X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=sql-classes.lisp;h=6bd0012f9809c2cbb3c32b2dd5293e2dfc0ac05a;hp=2831defc003504ff2c1f488793d013a80d612535;hb=e6ef11f4c42de5a6754f73d9a714a0213b3a0133;hpb=e9270445eaef612cf34fc247b45eae885a81be19 diff --git a/sql-classes.lisp b/sql-classes.lisp index 2831def..6bd0012 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -25,110 +25,137 @@ (defun current-srl! (srl) (setq *current-srl* srl)) -(defmacro query-string (table fields &optional srl where-name where-value - &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~)~^,~}" +(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~)" + (if distinct "DISTINCT " "") fields table)) + (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}" order) "")) - (%%lrl (format nil " and ~:@(~A~)<=" lrl)) + (%%lrl (format nil " AND ~:@(~A~)<=" lrl)) (%%where (when where-name - (format nil " where ~:@(~A~)~A" where-name - (if like " like " ""))))) - `(concatenate - 'string - ,%%fields - ,@(when %%where (list %%where)) - ,@(when %%where - `((typecase ,where-value - #+ignore - (fixnum - (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'")) - (number - (concatenate 'string "='" (write-to-string ,where-value) "'")) - (null - " is null") - (t - (format nil ,(if like "'%~A%'" "='~A'") ,where-value))))) - (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "") - ,@(when %%order (list %%order)) - ,@(when single (list " limit 1"))))) - -(defun query-string-eval (table fields &optional srl where-name where-value - &key (lrl "KCUILRL") single distinct order like) + (format nil " WHERE ~:@(~A~)~A" where-name + (if like " like " "")))) + (%filter (gensym "FILTER-")) + (%single (gensym "SINGLE-")) + (%limit (gensym "LIMIT-"))) + `(let ((,%limit ,limit) + (,%single ,single) + (,%filter ,filter)) + (concatenate + 'string + ,%%fields + ,@(when %%where (list %%where)) + ,@(when %%where + `((typecase ,where-value + #+ignore + (fixnum + (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'")) + (number + (concatenate 'string "='" (write-to-string ,where-value) "'")) + (null + " IS NULL") + (t + (format nil ,(if like "'%~A%'" "='~A'") ,where-value))))) + (if ,%filter (concatenate 'string + ,(if %%where " AND " " WHERE ") + ,%filter) "") + (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "") + ,@(when %%order (list %%order)) + (cond + ((and ,%single ,%limit) + (error "Can't set single (~S) and limit (~S)" ,%single ,%limit)) + (,%single + " LIMIT 1") + (,%limit + (format nil " LIMIT ~D" ,%limit)) + (t + "")))))) + +(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 srl (format nil " and ~:@(~A~)<=~D" lrl srl) "") - (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) "") - (if single " limit 1" ""))) + (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) ""))) (defmacro umlisp-query (table fields srl where-name where-value &key (lrl "KCUILRL") single distinct order like - (query-cmd 'mutex-sql-query)) + limit filter (query-cmd 'mutex-sql-query)) "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 - :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like))) + :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like + :filter ,filter :limit ,limit))) (defmacro umlisp-query-eval (table fields srl where-name where-value - &key (lrl "KCUILRL") single distinct order like) + &key (lrl "KCUILRL") single distinct order like + filter limit) "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 - :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like))) + :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like + :filter ,filter :limit ,limit))) ;; only WHERE-VALUE and SRL are evaluated (defmacro collect-umlisp-query ((table fields srl where-name where-value &key (lrl "KCUILRL") distinct single - order like (query-cmd 'mutex-sql-query)) + order like (query-cmd 'mutex-sql-query) + filter limit) &body body) (let ((value (gensym)) (r (gensym))) (if single - `(let* ((,value ,where-value) - (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value - :lrl ,lrl :single ,single - :distinct ,distinct :order ,order - :like ,like - :query-cmd ,query-cmd)))) - ,@(unless where-name `((declare (ignore ,value)))) - (when tuple - (destructuring-bind ,fields tuple - ,@body))) + (if (and limit (> limit 1)) + (error "Can't set limit along with single.") + `(let* ((,value ,where-value) + (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value + :lrl ,lrl :single ,single + :distinct ,distinct :order ,order + :like ,like :filter ,filter + :query-cmd ,query-cmd)))) + ,@(unless where-name `((declare (ignore ,value)))) + (when tuple + (destructuring-bind ,fields tuple + ,@body)))) `(let ((,value ,where-value)) ,@(unless where-name `((declare (ignore ,value)))) (let ((,r '())) (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like)) + :order ,order :filter ,filter :like ,like + :limit ,limit)) (push (destructuring-bind ,fields tuple ,@body) ,r)) (nreverse ,r)) #+ignore (loop for tuple in (umlisp-query ,table ,fields ,srl ,where-name ,value :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like) + :order ,order :like ,like :filter ,filter :limit ,limit) collect (destructuring-bind ,fields tuple ,@body)))))) (defmacro collect-umlisp-query-eval ((table fields srl where-name where-value &key (lrl "KCUILRL") distinct single - order like) + order like filter limit) &body body) (let ((value (gensym)) (r (gensym)) @@ -138,7 +165,8 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value :lrl ,lrl :single ,single :distinct ,distinct :order ,order - :like ,like)))) + :like ,like :filter ,filter + :limit ,limit)))) (when tuple (destructuring-bind ,eval-fields tuple ,@body))) @@ -146,14 +174,16 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (,r '())) (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like)) + :order ,order :like ,like + :filter ,filter :limit ,limit)) (push (destructuring-bind ,eval-fields tuple ,@body) ,r)) (nreverse ,r) #+ignore (loop for tuple in (umlisp-query-eval ,table ,fields ,srl ,where-name ,value :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like) + :order ,order :like ,like :filter ,filter + :limit ,limit) collect (destructuring-bind ,eval-fields tuple ,@body)))))) ;;; @@ -174,6 +204,16 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (setq ,sui (parse-sui ,sui)) ,sui)) +(defmacro ensure-aui-integer (aui) + `(if (stringp ,aui) + (setq ,aui (parse-aui ,aui)) + ,aui)) + +(defmacro ensure-rui-integer (rui) + `(if (stringp ,rui) + (setq ,rui (parse-rui ,rui)) + ,rui)) + (defmacro ensure-tui-integer (tui) `(if (stringp ,tui) (setq ,tui (parse-tui ,tui)) @@ -184,61 +224,101 @@ 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" (ensure-cui-integer cui) (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) "")))))) + (collect-umlisp-query (mrconso (str) srl cui cui :distinct t + :filter " KPFENG=1" :single t) + str) + (collect-umlisp-query (mrconso (str) srl cui cui :distinct t + :single t) + 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" (ensure-lui-integer lui) - (collect-umlisp-query (mrconso (cui kcuilrl) srl lui lui - :distinct t) - (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))))) + (or + (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui + :filter " KPFENG=1" :single t) + (make-instance 'ucon :cui (ensure-integer cui) + :pfstr str :lrl (ensure-integer kcuilrl))) + (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui + :single t) + (make-instance 'ucon :cui (ensure-integer cui) + :pfstr str :lrl (ensure-integer kcuilrl))))) (defun find-ucon-sui (sui &key (srl *current-srl*)) "Find list of ucon for sui" @@ -249,7 +329,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-aui (aui &key (srl *current-srl*)) "Find list of ucon for aui" - (ensure-sui-integer aui) + (ensure-aui-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)))) @@ -323,24 +403,21 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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))) + (make-instance 'udoc :dockey key :dvalue value :dtype 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))) + (make-instance 'udoc :dockey dockey :dvalue value :dtype 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-key-value (dockey value) + (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value)) + (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl))) (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))) + (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl))) (defun find-usty-cui (cui &key (srl *current-srl*)) "Return a list of usty for cui" @@ -354,14 +431,28 @@ 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 + 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" + (ensure-rui-integer rui) + (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) + srl rui rui :lrl "KSRL" :single t) + (make-instance 'urel :cui1 cui1 :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 + :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)))) (defun find-cui2-urel-cui (cui &key (srl *current-srl*)) @@ -376,8 +467,10 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-cui-integer cui2) (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) + (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2) + :stype2 stype2 :rui (ensure-integer 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)))) @@ -511,28 +604,28 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-uso-cuisui (cui sui &key (srl *current-srl*)) (ensure-sui-integer sui) (ensure-cui-integer cui) - (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui - (make-cuisui cui sui) :lrl srl) + (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str) + srl kcuisui (make-cuisui cui sui) :lrl srl) (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty - :cui cui :sui sui :saui saui :sdui sdui :scui scui))) + :cui cui :sui sui :saui saui :sdui sdui :scui scui + :lat lat :str str))) + +(defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit) + (ensure-cui-integer cui) + (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui) + srl cui cui :lrl srl :limit limit + :filter (when english-only "LAT='ENG'")) + (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty + :cui cui :sui sui :saui saui :sdui sdui :scui scui + :lat lat :str str))) (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) 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))) - -(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) @@ -551,11 +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) @@ -588,7 +681,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (find-usty-tui tui))) (defun find-usab-all () - "Find usab for a key" + "Return all usab objects" (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 ssn scit) nil nil nil) @@ -641,6 +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*)) @@ -649,11 +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" @@ -679,11 +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" @@ -724,10 +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)))) @@ -746,9 +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) @@ -758,9 +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" @@ -961,25 +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))))