
+ (sql-insert-values conn file)))
(defun sql-create-indexes (conn &optional (indexes +index-cols+))
"SQL Databases: create all indexes"
- (mapcar
- (lambda (idx)
- (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn))
- 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"))
+ (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 translate-all-files (&optional (extension ".trans"))
"Copy translated files and return postgresql copy commands to import"
(make-noneng-index-file extension)
- (map 'nil (lambda (f) (translate-file f extension)) *umls-files*))
+ (dolist (f *umls-files*) (translate-umls-file f extension)))
-(defun translate-file (file extension)
+(defun translate-file (filename extension files)
"Translate a umls file into a format suitable for sql copy cmd"
- (let ((path (umls-pathname (umls-file-fil file) extension)))
+ (let ((path (umls-pathname filename extension))
+ (input-files (mklist files)))
(if (probe-file path)
- (progn
- (format t "File ~A already exists: skipping~%" path)
- nil)
- (with-open-file (ostream path :direction :output)
- (with-umls-file (line (umls-file-fil file))
- (umls-translate file line ostream)
- (princ #\newline ostream))
- t))))
+ (format t "File ~A already exists: skipping~%" path)
+ (dolist (input-file input-files)
+ (with-open-file (ostream :direction :output)
+ (with-umls-file (line (umls-file-fil input-file))
+ (umls-translate file line ostream)
+ (princ #\newline ostream)))))))
+
+(defun translate-umls-file (file extension)
+ "Translate a umls file into a format suitable for sql copy cmd"
+ (translate-file (umls-file-fil file) extension (umls-file-fil file)))
(defun make-noneng-index-file (extension)
"Make non-english index file"
- (let* ((outfile (find-umls-file "MRXW.NONENG"))
- (path (umls-pathname (umls-file-fil outfile) extension)))
-
- (if (probe-file path)
- (progn
- (format t "File ~A already exists: skipping~%" path)
- nil)
- (progn
- (with-open-file (ostream path :direction :output)
- (dolist (inputfile (noneng-lang-index-files))
- (with-umls-file (line (umls-file-fil inputfile))
- (umls-translate outfile line ostream) ;; use outfile for custom cols
- (princ #\newline ostream))))
- t))))
+ (translate-file (find-umls-file "MRXW.NONENG" extension
+ (noneng-lang-index-files))))
(defun pg-copy-cmd (file extension)
"Return postgresql copy statement for a file"
- (format nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
- (umls-file-table file) (umls-pathname (umls-file-fil file) extension)))
+ (format
+ nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
+ (umls-file-table file) (umls-pathname (umls-file-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 (umls-file-fil file) extension) (umls-file-table file)))
-
-(defun umls-translate-old (file line)
- "Translate a single line for sql output"
- (string-trim-last-character
- (concatenate 'string
- (mapcar2-append-string
- (lambda (col value)
- (concatenate
- 'string
- (if (eq (umls-col-datatype col) 'sql-u)
- (format nil "~d" (parse-ui value ""))
- (escape-backslashes value))
- "|"))
- (remove-custom-cols (umls-file-colstructs file))
- line)
- (custom-col-values-old (custom-colstructs-for-file file) line "|" nil))))
-
-(defun concat-separated-strings (separator &rest lists)
- (format nil (format nil "~~{~~A~~^~A~~}" separator) (mapappend #'identity lists)))
-
-(defun print-separated-strings (strm separator &rest lists)
- (declare (optimize (speed 3) (safety 0) (space 0) (debug 0) (compilation-speed 0)))
- (do* ((rest-lists lists (cdr rest-lists))
- (list (car rest-lists) (car rest-lists))
- (last-list (null (cdr rest-lists)) (null (cdr rest-lists))))
- ((null list) strm)
- (do* ((lst list (cdr lst))
- (elem (car lst) (car lst))
- (last-elem (null (cdr lst)) (null (cdr lst))))
- ((null lst))
- (write-string elem strm)
- (unless (and last-elem last-list)
- (write-string separator strm)))))
+ (format
+ nil
+ "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
+ (umls-pathname (umls-file-fil file) extension) (umls-file-table file)))
(defun col-value (col value)
(if (eq (umls-col-datatype col) 'sql-u)
(defun max-umls-row ()
"Return length of longest row"
- (if t
- 6000 ;;; hack to use on systems without MRCOLS/MRFILES -- ok for UMLS2001
- (progn
- (unless *umls-files*
- (init-umls))
- (let ((rowsizes '()))
- (dolist (file *umls-files*)
- (let ((row 0)
- (fields (umls-file-colstructs file)))
- (dolist (field fields)
- (incf row (1+ (umls-col-max field))))
- (push row rowsizes)))
- (car (sort rowsizes #'>))))))
+ (unless *umls-files*
+ (init-umls))
+ (let ((rowsizes '()))
+ (dolist (file *umls-files*)
+ (let ((row 0)
+ (fields (umls-file-colstructs file)))
+ (dolist (field fields)
+ (incf row (1+ (umls-col-max field))))
+ (push row rowsizes)))
+ (car (sort rowsizes #'>))))
projects / umlisp.git / commitdiff