X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=sql-classes.lisp;h=2831defc003504ff2c1f488793d013a80d612535;hb=9b9c48233072a8f64c9677d9b92b5eb956f4079d;hp=525aa9cb8f32bfc05d1ecdd8bdbd0c102adba9e4;hpb=eadf93ecf9164f5e0a1ec0be102624d1a383f677;p=umlisp.git diff --git a/sql-classes.lisp b/sql-classes.lisp index 525aa9c..2831def 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -10,7 +10,7 @@ ;;;; $Id$ ;;;; ;;;; This file, part of UMLisp, is -;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D. +;;;; Copyright (c) 2000-2006 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. @@ -59,7 +59,7 @@ &key (lrl "KCUILRL") single distinct order like) (concatenate 'string - (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)" + (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)" (if distinct "distinct " "") fields table) (if where-name (format nil " where ~:@(~A~)" where-name) "") (if where-name @@ -82,7 +82,7 @@ "Query the UMLisp database. Return a list of umlisp objects whose name is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" `(,query-cmd - (query-string ,table ,fields ,srl ,where-name ,where-value + (query-string ,table ,fields ,srl ,where-name ,where-value :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like))) (defmacro umlisp-query-eval (table fields srl where-name where-value @@ -90,7 +90,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Query the UMLisp database. Return a list of umlisp objects whose name is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" `(mutex-sql-query - (query-string-eval ,table ,fields ,srl ,where-name ,where-value + (query-string-eval ,table ,fields ,srl ,where-name ,where-value :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like))) ;; only WHERE-VALUE and SRL are evaluated @@ -99,7 +99,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" order like (query-cmd 'mutex-sql-query)) &body body) (let ((value (gensym)) - (r (gensym))) + (r (gensym))) (if single `(let* ((,value ,where-value) (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value @@ -187,9 +187,21 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-cui (cui &key (srl *current-srl*)) "Find ucon for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl cui cui :single t) - (make-instance 'ucon :cui cui :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (unless cui (return-from find-ucon-cui nil)) + + (let ((tuple (car (mutex-sql-query + (format nil + "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A" + cui (if srl (format nil " AND SRL<=~D" srl) "")))))) + (unless tuple + (setq tuple (car (mutex-sql-query + (format nil + "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D" + cui (if srl (format nil " AND SRL<=~D" srl) nil)))))) + (unless tuple + (return-from find-ucon-cui nil)) + (make-instance 'ucon :cui cui :pfstr (second tuple) + :lrl (ensure-integer (first tuple))))) (defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*)) "Find ucon for a cui" @@ -201,23 +213,45 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-pfstr-cui (cui &key (srl *current-srl*)) "Find preferred string for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t) - kpfstr)) - + (or + (caar (mutex-sql-query + (format nil "SELECT DISTINCT str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A LIMIT 1" + cui (if srl (format nil " AND SRL<=~D" srl) "")))) + (caar (mutex-sql-query + (format nil "SELECT DISTINCT str FROM MRCONSO WHERE CUI=~D~A LIMIT 1" + cui (if srl (format nil " AND SRL<=~D" srl) "")))))) (defun find-ucon-lui (lui &key (srl *current-srl*)) "Find list of ucon for lui" (ensure-lui-integer lui) - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui + (collect-umlisp-query (mrconso (cui kcuilrl) srl lui lui :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl))) + (unless lui (return-from find-ucon-lui nil)) + + (let ((tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D AND KPFENG=1~A ORDER BY kcuilrl ASC LIMIT 1" + lui (if srl (format nil " AND SRL<=~D" srl) ""))))) + (unless tuple + (setq tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D~A ORDER BY kcuilrl ASC LIMIT 1" + lui (if srl (format nil " AND SRL<=~D" srl) ""))))) + (unless tuple + (return-from find-ucon-lui nil)) + (make-instance 'ucon :cui (first tuple) :pfstr (third tuple) + :lrl (ensure-integer (third tuple))))) (defun find-ucon-sui (sui &key (srl *current-srl*)) "Find list of ucon for sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr + (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl)))) + +(defun find-ucon-aui (aui &key (srl *current-srl*)) + "Find list of ucon for aui" + (ensure-sui-integer aui) + (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-ucon-cuisui (cui sui &key (srl *current-srl*)) @@ -225,38 +259,38 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-cui-integer cui) (ensure-sui-integer sui) (when (and cui sui) - (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl kcuisui + (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui (make-cuisui cui sui)) (make-instance 'ucon :cui cui - :pfstr kpfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl))))) (defun find-ucon-str (str &key (srl *current-srl*)) "Find ucon that are exact match for str" - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr + (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-ucon-all (&key (srl *current-srl*)) "Return list of all ucon's" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query 'list #'(lambda (tuple) - (destructuring-bind (cui pfstr cuilrl) tuple + (destructuring-bind (cui cuilrl) tuple (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl)))) - (query-string mrconso (cui kpfstr kcuilrl) srl nil nil + :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer cuilrl)))) + (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc) :distinct t) :database db))) (defun find-ucon-all2 (&key (srl *current-srl*)) "Return list of all ucon's" - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc) :distinct t) (make-instance 'ucon :cui (ensure-integer cui) - :pfstr kpfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-cui-ucon-all (&key (srl *current-srl*)) @@ -268,14 +302,14 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun map-ucon-all (fn &key (srl *current-srl*)) "Map a function over all ucon's" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query nil #'(lambda (tuple) - (destructuring-bind (cui pfstr cuilrl) tuple + (destructuring-bind (cui cuilrl) tuple (funcall fn (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer cuilrl))))) - (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc) :distinct t) :database db))) @@ -283,8 +317,30 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-udef-cui (cui &key (srl *current-srl*)) "Return a list of udefs for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrdef (sab def) srl cui cui :lrl "KSRL") - (make-instance 'udef :sab sab :def def))) + (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL") + (make-instance 'udef :sab sab :def def :suppress suppress))) + +(defun find-udoc-key (key) + "Return list of abbreviation documentation for a key" + (collect-umlisp-query (mrdoc (value type expl) nil dockey key) + (make-instance 'udoc :key key :value value :type type :expl expl))) + +(defun find-udoc-value (value) + "Return abbreviation documentation" + (collect-umlisp-query (mrdoc (dockey type expl) nil value value) + (make-instance 'udoc :key dockey :value value :type type :expl expl))) + +(defun find-udoc-key-value (key value) + (let ((tuple (car (mutex-sql-query + (format nil "SELECT TYPE,EXPL FROM MRDOC WHERE DOCKEY='~A' AND VALUE='~A'" + key value))))) + (when tuple + (make-instance 'udoc :key key :value value :type (first tuple) :expl (second tuple))))) + +(defun find-udoc-all () + "Return all abbreviation documentation" + (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil) + (make-instance 'udoc :key dockey :value value :type type :expl expl))) (defun find-usty-cui (cui &key (srl *current-srl*)) "Return a list of usty for cui" @@ -301,11 +357,12 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-urel-cui (cui &key (srl *current-srl*)) "Return a list of urel for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1 - cui :lrl "KSRL") - (make-instance 'urel :cui1 cui :rel rel - :cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl - :mg mg :pfstr2 kpfstr2))) + (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) + srl cui1 cui :lrl "KSRL") + (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel + :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2 + :rui rui :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir + :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2)))) (defun find-cui2-urel-cui (cui &key (srl *current-srl*)) "Return a list of urel for cui" @@ -317,11 +374,12 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-urel-cui2 (cui2 &key (srl *current-srl*)) "Return a list of urel for cui2" (ensure-cui-integer cui2) - (collect-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2 - cui2 :lrl "KSRL") - (make-instance 'urel :cui2 cui2 :rel rel - :cui1 (ensure-integer cui1) :rela rela :sab sab :sl sl - :mg mg :pfstr2 kpfstr2))) + (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) + srl cui2 cui2 :lrl "KSRL") + (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2) :stype2 stype2 :rui rui :srui srui + :stype1 stype1 :cui1 (ensure-integer cui1) :aui1 (ensure-integer aui1) + :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf + :pfstr2 (find-pfstr-cui cui2)))) (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*)) (ensure-cui-integer cui2) @@ -332,39 +390,33 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucoc-cui (cui &key (srl *current-srl*)) "Return a list of ucoc for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1 + (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1 cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) (when (eql 0 cui2) (setq cui2 nil)) - (make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2) - :soc soc :cot cot :cof (ensure-integer cof) :coa coa - :pfstr2 kpfstr2))) + (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1) + :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) + :cot cot :cof (ensure-integer cof) :coa coa :sab sab + :pfstr2 (find-pfstr-cui cui2)))) (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*)) "Return a list of ucoc for cui2" (ensure-cui-integer cui2) - (collect-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2 + (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2 cui2 :lrl klrl :order (cof asc)) (when (zerop cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2 - :soc soc :cot cot :cof (ensure-integer cof) :coa coa - :pfstr2 kpfstr2))) + :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2) + :sab sab :cot cot :cof (ensure-integer cof) :coa coa + :pfstr2 (find-pfstr-cui cui2)))) (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*)) "List of ucon with co-occurance cui2" (ensure-cui-integer cui2) - (mapcar + (mapcar #'(lambda (cui) (find-ucon-cui cui :srl srl)) (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl))))) -(defun find-ulo-cui (cui &key (srl *current-srl*)) - "Return a list of ulo for cui" - (ensure-cui-integer cui) - (collect-umlisp-query (mrlo (isn fr un sui sna soui) srl cui cui - :lrl "KLRL") - (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un - :sui (ensure-integer sui) :sna sna :soui soui))) - (defun find-uterm-cui (cui &key (srl *current-srl*)) "Return a list of uterm for cui" @@ -377,7 +429,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-uterm-lui (lui &key (srl *current-srl*)) "Return a list of uterm for lui" (ensure-lui-integer lui) - (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui + (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui :lrl kluilrl :distinct t) (make-instance 'uterm :cui (ensure-integer cui) :lui lui :lat lat :ts ts :lrl (ensure-integer kluilrl)))) @@ -396,36 +448,37 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Return a list of ustr for cui/lui" (ensure-cui-integer cui) (ensure-lui-integer lui) - (collect-umlisp-query (mrconso (sui stt str ksuilrl) srl kcuilui + (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui (make-cuilui cui lui) :lrl ksuilrl) (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui - :cuisui (make-cuisui cui sui) :stt stt :str str + :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress :lrl (ensure-integer ksuilrl)))) (defun find-ustr-cuisui (cui sui &key (srl *current-srl*)) "Return the single ustr for cuisui" (ensure-cui-integer cui) (ensure-sui-integer sui) - (collect-umlisp-query (mrconso (lui stt str ksuilrl) srl kcuisui + (collect-umlisp-query (mrconso (lui stt str suppress ksuilrl) srl kcuisui (make-cuisui cui sui) :lrl lsuilrl :single t) (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui) - :lui (ensure-integer lui) :stt stt :str str + :lui (ensure-integer lui) :stt stt :str str :suppress suppress :lrl (ensure-integer ksuilrl)))) (defun find-ustr-sui (sui &key (srl *current-srl*)) "Return the list of ustr for sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrconso (cui lui stt str ksuilrl) srl sui sui + (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui :lrl ksuilrl) (make-instance 'ustr :sui sui :cui cui :stt stt :str str :cuisui (make-cuisui (ensure-integer cui) sui) + :suppress suppress :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl)))) - + (defun find-ustr-sab (sab &key (srl *current-srl*)) "Return the list of ustr for sab" (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl) (let ((cuisui (ensure-integer kcuisui))) - (apply #'find-ustr-cuisui + (apply #'find-ustr-cuisui (append (multiple-value-list (decompose-cuisui cuisui)) (list :srl srl)))))) @@ -433,17 +486,18 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ustr-all (&key (srl *current-srl*)) "Return list of all ustr's" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query 'list #'(lambda (tuple) - (destructuring-bind (cui lui sui stt ksuilrl pfstr) tuple + (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple (make-instance 'ustr :cui (ensure-integer cui) :lui (ensure-integer lui) :sui (ensure-integer sui) - :stt stt :str pfstr + :stt stt :str (find-pfstr-cui cui) :cuisui (make-cuisui (ensure-integer cui) (ensure-integer sui)) + :suppress suppress :lrl (ensure-integer ksuilrl)))) - (query-string mrconso (cui lui sui stt ksuilrl kpfstr) srl nil nil :lrl ksuilrl + (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl :distinct t :order (sui asc)) :database db))) @@ -472,13 +526,31 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*)) (ensure-cui-integer cui) (ensure-sui-integer sui) - (collect-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc) + (collect-umlisp-query (mrcxt (sab rank code cxn cxl cxs cui2 hcd rela xc) srl kcuisui (make-cuisui cui sui) :lrl ksrl) - (make-instance 'ucxt :sab sab :code code + (make-instance 'ucxt :sab sab :code code + :rank rank :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd - :rela rela :xc xc :rnk (ensure-integer rnk) + :rela rela :xc xc :cui2 (ensure-integer cui2)))) +(defun find-uhier-cui (cui &key (srl *current-srl*)) + (ensure-cui-integer cui) + (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf) + srl cui cui :lrl ksrl) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + +(defun find-uhier-all (&key (srl *current-srl*)) + (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf) + srl nil nil :lrl ksrl) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*)) (ensure-cui-integer cui) (ensure-lui-integer lui) @@ -495,7 +567,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "' and lui='0' and sui='0'"))) (when srl (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3))) - (loop for tuple in (mutex-sql-query ls) collect + (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))))) @@ -519,28 +591,30 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Find usab for a key" (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat - cenc curver sabin) nil nil nil) - (make-instance 'usab :vcui (ensure-integer vcui) + cenc curver sabin ssn scit) nil nil nil) + (make-instance 'usab :vcui (ensure-integer vcui) :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son :sf sf :sver sver :vstart vstart :vend vend :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))) + :curver curver :sabin sabin :ssn ssn :scit scit))) (defun find-usab-by-key (key-name key) "Find usab for a key" (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart - vend 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 :vstart vstart :vend vend :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))) + vend imeta rmeta slc scc srl tfr cfr cxty + ttyl atnl lat cenc curver sabin + ssn scit) + 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 :vstart vstart :vend vend :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 + :ssn ssn :scit scit))) (defun find-usab-rsab (rsab) "Find usab for rsab" @@ -553,6 +627,20 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-cui-max () (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON")))) +(defun find-umap-cui (cui) + (ensure-cui-integer cui) + (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr + fromtype fromrule fromres rel rela toid tosid + toexpr totype torule tores maprule maptype + mapatn mapatv cvf) + nil mapsetcui cui) + (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid + :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid + :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres + :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype + :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn + :mapatv mapatv :cvf cvf))) + ;;;; Cross table find functions (defun find-ucon-tui (tui &key (srl *current-srl*)) @@ -560,7 +648,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-tui-integer tui) (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc)) (find-ucon-cui (ensure-integer cui) :srl srl))) - + (defun find-ucon-word (word &key (srl *current-srl*) (like nil)) "Return list of ucons that match word. Optionally, use SQL's LIKE syntax" (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t @@ -636,34 +724,44 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" ;;; Multiword lookup and score functions (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl - only-exact-if-match) + only-exact-if-match limit) (let ((uobjs '())) (dolist (word (delimited-string-to-list str #\space)) (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl)))) - (let ((sorted + (let ((sorted (funcall sort-fun str (delete-duplicates uobjs :test #'= :key key)))) - (if (and (plusp (length sorted)) - only-exact-if-match - (multiword-match str (pfstr (first sorted)))) - (first sorted) - sorted)))) - + (let ((len (length sorted))) + (cond + ((zerop len) + (return-from find-uobj-multiword nil)) + ((and only-exact-if-match (multiword-match str (pfstr (first sorted)))) + (first sorted)) + (limit + (if (and (plusp limit) (> len limit)) + (subseq sorted 0 limit) + limit)) + (t + sorted)))))) + (defun find-ucon-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str - #'cui srl only-exact-if-match)) + #'cui srl only-exact-if-match limit)) (defun find-uterm-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str - #'lui srl only-exact-if-match)) + #'lui srl only-exact-if-match limit)) (defun find-ustr-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str - #'sui srl only-exact-if-match)) - + #'sui srl only-exact-if-match limit)) + (defun sort-score-pfstr-str (str uobjs) "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr" (sort-score-umlsclass-str uobjs str #'pfstr)) @@ -676,7 +774,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Sort a list of objects based on scoring to a string" (let ((scored '())) (dolist (obj objs) - (push (list obj (score-multiword-match str (funcall lookup-func obj))) + (push (list obj (score-multiword-match str (funcall lookup-func obj))) scored)) (mapcar #'car (sort scored #'> :key #'cadr)))) @@ -697,7 +795,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-labr-eui (eui) (ensure-eui-integer eui) - (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui) + (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui) (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2 :eui2 (ensure-integer eui2)))) @@ -746,7 +844,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ltrm-eui (eui) (ensure-eui-integer eui) - (collect-umlisp-query (lrtrm (bas gen) nil eui eui) + (collect-umlisp-query (lrtrm (bas gen) nil eui eui) (make-instance 'ltrm :eui eui :bas bas :gen gen))) (defun find-ltyp-eui (eui) @@ -799,18 +897,18 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (with-sql-connection (conn) (ignore-errors (sql-execute "drop table USTATS" conn)) (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn) - - (dotimes (srl 4) + + (dotimes (srl 5) (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl) (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl) (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl) (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl) (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl) - (insert-ustats-count conn "Context Count" "MRCXT" "*" "KSRL" srl) + (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl) + (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl) + (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl) (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl) (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl) - #+ignore - (insert-ustats-count conn "Locator Count" "MRLO" "*" "KLRL" srl) (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl) (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl) (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl) @@ -828,13 +926,13 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-count-table (conn table srl count-variable srl-control) (cond ((stringp srl-control) - (ensure-integer - (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d" + (ensure-integer + (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d" count-variable table srl-control srl) conn)))) ((null srl-control) (ensure-integer - (caar (sql-query (format nil "select count(~a) from ~a" + (caar (sql-query (format nil "select count(~a) from ~a" count-variable table ) conn)))) (t @@ -842,8 +940,8 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" 0))) (defun insert-ustats (conn name count srl) - (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)" - name count (if srl srl 3)) + (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)" + name count (if srl srl 3)) conn)) (defun find-ustats-all (&key (srl *current-srl*)) @@ -858,7 +956,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (make-instance 'ustats :name name :hits (ensure-integer count) :srl (ensure-integer srl))))) - + (defun find-ustats-srl (srl) (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc)) (make-instance 'ustats :name name :hits (ensure-integer count))))