X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=sql-classes.lisp;h=d1e19f3fea74dd3a36293dab1793f3b24250fad4;hp=f6f306ecb204ce8162f92bcf39b9dad8d01a5d3c;hb=HEAD;hpb=357dad37300c0f2cc45156dae18bd89265c20431 diff --git a/sql-classes.lisp b/sql-classes.lisp index f6f306e..d086fd4 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -7,10 +7,8 @@ ;;;; Author: Kevin M. Rosenberg ;;;; Created: Apr 2000 ;;;; -;;;; $Id$ -;;;; ;;;; This file, part of UMLisp, is -;;;; Copyright (c) 2000-2006 by Kevin M. Rosenberg, M.D. +;;;; Copyright (c) 2000-2010 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. @@ -22,21 +20,21 @@ (defvar *current-srl* nil) (defun current-srl () *current-srl*) -(defun current-srl! (srl) +(defun set-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 limit +(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)) - (%%where (when where-name - (format nil " WHERE ~:@(~A~)~A" where-name - (if like " like " "")))) + (if distinct "DISTINCT " "") (sqlname fields) table)) + (%%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" (sqlname where-name) + (if like " like " "")))) (%filter (gensym "FILTER-")) (%single (gensym "SINGLE-")) (%limit (gensym "LIMIT-"))) @@ -65,7 +63,7 @@ ,@(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 @@ -73,22 +71,22 @@ (t "")))))) -(defun query-string-eval (table fields &optional srl where-name where-value - &key (lrl "KCUILRL") single distinct order like limit filter) +(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) "") + (if distinct "DISTINCT " "") (sqlname fields) table) + (if where-name (format nil " WHERE ~:@(~A~)" (sqlname where-name)) "") (if where-name (format nil - (typecase where-value - (number "='~D'") - (null " IS NULL") - (t - (if like " LINK '%~A%""='~A'"))) - where-value) + (typecase where-value + (number "='~D'") + (null " IS NULL") + (t + (if like " LIKE '%~A%'" "='~A'"))) + where-value) "") (if filter (concatenate 'string " AND " filter) nil) (if srl (format nil " AND ~:@(~A~)<=~D" lrl srl) "") @@ -97,7 +95,7 @@ (defmacro umlisp-query (table fields srl where-name where-value - &key (lrl "KCUILRL") single distinct order like + &key (lrl "KCUILRL") single distinct order like 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" @@ -107,7 +105,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :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" @@ -118,12 +116,12 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" ;; 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) + &key (lrl "KCUILRL") distinct single + order like (query-cmd 'mutex-sql-query) filter limit) - &body body) + &body body) (let ((value (gensym)) - (r (gensym))) + (r (gensym))) (if single (if (and limit (> limit 1)) (error "Can't set limit along with single.") @@ -137,54 +135,54 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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 :filter ,filter :like ,like + `(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 :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 :filter ,filter :limit ,limit) - collect (destructuring-bind ,fields tuple ,@body)))))) + (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 :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 filter limit) - &body body) + &key (lrl "KCUILRL") distinct single + order like filter limit) + &body body) (let ((value (gensym)) - (r (gensym)) - (eval-fields (cadr fields))) + (r (gensym)) + (eval-fields (cadr fields))) (if single - `(let* ((,value ,where-value) - (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value - :lrl ,lrl :single ,single - :distinct ,distinct :order ,order - :like ,like :filter ,filter + `(let* ((,value ,where-value) + (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value + :lrl ,lrl :single ,single + :distinct ,distinct :order ,order + :like ,like :filter ,filter :limit ,limit)))) - (when tuple - (destructuring-bind ,eval-fields tuple - ,@body))) - `(let ((,value ,where-value) - (,r '())) - (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value - :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like + (when tuple + (destructuring-bind ,eval-fields tuple + ,@body))) + `(let ((,value ,where-value) + (,r '())) + (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value + :lrl ,lrl :single ,single :distinct ,distinct + :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 :filter ,filter + (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 :filter ,filter :limit ,limit) - collect (destructuring-bind ,eval-fields tuple ,@body)))))) + collect (destructuring-bind ,eval-fields tuple ,@body)))))) ;;; ;;; Read from SQL database @@ -224,25 +222,83 @@ 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)) - (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-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-cuisui (cuisui &key sab (srl *current-srl*)) + "Find uconso for a cuisui." + (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 kcuisui cuisui + :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)) + (unless sui + (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" @@ -253,7 +309,13 @@ 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" @@ -274,31 +336,34 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-sui-integer sui) (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)))) + :lrl (ensure-integer kcuilrl)))) (defun find-ucon-aui (aui &key (srl *current-srl*)) "Find list of ucon for 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)))) + :lrl (ensure-integer kcuilrl)))) -(defun find-ucon-cuisui (cui sui &key (srl *current-srl*)) +(defun find-ucon-cuisui (cuisui &key (srl *current-srl*)) + "Find ucon for cui/sui" + (collect-umlisp-query (mrconso (cui kcuilrl) srl kcuisui cuisui) + (make-instance 'ucon :cui cui + :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl)))) + +(defun find-ucon-cui-sui (cui sui &key (srl *current-srl*)) "Find ucon for cui/sui" (ensure-cui-integer cui) (ensure-sui-integer sui) (when (and cui sui) - (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui - (make-cuisui cui sui)) - (make-instance 'ucon :cui cui - :pfstr (find-pfstr-cui cui) - :lrl (ensure-integer kcuilrl))))) + (find-ucon-cui-sui cui sui :srl srl))) (defun find-ucon-str (str &key (srl *current-srl*)) "Find ucon that are exact match for str" (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)))) + :lrl (ensure-integer kcuilrl)))) (defun find-ucon-all (&key (srl *current-srl*)) "Return list of all ucon's" @@ -306,27 +371,27 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query 'list #'(lambda (tuple) - (destructuring-bind (cui cuilrl) tuple - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr (find-pfstr-cui cui) + (destructuring-bind (cui cuilrl) tuple + (make-instance 'ucon :cui (ensure-integer cui) + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer cuilrl)))) (query-string mrconso (cui kcuilrl) srl nil nil - :order (cui asc) :distinct t) + :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 kcuilrl) srl nil nil :order (cui asc) - :distinct t) + :distinct t) (make-instance 'ucon :cui (ensure-integer cui) - :pfstr (find-pfstr-cui cui) - :lrl (ensure-integer kcuilrl)))) + :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl)))) (defun find-cui-ucon-all (&key (srl *current-srl*)) "Return list of CUIs for all ucons" (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc) - :distinct t) - cui)) + :distinct t) + cui)) (defun map-ucon-all (fn &key (srl *current-srl*)) "Map a function over all ucon's" @@ -334,19 +399,20 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query nil #'(lambda (tuple) - (destructuring-bind (cui cuilrl) tuple - (funcall fn (make-instance 'ucon :cui (ensure-integer cui) - :pfstr (find-pfstr-cui cui) - :lrl (ensure-integer cuilrl))))) + (destructuring-bind (cui cuilrl) tuple + (funcall fn (make-instance 'ucon :cui (ensure-integer cui) + :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer cuilrl))))) (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc) - :distinct t) + :distinct t) :database db))) (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 suppress) srl cui cui :lrl "KSRL") + (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL" + :distinct t) (make-instance 'udef :sab sab :def def :suppress suppress))) (defun find-udoc-key (key) @@ -377,78 +443,82 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-usty-word (word &key (srl *current-srl*)) "Return a list of usty that match word" (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t - :distinct t) + :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" (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) + 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 (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir - :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2)))) + :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)))) (defun find-cui2-urel-cui (cui &key (srl *current-srl*)) "Return a list of urel for cui" (ensure-cui-integer cui) (collect-umlisp-query (mrrel (cui2) srl cui1 - cui :lrl "KSRL") - cui2)) + cui :lrl "KSRL") + cui2)) (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 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) - srl cui2 cui2 :lrl "KSRL") + srl cui2 cui2 :lrl "KSRL") (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) + :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)))) + :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) (loop for cui in (remove-duplicates - (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl))) - collect (find-ucon-cui cui :srl srl))) + (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl))) + collect (find-ucon-cui cui :srl srl))) -(defun find-ucoc-cui (cui &key (srl *current-srl*)) +#+mrcoc (defun find-ucoc-cui (cui &key (srl *current-srl*)) "Return a list of ucoc for cui" (ensure-cui-integer cui) (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1 - cui :lrl klrl :order (cof asc)) + cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) (when (eql 0 cui2) (setq cui2 nil)) (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)))) + :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*)) +#+mrcoc (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 aui1 aui2 sab cot cof coa) srl cui2 - cui2 :lrl klrl :order (cof asc)) + cui2 :lrl klrl :order (cof asc)) (when (zerop cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2 - :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2) - :sab sab :cot cot :cof (ensure-integer cof) :coa coa - :pfstr2 (find-pfstr-cui cui2)))) + :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*)) +#+mrcoc (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*)) "List of ucon with co-occurance cui2" (ensure-cui-integer cui2) (mapcar @@ -460,66 +530,67 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Return a list of uterm for cui" (ensure-cui-integer cui) (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui - :lrl kluilrl :distinct t) + :lrl kluilrl :distinct t) (make-instance 'uterm :lui (ensure-integer lui) :cui cui - :lat lat :ts ts :lrl (ensure-integer kluilrl)))) + :lat lat :ts ts :lrl (ensure-integer kluilrl)))) (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 - :lrl kluilrl :distinct t) + :lrl kluilrl :distinct t) (make-instance 'uterm :cui (ensure-integer cui) :lui lui - :lat lat :ts ts :lrl (ensure-integer kluilrl)))) + :lat lat :ts ts :lrl (ensure-integer kluilrl)))) (defun find-uterm-cuilui (cui lui &key (srl *current-srl*)) "Return single uterm for cui/lui" (ensure-cui-integer cui) (ensure-lui-integer lui) (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui - (make-cuilui cui lui) - :lrl kluilrl :single t) + (make-cuilui cui lui) + :lrl kluilrl :single t) (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts - :lrl (ensure-integer kluilrl)))) + :lrl (ensure-integer kluilrl)))) (defun find-ustr-cuilui (cui lui &key (srl *current-srl*)) "Return a list of ustr for cui/lui" (ensure-cui-integer cui) (ensure-lui-integer lui) (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 :suppress suppress - :lrl (ensure-integer ksuilrl)))) + (make-cuilui cui lui) :lrl ksuilrl :distinct t) + (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui + :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress + :lrl (ensure-integer ksuilrl)))) + +(defun find-ustr-cuisui (cuisui &key (srl *current-srl*)) + "Return the single ustr for cuisui" + (collect-umlisp-query (mrconso (cui lui sui stt str suppress ksuilrl) srl kcuisui + cuisui :lrl ksuilrl :single t) + (make-instance 'ustr :sui sui :cui cui :cuisui cuisui + :lui (ensure-integer lui) :stt stt :str str :suppress suppress + :lrl (ensure-integer ksuilrl)))) -(defun find-ustr-cuisui (cui sui &key (srl *current-srl*)) +(defun find-ustr-cui-sui (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 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 :suppress suppress - :lrl (ensure-integer ksuilrl)))) + (find-ustr-cuisui (make-cuisui cui sui) :srl srl)) (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 suppress ksuilrl) srl sui sui - :lrl ksuilrl) + :lrl ksuilrl :distinct t) (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)))) + :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 - (append - (multiple-value-list (decompose-cuisui cuisui)) - (list :srl srl)))))) + (find-ustr-cuisui cuisui :srl srl)))) (defun find-ustr-all (&key (srl *current-srl*)) "Return list of all ustr's" @@ -527,17 +598,17 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query 'list #'(lambda (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 (find-pfstr-cui cui) - :cuisui (make-cuisui (ensure-integer cui) - (ensure-integer sui)) - :suppress suppress - :lrl (ensure-integer ksuilrl)))) + (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 (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) srl nil nil :lrl ksuilrl - :distinct t - :order (sui asc)) + :distinct t + :order (sui asc)) :database db))) (defun find-string-sui (sui &key (srl *current-srl*)) @@ -549,76 +620,65 @@ 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 lat str) + (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str ts) 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 - :lat lat :str str))) + :cui cui :sui sui :saui saui :sdui sdui :scui scui + :lat lat :str str :ts ts))) (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) + (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui ts) 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))) + :lat lat :str str :ts ts))) (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) + str ts) 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 :ts ts))) (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) + 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))) + :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) + 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))) + :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*)) +(defun find-usat-ui (cui &optional lui sui &key (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 ")) (cond (sui (string-append ls "KCUISUI='" - (integer-string (make-cuisui cui sui) 14) - "'")) + (integer-string (make-cuisui cui sui) 14) + "'")) (lui (string-append ls "KCUILUI='" - (integer-string (make-cuilui cui lui) 14) - "' and sui='0'")) + (integer-string (make-cuilui cui lui) 14) + "' and sui='0'")) (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7) - "' and lui='0' and sui='0'"))) + "' 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 - (destructuring-bind (code atn sab atv) tuple - (make-instance 'usat :code code :atn atn :sab sab :atv atv))))) + (destructuring-bind (code atn sab atv) tuple + (make-instance 'usat :code code :atn atn :sab sab :atv atv))))) (defun find-usty-tui (tui) "Find usty for tui" @@ -639,37 +699,38 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-usab-all () "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) + rmeta slc scc srl tfr cfr cxty ttyl atnl lat + 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 :ssn ssn :scit scit))) - -(defun find-usab-by-key (key-name key) + :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-by-key (key-name key &key current) "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 - ssn scit) - nil key-name key :single t) + vend imeta rmeta slc scc srl tfr cfr cxty + ttyl atnl lat cenc curver sabin + ssn scit) + nil key-name key :single t + :filter (when current "RMETA=''")) (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) + :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 &key (current t)) "Find usab for rsab" (find-usab-by-key 'rsab rsab)) -(defun find-usab-vsab (vsab) +(defun find-usab-vsab (vsab &key (current t)) "Find usab for vsab" (find-usab-by-key 'vsab vsab)) @@ -679,24 +740,24 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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) + 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))) + :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))) (defun find-usmap-cui (cui) (ensure-cui-integer cui) (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf) - nil mapsetcui cui) + nil mapsetcui cui) (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab - :fromexpr fromexpr :fromtype fromtype - :rel rel :rela rela :toexpr toexpr :totype totype + :fromexpr fromexpr :fromtype fromtype + :rel rel :rela rela :toexpr toexpr :totype totype :cvf cvf))) ;;;; Cross table find functions @@ -707,71 +768,138 @@ 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 '(kcuisui) srl 'wd word :like like + :lrl 'klrl :order '(kcuisui asc)) + (find-uconso-cuisui kcuisui :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" (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t - :lrl 'klrl :order '(cui asc)) + :lrl 'klrl :order '(cui asc)) (find-ucon-cui cui :srl srl))) (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil)) "Return list of cui that match word, optionally use SQL's LIKE syntax" (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t - :lrl 'klrl :order '(cui asc)) - cui)) + :lrl 'klrl :order '(cui asc)) + cui)) (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil)) "Return list of cui that match word, optionally use SQL's LIKE syntax" (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t - :lrl 'klrl :order '(cui asc)) - lui)) + :lrl 'klrl :order '(cui asc)) + lui)) (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil)) "Return list of cui that match word, optionally use SQL's LIKE syntax" (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t - :lrl 'klrl :order '(cui asc)) - sui)) + :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 (kcuisui) srl wd word :lrl klrl + :order (cui asc sui asc)) + (find-ustr-cuisui kcuisui :srl srl))))) (defun find-ustr-normalized-word (word &key (srl *current-srl*)) "Return list of ustrs that match word" - (collect-umlisp-query (mrxnw_eng (cui sui) srl nwd word :lrl klrl - :order (cui asc sui asc)) - (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl))) + (collect-umlisp-query (mrxnw_eng (kcuisui) srl nwd word :lrl klrl + :order (cui asc sui asc)) + (find-ustr-cuisui kcuisui :srl srl))) (defun find-uterm-word (word &key (srl *current-srl*)) "Return list of uterms that match word" (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl - :order (cui asc lui asc)) + :order (cui asc lui asc)) (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl))) (defun find-uterm-normalized-word (word &key (srl *current-srl*)) "Return list of uterms that match word" (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl - :order (cui asc lui asc)) + :order (cui asc lui asc)) (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl))) (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil)) "Return list of ucons that match non-english word" (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like - :distinct t :lrl 'klrl :order '(cui asc)) + :distinct t :lrl 'klrl :order '(cui asc)) (find-ucon-cui cui :srl srl))) (defun find-ustr-noneng-word (word &key (srl *current-srl*)) "Return list of ustrs that match non-english word" - (collect-umlisp-query (mrxw_noneng (cui sui) srl wd word :lrl klrl - :order (cui asc sui asc)) - (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl))) + (collect-umlisp-query (mrxw_noneng (kcuisui) srl wd word :lrl klrl + :order (cui asc sui asc)) + (find-ustr-cuisui kcuisui :srl srl))) ;; Special tables @@ -782,13 +910,14 @@ 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 (nconc uobjs + (kmrcl:flatten (apply obj-lookup-fun word :srl srl extra-lookup-args))))) (let ((sorted - (funcall sort-fun str - (delete-duplicates uobjs :test #'= :key key)))) + (funcall sort-fun str + (delete-duplicates uobjs :test #'= :key key)))) (let ((len (length sorted))) (cond ((zerop len) @@ -803,22 +932,34 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" sorted)))))) (defun find-ucon-multiword (str &key (srl *current-srl*) - (only-exact-if-match t) - limit) + (only-exact-if-match t) + 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) + (only-exact-if-match t) limit) (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str - #'lui srl only-exact-if-match limit)) + #'lui srl only-exact-if-match limit)) (defun find-ustr-multiword (str &key (srl *current-srl*) - (only-exact-if-match t) - limit) + (only-exact-if-match t) + 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" @@ -847,7 +988,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-lexterm-word (wrd) (collect-umlisp-query (lrwd (eui) nil wrd wrd) (make-instance 'lexterm :eui (ensure-integer eui) - :wrd (copy-seq wrd)))) + :wrd (copy-seq wrd)))) ;; LEX SQL Read functions @@ -855,18 +996,18 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-eui-integer 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)))) + :eui2 (ensure-integer eui2)))) (defun find-labr-bas (bas) (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas) (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2 - :bas (copy-seq bas) :eui2 (ensure-integer eui2)))) + :bas (copy-seq bas) :eui2 (ensure-integer eui2)))) (defun find-lagr-eui (eui) (ensure-eui-integer eui) (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui) (make-instance 'lagr :eui eui :str str :sca sca :agr agr - :cit cit :bas bas))) + :cit cit :bas bas))) (defun find-lcmp-eui (eui) (ensure-eui-integer eui) @@ -882,13 +1023,13 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-eui-integer eui) (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui) (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2 - :eui2 (ensure-integer eui2)))) + :eui2 (ensure-integer eui2)))) (defun find-lprn-eui (eui) (ensure-eui-integer eui) (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui) (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd - :cas cas :pos pos :qnt qnt :fea fea))) + :cas cas :pos pos :qnt qnt :fea fea))) (defun find-lprp-eui (eui) (ensure-eui-integer eui) @@ -912,26 +1053,26 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-lwd-wrd (wrd) (make-instance 'lwd :wrd wrd - :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd) - (ensure-integer eui)))) + :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd) + (ensure-integer eui)))) ;;; Semantic Network SQL access functions (defun find-sdef-ui (ui) (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin) - nil ui ui :single t) + nil ui ui :single t) (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn - :def def :ex ex :un un :rh rh :abr abr :rin rin))) + :def def :ex ex :un un :rh rh :abr abr :rin rin))) (defun find-sstre1-ui (ui) (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui) (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2) - :ui3 (ensure-integer ui3)))) + :ui3 (ensure-integer ui3)))) (defun find-sstre1-ui2 (ui2) (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2) (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2 - :ui3 (ensure-integer ui3)))) + :ui3 (ensure-integer ui3)))) (defun find-sstr-rl (rl) (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl) @@ -951,93 +1092,52 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" ;;; ************************** -(defun make-ustats () - (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 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 "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) - (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) - (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl) - (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl) - (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl) - (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl) - (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl)) - (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn)) - (find-ustats-all)) - -(defun insert-ustats-count (conn name table count-variable srl-control srl) - (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl)) - (defun find-count-table (conn table srl count-variable srl-control) + (with-sql-connection (conn) (cond ((stringp srl-control) (ensure-integer (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d" - count-variable table srl-control srl) - conn)))) + count-variable table srl-control srl) + conn)))) ((null srl-control) (ensure-integer (caar (sql-query (format nil "select count(~a) from ~a" - count-variable table ) - conn)))) + count-variable table ) + conn)))) (t (error "Unknown srl-control") - 0))) + 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)) - conn)) + name count (if srl srl 3)) + conn)) (defun find-ustats-all (&key (srl *current-srl*)) (if srl (collect-umlisp-query (ustats (name count srl) nil srl srl - :order (name asc)) - (make-instance 'ustats :name name - :hits (ensure-integer count) - :srl (ensure-integer srl))) + :order (name asc)) + (make-instance 'ustats :name name + :hits (ensure-integer count) + :srl (ensure-integer srl))) (collect-umlisp-query (ustats (name count srl) nil nil nil - :order (name asc)) - (make-instance 'ustats :name name - :hits (ensure-integer count) - :srl (ensure-integer srl))))) + :order (name asc)) + (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)))) - - - -(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)))) + (make-instance 'ustats :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-urank-sab (sab &key (srl *current-srl*)) + (collect-umlisp-query (mrrank (rank sab suppress tty) nil sab sab) + (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress))) -(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)))) +(defun find-urank-all (&key (srl *current-srl*)) + (if srl + (collect-umlisp-query (mrrank (rank sab suppress tty) nil ksrl srl) + (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress)) + (collect-umlisp-query (mrrank (rank sab suppress tty ksrl) nil nil nil) + (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress))))