X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=sql-classes.lisp;h=6bd0012f9809c2cbb3c32b2dd5293e2dfc0ac05a;hb=e6ef11f4c42de5a6754f73d9a714a0213b3a0133;hp=1187d5931bd9bc52a0791c43752dbaa434b2e865;hpb=756b9f208a0f807c326b0ecc6d29bfc73967440e;p=umlisp.git diff --git a/sql-classes.lisp b/sql-classes.lisp index 1187d59..6bd0012 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -25,7 +25,7 @@ (defun current-srl! (srl) (setq *current-srl* srl)) -(defmacro query-string (table fields &optional srl where-name where-value +(defmacro query-string (table fields srl where-name where-value &key (lrl "KCUILRL") single distinct order like limit filter) (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)" @@ -35,7 +35,7 @@ "")) (%%lrl (format nil " AND ~:@(~A~)<=" lrl)) (%%where (when where-name - (format nil " where ~:@(~A~)~A" where-name + (format nil " WHERE ~:@(~A~)~A" where-name (if like " like " "")))) (%filter (gensym "FILTER-")) (%single (gensym "SINGLE-")) @@ -55,7 +55,7 @@ (number (concatenate 'string "='" (write-to-string ,where-value) "'")) (null - " is null") + " IS NULL") (t (format nil ,(if like "'%~A%'" "='~A'") ,where-value))))) (if ,%filter (concatenate 'string @@ -65,7 +65,7 @@ ,@(when %%order (list %%order)) (cond ((and ,%single ,%limit) - (error "Can't set single and limit")) + (error "Can't set single (~S) and limit (~S)" ,%single ,%limit)) (,%single " LIMIT 1") (,%limit @@ -73,27 +73,27 @@ (t "")))))) -(defun query-string-eval (table fields &optional srl where-name where-value +(defun query-string-eval (table fields srl where-name where-value &key (lrl "KCUILRL") single distinct order like limit filter) (when single (setq limit 1)) (concatenate 'string - (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)" - (if distinct "distinct " "") fields table) - (if where-name (format nil " where ~:@(~A~)" where-name) "") + (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)" + (if distinct "DISTINCT " "") fields table) + (if where-name (format nil " WHERE ~:@(~A~)" where-name) "") (if where-name (format nil (typecase where-value (number "='~D'") - (null " is null") + (null " IS NULL") (t - (if like " like '%~A%""='~A'"))) + (if like " LINK '%~A%""='~A'"))) where-value) "") (if filter (concatenate 'string " AND " filter) nil) - (if srl (format nil " and ~:@(~A~)<=~D" lrl srl) "") - (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) "") - (if limit (format nil " limit ~D" limit) ""))) + (if srl (format nil " AND ~:@(~A~)<=~D" lrl srl) "") + (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}" order) "") + (if limit (format nil " LIMIT ~D" limit) ""))) (defmacro umlisp-query (table fields srl where-name where-value @@ -224,31 +224,70 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (setq ,eui (parse-eui ,eui)) ,eui)) -(defun find-ucon-cui (cui &key (srl *current-srl*)) - "Find ucon for a cui" +(defun make-ucon-cui (cui) + (ensure-cui-integer cui) + (when cui + (make-instance 'ucon :cui cui))) + +(defun find-ucon-cui (cui &key (srl *current-srl*) without-pfstr) + "Find ucon for a cui. If set SAB, the without-pfstr is on by default" (ensure-cui-integer cui) (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" + (if without-pfstr + (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t) + (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl) + :pfstr nil))) + (or + (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t :filter "KPFENG=1") + (make-instance 'ucon :cui cui :pfstr str + :lrl kcuilrl)) + (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t) + (make-instance 'ucon :cui cui :pfstr str + :lrl kcuilrl)))) + +(defun find-uconso-cui (cui &key sab (srl *current-srl*)) + "Find uconso for a cui." (ensure-cui-integer cui) - (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t) - (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl) - :pfstr nil))) + (unless cui (return-from find-uconso-cui nil)) + + (collect-umlisp-query (mrconso (lat ts lui stt sui ispref aui saui scui sdui sab tty code str + srl suppress cvf kpfeng kcuisui kcuilui kcuilrl + kluilrl ksuilrl) srl cui cui + :filter (if sab (concatenate 'string "SAB='" sab "'") nil)) + (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref + :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code + :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng + :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl + :ksuilrl ksuilrl))) + + +(defun find-uconso-code (code &key first sab (srl *current-srl*) (like nil)) + "Return list of uconso objects that match code. Optional, filter for SAB. Optionally, use SQL's LIKE syntax" + (collect-umlisp-query (mrconso (cui sab) srl code code :like like :distinct t + :lrl klrl + :filter (if sab (concatenate 'string "SAB='" sab "'") nil)) + (let ((uconsos (find-uconso-cui cui :sab sab :srl srl))) + (if first + (first uconsos) + uconsos)))) + +(defun find-uconso-sui (sui &key sab (srl *current-srl*)) + "Find uconso for a sui. If set SAB, the without-pfstr is on by default" + (ensure-sui-integer sui) + (unless (and sui (stringp sab)) + (return-from find-uconso-sui nil)) + + (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str + srl suppress cvf kpfeng kcuisui kcuilui kcuilrl + kluilrl ksuilrl) srl sui sui + :distinct t + :filter (if sab (concatenate 'string "SAB='" sab "'") nil)) + (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref + :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code + :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng + :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl + :ksuilrl ksuilrl))) (defun find-pfstr-cui (cui &key (srl *current-srl*)) "Find preferred string for a cui" @@ -259,7 +298,13 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" str) (collect-umlisp-query (mrconso (str) srl cui cui :distinct t :single t) - str))) + str))) + +(defun find-lrl-cui (cui &key (srl *current-srl*)) + "Find LRL for a cui" + (ensure-cui-integer cui) + (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :distinct t :single t) + (ensure-integer kcuilrl))) (defun find-ucon-lui (lui &key (srl *current-srl*)) "Find list of ucon for lui" @@ -386,15 +431,19 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :distinct t) (make-instance 'usty :tui (ensure-integer tui) :sty sty))) -(defun find-urel-cui (cui &key (srl *current-srl*)) +(defun find-urel-cui (cui &key (srl *current-srl*) filter without-pfstr2) "Return a list of urel for cui" (ensure-cui-integer cui) (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 (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir - :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2)))) + srl cui1 cui :lrl "KSRL" :filter filter) + (let ((rel + (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel + :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2 + :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir + :suppress suppress :cvf cvf))) + (unless without-pfstr2 + (setf (slot-value rel 'pfstr2) (find-pfstr-cui cui2))) + rel))) (defun find-urel-rui (rui &key (srl *current-srl*)) "Return the urel for a rui" @@ -572,22 +621,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-uso-aui (aui &key (srl *current-srl*)) (ensure-sui-integer aui) - (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat str) srl aui - aui :lrl srl :single t) + (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat + str) srl aui aui :lrl srl :single t) (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty - :sui sui :saui saui :sdui sdui :scui scui - :lat lat :str str))) - -(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*)) - (ensure-cui-integer cui) - (ensure-sui-integer sui) - (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 - :rank rank - :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd - :rela rela :xc xc - :cui2 (ensure-integer cui2)))) + :sui sui :saui saui :sdui sdui :scui scui :lat lat + :str str))) (defun find-uhier-cui (cui &key (srl *current-srl*)) (ensure-cui-integer cui) @@ -606,11 +644,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :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*)) +(defun find-usat-ui (cui &key lui sui (srl *current-srl*)) (ensure-cui-integer cui) (ensure-lui-integer lui) (ensure-sui-integer sui) - (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where ")) + (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE ")) (cond (sui (string-append ls "KCUISUI='" (integer-string (make-cuisui cui sui) 14) @@ -696,6 +734,15 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn :mapatv mapatv :cvf cvf))) +(defun find-usmap-cui (cui) + (ensure-cui-integer cui) + (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf) + nil mapsetcui cui) + (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab + :fromexpr fromexpr :fromtype fromtype + :rel rel :rela rela :toexpr toexpr :totype totype + :cvf cvf))) + ;;;; Cross table find functions (defun find-ucon-tui (tui &key (srl *current-srl*)) @@ -704,11 +751,59 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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 - :lrl 'klrl :order '(cui asc)) - (find-ucon-cui cui :srl srl))) +(defun mrconso-query-word-cui (word sab srl like) + (format nil "SELECT DISTINCT c.cui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.cui=c.cui~A~A" + (if like " LIKE " "=") + (clsql-sys::sql-escape-quotes word) + (etypecase sab + (string + (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab))) + (cons + (format nil " AND c.sab IN (~{'~A'~^,~})" + (mapcar 'clsql-sys::sql-escape-quotes sab))) + (null + "")) + (if srl (format nil " AND KCUILRL <= ~A" srl) ""))) + +(defun mrconso-query-word-sui (word sab srl like) + (format nil "SELECT DISTINCT c.sui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.sui=c.sui~A~A" + (if like " LIKE " "=") + (clsql-sys::sql-escape-quotes word) + (etypecase sab + (string + (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab))) + (cons + (format nil " AND c.sab IN (~{'~A'~^,~})" + (mapcar 'clsql-sys::sql-escape-quotes sab))) + (null + "")) + (if srl (format nil " AND KCUILRL <= ~A" srl) ""))) + +(defun find-uconso-word (word &key sab (srl *current-srl*) (like nil)) + "Return list of uconso that match word. Optionally, matching SAB. Optionally, use SQL's LIKE syntax" + (cond + (sab + (let ((sui-query (mrconso-query-word-sui word sab srl like)) + (uconsos nil)) + (dolist (sui (remove-duplicates (sort (mapcar 'car (mutex-sql-query sui-query)) #'<))) + (setq uconsos (nconc uconsos (find-uconso-sui sui :sab sab)))) + (remove-duplicates uconsos :key 'cui))) + (t + (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t + :lrl 'klrl :order '(cui asc)) + (find-uconso-cui cui :srl srl))))) + +(defun find-ucon-word (word &key sab (srl *current-srl*) (like nil)) + "Return list of ucon that match word in matching SAB. Optionally, use SQL's LIKE syntax" + (cond + (sab + (let ((query (mrconso-query-word-cui word sab srl like))) + (loop for tuple in (mutex-sql-query query) + collect (make-instance 'ucon :cui (first tuple))))) + (t + (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t + :lrl 'klrl :order '(cui asc)) + (find-ucon-cui cui :srl srl))))) (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil)) "Return list of ucons that match word, optionally use SQL's LIKE syntax" @@ -734,11 +829,30 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :lrl 'klrl :order '(cui asc)) sui)) -(defun find-ustr-word (word &key (srl *current-srl*)) - "Return list of ustrs that match word" - (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl - :order (cui asc sui asc)) - (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl))) +(defun find-ustr-word (word &key sab (srl *current-srl*) (like nil)) + "Return list of ustr that match word in matching SAB. Optionally, use SQL's LIKE syntax" + (cond + (sab + (let ((query (format nil "SELECT c.sui,c.cui,c.lui,c.str,c.lrl,c.stt,c.suppress,c.cuisui FROM MRCONSO c,MRXW_ENG x WHERE x.WD ~A '~A' AND x.cui=c.cui AND x.lui=c.lui AND x.sui=c.sui~A~A" + (if like "LIKE" "=") + (clsql-sys::sql-escape-quotes word) + (typecase sab + (string + (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab))) + (cons + (format nil " AND c.sab IN (~('~A'~^,~))" + (mapcar 'clsql-sys::sql-escape-quotes sab))) + (null + "")) + (if srl (format nil " AND KCUILRL <= ~D" srl) "")))) + (loop for tuple in (mutex-sql-query query) + collect (destructuring-bind (sui cui lui str lrl stt suppress cuisui) tuple + (make-instance 'ustr :sui sui :cui cui :lui lui :str str :lrl lrl + :stt stt :suppress suppress :cuisui cuisui))))) + (t + (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl + :order (cui asc sui asc)) + (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl))))) (defun find-ustr-normalized-word (word &key (srl *current-srl*)) "Return list of ustrs that match word" @@ -779,10 +893,10 @@ 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 limit) + only-exact-if-match limit &key extra-lookup-args) (let ((uobjs '())) (dolist (word (delimited-string-to-list str #\space)) - (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl)))) + (setq uobjs (append uobjs (apply obj-lookup-fun word :srl srl extra-lookup-args)))) (let ((sorted (funcall sort-fun str (delete-duplicates uobjs :test #'= :key key)))) @@ -801,9 +915,19 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-multiword (str &key (srl *current-srl*) (only-exact-if-match t) - limit) + limit + sab) (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str - #'cui srl only-exact-if-match limit)) + #'cui srl only-exact-if-match limit + :extra-lookup-args (list :sab sab))) + +(defun find-uconso-multiword (str &key (srl *current-srl*) + (only-exact-if-match t) + limit + sab) + (find-uobj-multiword str #'find-uconso-word #'sort-score-pfstr-str + #'cui srl only-exact-if-match limit + :extra-lookup-args (list :sab sab))) (defun find-uterm-multiword (str &key (srl *current-srl*) (only-exact-if-match t) @@ -813,9 +937,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ustr-multiword (str &key (srl *current-srl*) (only-exact-if-match t) - limit) + limit + sab) (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str - #'sui srl only-exact-if-match limit)) + #'sui srl only-exact-if-match limit + :extra-lookup-args (list :sab sab))) (defun sort-score-pfstr-str (str uobjs) "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr" @@ -1016,25 +1142,3 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc)) (make-instance 'ustats :name name :hits (ensure-integer count)))) - - -(defun find-bsab-sab (sab) - (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t) - (make-instance 'bsab :sab sab :name name :hits (ensure-integer count)))) - -(defun find-bsab-all () - (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc)) - (make-instance 'bsab :sab sab :name name :hits (ensure-integer count)))) - -(defun find-btty-tty (tty) - (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t) - (make-instance 'btty :tty tty :name name :hits (ensure-integer count)))) - -(defun find-btty-all () - (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc)) - (make-instance 'btty :tty tty :name name :hits (ensure-integer count)))) - -(defun find-brel-rel (rel) - (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel) - (make-instance 'brel :sab sab :sl sl :rel rel :rela rela - :hits (ensure-integer count))))